HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones

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Giebelhaus" }, { "@type": "Person", "name": "Lauren A.E. Erland" }, { "@type": "Person", "name": "Susan J. Murch" } ], "publisher": { "@type": "Organization", "name": "F1000Research", "logo": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 480, "width": 60 } }, "image": { "@type": "ImageObject", "url": "https://f1000research.com/img/AMP/F1000Research_image.png", "height": 1200, "width": 150 }, "description": " Background Metabolomics is the simultaneous determination of all metabolites in a system. Despite significant advances in the field, compound identification remains a challenge. Prior knowledge of the compound classes of interest can improve metabolite identification. Hormones are a small signaling molecules, which function in coordination to direct all aspects of development, function and reproduction in living systems and which also pose challenges as environmental contaminants. Hormones are inherently present at low levels in tissues, stored in many forms and mobilized rapidly in response to a stimulus making them difficult to measure, identify and quantify. Methods An in-depth literature review was performed for known hormones, their precursors, metabolites and conjugates in plants to generate the database and an RShiny App developed to enable web-based searches against the database. An accompanying liquid chromatography – mass spectrometry (LC-MS) protocol was developed with retention time prediction in Retip. A meta-analysis of 14 plant metabolomics studies was used for validation. Results We developed HormonomicsDB, a tool which can be used to query an untargeted mass spectrometry (MS) dataset against a database of more than 200 known hormones, their precursors and metabolites. The protocol encompasses sample preparation, analysis, data processing and hormone annotation and is designed to minimize degradation of labile hormones. The plant system is used a model to illustrate the workflow and data acquisition and interpretation. Analytical conditions were standardized to a 30 min analysis time using a common solvent system to allow for easy transfer by a researcher with basic knowledge of MS. Incorporation of synthetic biotransformations enables prediction of novel metabolites. Conclusions HormonomicsDB is suitable for use on any LC-MS based system with compatible column and buffer system, enables the characterization of the known hormonome across a diversity of samples, and hypothesis generation to reveal knew insights into hormone signaling networks. 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F1000Research 2024, 11 :1191 ( https://doi.org/10.12688/f1000research.124194.2 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. Close Copy Citation Details Export Export Citation Sciwheel EndNote Ref. Manager Bibtex ProCite Sente EXPORT Select a format first Track Share ▬ ✚ Software Tool Article Revised HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] Ryland T. Giebelhaus https://orcid.org/0000-0002-7625-3077 1 , Lauren A.E. Erland 1,2 , Susan J. Murch https://orcid.org/0000-0001-5803-9483 1 Ryland T. Giebelhaus https://orcid.org/0000-0002-7625-3077 1 , Lauren A.E. Erland 1,2 , Susan J. Murch https://orcid.org/0000-0001-5803-9483 1 PUBLISHED 08 Apr 2024 Author details Author details 1 Chemistry, University of British Columbia, Kelowna, British Columbia, V1V1V7, Canada 2 Agriculture, University of the Fraser Valley, Chilliwack, British Columbia, V2R 0N3, Canada Ryland T. Giebelhaus Roles: Data Curation, Formal Analysis, Methodology, Resources, Software, Writing – Original Draft Preparation, Writing – Review & Editing Lauren A.E. Erland Roles: Conceptualization, Data Curation, Formal Analysis, Methodology, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Susan J. Murch Roles: Conceptualization, Data Curation, Funding Acquisition, Methodology, Project Administration, Supervision, Validation, Writing – Original Draft Preparation, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the Plant Science gateway. Abstract Background Metabolomics is the simultaneous determination of all metabolites in a system. Despite significant advances in the field, compound identification remains a challenge. Prior knowledge of the compound classes of interest can improve metabolite identification. Hormones are a small signaling molecules, which function in coordination to direct all aspects of development, function and reproduction in living systems and which also pose challenges as environmental contaminants. Hormones are inherently present at low levels in tissues, stored in many forms and mobilized rapidly in response to a stimulus making them difficult to measure, identify and quantify. Methods An in-depth literature review was performed for known hormones, their precursors, metabolites and conjugates in plants to generate the database and an RShiny App developed to enable web-based searches against the database. An accompanying liquid chromatography – mass spectrometry (LC-MS) protocol was developed with retention time prediction in Retip. A meta-analysis of 14 plant metabolomics studies was used for validation. Results We developed HormonomicsDB, a tool which can be used to query an untargeted mass spectrometry (MS) dataset against a database of more than 200 known hormones, their precursors and metabolites. The protocol encompasses sample preparation, analysis, data processing and hormone annotation and is designed to minimize degradation of labile hormones. The plant system is used a model to illustrate the workflow and data acquisition and interpretation. Analytical conditions were standardized to a 30 min analysis time using a common solvent system to allow for easy transfer by a researcher with basic knowledge of MS. Incorporation of synthetic biotransformations enables prediction of novel metabolites. Conclusions HormonomicsDB is suitable for use on any LC-MS based system with compatible column and buffer system, enables the characterization of the known hormonome across a diversity of samples, and hypothesis generation to reveal knew insights into hormone signaling networks. READ ALL READ LESS Keywords Plant metabolomics, phytohormones, synthetic biotransformations, hormonomics Corresponding Author(s) Susan J. Murch ( [email protected] ) Close Corresponding author: Susan J. Murch Competing interests: No competing interests were disclosed. Grant information: Financial support was provided by the Natural Sciences and Engineering Research Council of Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2024 Giebelhaus RT et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. How to cite: Giebelhaus RT, Erland LAE and Murch SJ. HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.12688/f1000research.124194.2 ) First published: 18 Oct 2022, 11 :1191 ( https://doi.org/10.12688/f1000research.124194.1 ) Latest published: 08 Apr 2024, 11 :1191 ( https://doi.org/10.12688/f1000research.124194.2 ) Revised Amendments from Version 1 We appreciate the reviewers’ comments and great suggestions. We have clarified the relationship between Daltons and ppm and included a table of recommended mass tolerances for different types of mass spectrometers in a Supplemental document. This is available at ( https://doi.org/10.5683/SP3/SIGTUN ) and is described in the data availability statement. This document which outlines how users should select mass tolerances for searching, based on their mass detector. The Supporting Information is based on previously published work, and we are providing a summary of this information, therefore we felt was not appropriate to include in the main body of the text. Some editorial comments have been added to improve clarity. We have also clarified some questions both reviewers had regarding how to utilize the retention time predictions, and when to use the biotransformations option in the software. Additionally, we have updated Figure 1 in the manuscript to reflect these changes to the tool and have updated the tool to v1.5 after this round of revision. Figures 3, 4, and 5 were out of order and this has since been corrected, with no changes to the content of these figures. Some of the suggestions will be incorporated into future versions of the analytical tool and database. We appreciate the reviewers’ comments and great suggestions. We have clarified the relationship between Daltons and ppm and included a table of recommended mass tolerances for different types of mass spectrometers in a Supplemental document. This is available at ( https://doi.org/10.5683/SP3/SIGTUN ) and is described in the data availability statement. This document which outlines how users should select mass tolerances for searching, based on their mass detector. The Supporting Information is based on previously published work, and we are providing a summary of this information, therefore we felt was not appropriate to include in the main body of the text. Some editorial comments have been added to improve clarity. We have also clarified some questions both reviewers had regarding how to utilize the retention time predictions, and when to use the biotransformations option in the software. Additionally, we have updated Figure 1 in the manuscript to reflect these changes to the tool and have updated the tool to v1.5 after this round of revision. Figures 3, 4, and 5 were out of order and this has since been corrected, with no changes to the content of these figures. Some of the suggestions will be incorporated into future versions of the analytical tool and database. See the authors' detailed response to the review by Jian You Wang See the authors' detailed response to the review by Ainsely Lewis and R.J. Neil Emery READ REVIEWER RESPONSES Introduction With the growth of interest in metabolomics studies has come an explosion in the development of tools and databases for the annotation, analysis and interpretation of untargeted datasets. Fundamental to the ability to appropriately identify and annotate features in a dataset is the development of libraries and databases as the economics of purchasing standards to validate feature identification in these datasets is not feasible. While many tools and databases have been developed to assist in identification of metabolites from untargeted mass spectrometry (MS), much of the focus has been on capturing the largest possible depth and breadth of metabolites in a system. 1 While this increases the likelihood of matches often times identification using large databases, particularly for mass to charge (m/z) and retention time (RT) data or identification to level three confidence, 2 it also often leads to large numbers of improbable identities. This has led to calls for more specific databases, for example by sample type of metabolite class of interest which can improve the quality of matches and simplify the process. 3 The ability to search a dataset against a smaller, more focused database can therefore be helpful in identification of biologically relevant features within a dataset. Hormonomics is a subset of metabolomics which has been defined as the study of the full spectrum of hormones, their conjugates and precursors in a living system. 4 , 5 The first hormonomics experiment is reported in Simura et al. 2018, where a targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) method was developed to rapidly profile 101 phytohormones in plant tissues, including the bioactive forms of the hormones, their precursors, and their catabolites, allowing for a quantitative view of the state of the hormonome in the tissue being sampled. 5 This approach was then expanded and adapted to an untargeted metabolomics work flow. 4 , 6 Hormones are not however exclusive to plants and in fact are best studied in mammalian systems having been defined as “substance [s] which, being produced in any one part of the organism, is transferred to another part and there influence a specific physiological process”. 7 Hormones are often hard to quantify due to their labile nature and presence at low concentrations. Additionally, hormones, and phytohormones particularly are known to undergo diverse biotransformations, many of which remain uncharacterized, but which may play essential roles in their biological activity. 4 , 8 To avoid undesired induction of signaling cascade during storage or transport phytohormones are modified or conjugated to deactivate the compounds, while also allowing for the rapid release of these compounds when needed. To gain a full understanding of the hormonome of a sample all these possible forms must be considered. We have developed a protocol using a standard buffer system, gradient and column which can be adopted for any LC-MS platform in coordination with the HormonomicsDB platform to specifically characterize the hormonome of a desired sample while also enabling discovery of novel phytohormone metabolites which may have physiological relevance. The inhouse hormonomics dataset described by Erland et al 2020a, b has been expanded and moved to a publicly accessible RShiny based web-tool “HormonomicsDB” ( http://hormonomicsDB.com ) which allows for the putative identification of phytohormones, their precursors, metabolites, conjugates in untargeted datasets. We also performed a meta-analysis of data from 14 plant metabolomics studies archived on the Metabolomics Workbench using the HormonomicsDB web-tool to demonstrate the utility of the approach in exploring the plant hormonome. 9 Our previously developed synthetic biotransformations algorithms 10 , 11 are additionally integrated into the tool to allow for prediction and discovery of novel metabolites from MS metabolomics data using m/z and RT for compound ID. Methods Code, availability and issue reporting The HormonomicsDB web-tool is available at http://hormonomicsdb.com/ ( Figure 1 ). The code was written using R ( https://www.r-project.org ) and RStudio ( https://rstudio.com ). To run the app, the RShiny package was utilized ( https://www.shiny.rstudio.com ). The code of the current version 1.4 reported in this manuscript is archived on GitHub.com : https://github.com/plantSMART-UBC/HormonomicsDB . Figure 1. Screenshot of the current version of HormonomicsDB (v1.5) as viewed in Google Chrome. Plant growth regulators A list of 249 plant phytohormones of interest was catalogued in a csv file, along with the class, monoisotopic mass, and M+H, m/z, InChI and SMILES terms. The list was expanded from those previously published in Erland et al. 2020 and Simura et al. 2018. 4 , 5 For each database entry, 7 common adducts and 27 synthetic biotransformations ( Table 1 ) are calculated. 4 , 12 Table 1. Description of the four searchable databases of plant growth regulators in HormonomicsDB. Database Name Database Description and Outputs PGR Monoisotopic Contains the monoisotopic mass of each archived plant growth regulator. Returns matches on the monoisotopic mass only. PGR M+H Contains the M+H adduct of each plant growth regulator and returns matches on this adduct only. PGR Adducts Contains and searches across 7 common adducts, M+H-2H 2 O, M+H-H 2 O, M+NH 4 -H 2 O, M+Li, M+NH 4 , M+CH 3 OH-H, and M+K, for all archived plant growth regulators. PGR Biotransformations Contains and searches across 27 common predicted biotransformations, M+CH 3 , M+C 6 H 12 O 6 , M+OH, M+COOH, M+NH 2 , M+NH 3 , M-H+OH, M-H+2OH, M-H+NH 2 , MCH 3 +H, M-CH 3 +OH, M-CH 3 +NH 2 , M-C 6 H 12 O 6 +H, MC 6 H 12 O 6 +OH, M-C 6 H 12 O 6 +NH 2 , M-C 6 H 12 O 6 +CH 3 , MOH+H 2 , M-OH+CH 3 , M-OH+C 6 H 12 O 6 , M-OH+COOH, MOH+NH 2 , M-OH+NH 3 , M-NH 2 +H 2 , M-NH 2 +CH 3 , MNH 2 +C 6 H 12 O 6 , M-NH 2 +COOH, and M-NH 2 +OH, for all archived plant growth regulators. PGR Monoisotopic contains the monoisotopic mass for each phytohormone, the PGR M+H contains the m/z of each phytohormone as an M+H adduct, the PGR adducts contains the m/z of 7 common adducts ( Table 1 ), and PGR biotransformations contains 27 common biotransformations ( Table 1 ) as M+H adducts. Data input and output User data is supplied via file upload as a comma separated value (CSV) file. A standard format is used for uploading data to HormonomicsDB, with m/z in the first column, RT in the second column, and sample intensities populating the remaining columns. Users can generate peak tables for upload to HormonomicsDB a number of ways, including with vendor software, or open source packages. These software take raw data files collected from individual chromatographic runs, and align the peaks to generate a single peak table which describes all the samples in the metabolomics experiment. These open source tools include XCMS (xcmsonline.scripps.edu), MetaboAnalyst ( metaboanalyst.com ), mzMine (mzmine.github.io), and Metaboseek ( metaboseek.com ). Given this, HormonomicsDB makes no assumptions about signal to noise (S/N) or other sensitivity figures of merit as these are typically made during this peak alignment step. The maximum file size for HormonomicsDB has been set to 10 Mb for the web tool, however, this can be increased as desired when running locally in R by editing the source code manually. To demonstrate the features of the app, example data is provided on the app’s website, of which the details of the data can be found elsewhere. 11 Prior to data upload, the user selects the databases that they wish to search against; PGR Monoisotopic, PGR M+H, PGR Adducts, or PGR Biotransformations ( Table 1 ) and mass tolerance, which can be given as ± Da or ppm (Supporting Information 37 ). The user can then view the data in the “Screener Output” tab on the app or downloaded as a CSV onto the user’s computer by clicking the “Download Results” on the “m/z Screener” tab. The databases queued against depend on the structure of the input data and the users hypothesis. Certain software, particularly for Fourier transform mass spectrometry (FT-MS) data, convert ion masses to monoisotopic mass before exporting a peak table. If this is the case, the user can queue against the “PGR Monoisotopic” database. HormonomicsDB custom search The HormonomicsDB code was modified to create the “Custom Database Search” feature which allows users to use the existing search algorithm and user interface to search against a user uploaded database rather than the internal list of compounds. To use this feature, the user first makes their own database of compounds in a CSV using the same standard format as the “m/z screener”. Metabolite identification and the metabolomics standards initiative HormonomicsDB putatively identifies metabolites on both m/z as well as RT. The query algorithm developed for HormonomicsDB first searches on m/z, selecting features that match to PGRs within the user specified search tolerance. Next these putatively identified PGRs are sorted on % RT match, calculating how close the experimental RT for the feature is to the predicted RT for the putatively identified PGR. HormonomicsDB putatively identifies metabolites to the metabolomics standards initiative (MSI) level 3, as two physicochemical properties, m/z and RT, are used to annotate compounds, without comparison to a chemical reference standard but which do not yield unambiguous matches. 2 Standardized untargeted hormonomics protocol An extraction protocol previously established for the extraction of phytohormones for LC-MS analysis was adapted for untargeted hormonomics. 12 – 15 For extraction, multiple different extraction solvents can be utilized to achieve the desired extraction. This includes water for polar extractions, as well as methanol for nonpolar extractions. Additionally, two extraction buffers used in previously published LC-MS protocols are recommended. The two extraction buffers are 0.5 N trichloroacetic acid (Fischer Scientific, Ottawa, ON, Canada) in 80% methanol (Optima, Fisher Scientific) and 50% methanol (MS Grade, Fisher Scientific, Canada; MeOH) and 4% acetic acid (glacial, Fisher Scientific, Canada) in Milli-Q water. All sample preparation is performed in a reduced light environment, under a red light. Approximately 100 mg of plant tissue was weighed into a 1.5 mL microcentrifuge tube ( Figure 2 ) and immediately stored on ice or in liquid nitrogen. Extraction buffer was added to the sample in a 3:1 volume (μL): mass (mg) ratio then homogenized on ice using a disposable tissue grinder (Kontes Pellet Pestle; Fisher). The resulting homogenate was vortexed for 30 seconds (Lab Dancer ©, VWR) then centrifuged for 3 minutes at 13,000 rpm (VWR Galaxy 16DH centrifuge). The supernatant was filtered using a 400 μL microcentrifuge filter (0.2 μm PVDF Ultrafree Centrifuge filter; Millipore, Etobicoke, ON, Canada) and centrifuged for 3 minutes at 13,000 rpm. If the sample matrix was complex, the filtrate could be further diluted with ultrapure water up to 1:10 filtrate: water. The filtrate was then aliquoted into an amber glass autosampler vial and stored at 4 °C prior to analysis. Figure 2. Standardized workflow for untargeted hormonomics analysis (Figure generated in BioRender). An untargeted metabolomics method previously established in Brown et al. 2012 was developed with slight modifications. 10 , 11 , 15 , 16 Separation was optimized for use with Waters Acquity UPLC BEH C18 column (2.1 × 150 mm × 1.7 μm) at a temperature of 30 °C. A volume of 5 μL was injected onto the column at the start of the gradient. The elution was performed using eluents consisting of 0.25% formic acid (Sigma) in ultrapure water (Eluent A); 100% acetonitrile (Eluent B) was used with the following gradient: 0.0-10.0 min, 95:5-5:95 v/v, 10.0-15.0 min, 5:95 v/v, 15.0-20.0min, 5:95-95:5 v/v, 20.025.0min, 95:5 v/v. The needle wash solvent and purge solvent were both 10:90% water: acetonitrile (v/v). A pre-inject wash of 5 seconds was performed, followed by a 10 second post-injection wash. The total runtime was 25 minutes and a flow rate of 0.25 mL/min was used. The method should be compatible with most mass spectrometry platforms. For acquisition of MS data we have tested data acquire on a Waters LCT Premier to good success using positive electrospray ionization and positive ion detection, with capillary voltage of 2.9 kV, cone voltage 60 V, source temperature 120 °C, desolvation temperature 250 °C, mass range of 100–1000 amu and a scan time of 0.1 s. Retention time prediction Using the validated method, a mixture of 46 known analytes were weighed then dissolved in the 0.5 N trichloroacetic acid and 80% methanol extraction buffer ( Table 2 ), each with a concentration of approximately 100 ng/mL were injected and eluted. Using the predicted M+H m/z for each analyte, extracted ion chromatograms were generated to determine the retention time of these analytes. These RTs were then catalogued in an Excel TM document. Table 2. Metabolites used to build the retention time prediction model. All RTs and ∆ RT given in minutes. Compound Predicted RT Experimental RT ∆ RT Histidine 2.45 1.23 1.22 Norepinepherine 3.57 1.35 2.22 Ascorbic Acid 2.74 1.85 0.89 5-Hydroxytryptophan 3.24 2.47 0.77 Zeatin 3.31 2.47 0.84 Phenylalanine 3.25 2.786 0.464 Indole 4.44 3.34 1.1 Caffeine 3.97 3.41 0.56 N-acetyl serotonin 5 3.704 1.296 4-chlorophenylalanine 3.99 3.81 0.18 Isopentenyl adenine 3.93 3.94 -0.01 Indole-3-acetic acid 4.2 3.94 0.26 6-Benzylaminopurine 4.53 4.07 0.46 Lidocaine 5.25 4.4 0.85 Coumaric acid 4.59 4.44 0.15 Gibberellin A3 5.63 4.492 1.138 Serotonin 4.52 4.51 0.01 5-chlorotryptamine 4.87 4.55 0.32 Vanillin 4.63 4.57 0.06 Strictosamide 4.85 4.621 0.229 Ferulic Acid 4.89 4.621 0.269 Anthranilic acid 4.58 4.69 -0.11 Melatonin 4.97 4.86 0.11 Kinetin 5.32 5.061 0.259 N-Feruloyl serotonin 4.67 5.079 -0.409 3-hydroxy tryptamine 5.64 5.281 0.359 Quercetin 4.92 5.3 -0.38 7-hydroxy mitragynine 5.41 5.648 -0.238 Mitragynine 5.73 5.65 0.08 Pipernal 6.04 5.85 0.19 Strychnine 4.67 5.9 -1.23 Reserpine 6 5.94 0.06 Indole-3-butyric acid 6.05 6.363 -0.313 Jasmonic acid 5.97 6.418 -0.448 1-Naphthaleneacetic acid 6.48 6.45 0.03 2-Naphthoxyacetic acid 6.43 6.8 -0.37 Ramelton 6.31 6.86 -0.55 Luzindole 6.87 6.86 0.01 Methyl Salicylate 6.9 7.17 -0.27 Melamine 6.49 7.68 -1.19 Brassinolide 5.91 7.76 -1.85 Paclobutrazol 7.16 7.89 -0.73 cis-4-Phenyl-2-propionamidotetralin (4-P-PDOT) 7.27 8.03 -0.76 Corticosterone 7.97 8.252 -0.282 Progesterone 6.95 8.33 -1.38 Nicotine 7.95 10.09 -2.14 Separation was performed according to the standardized protocol described above on a Waters Acquity I-Class ultra performance liquid chromatography system. Detection was on a Waters Xevo TQ-S in full scan mode (ESI+) using the following optimized settings: Mass range: 75.01100.0 m/z; capillary: 3.5 kV; cone voltage: 30.0 V; Source offset: 60.0 V; Source temperature: 150 °C; desolvation temperature: 400 °C; cone gas flow: 150 L/Hr; desolvation gas flow: 550 L/Hr; collision gas flow: 0.00 mL/min; nebulizer gas flow: 7.00 Bar. In addition to the injected samples, extraction solvent blanks and standards were injected between blocks of samples for quality control and to prevent carryover. In silico RT prediction was performed using the Retip package in the R environment. 17 The package used the in-house RT database as a training set and testing set for up to five ML methods; Random Forest (RF), bidirectional recurrent neural networks (BRNN), XGBoost, lightGBM, and Keras. Of these five models, two worked and were tested; RF and BRNN. The RF ML model was selected as the model to predict RTs for HormonomicsDB. Validation was performed by comparing the predicted RTs to experimental values of known compounds. Testing and validation To test and validate the tool, a previously published untargeted metabolomics dataset generated using the same chromatographic parameters as described above was analyzed using HormonomicsDB. 15 The purpose of testing and validating was to assess the tools querying ability to ensure fit for purpose, while processing a large dataset. Additionally, we wanted to compare HormonomicDBs outputs to a previously published list of putative metabolites to determine if the tool returning the desired outputs. This dataset was analyzed through HormonomicsDB using the ‘M+H’ database and a search tolerance of ± 0.02 Da. The putative hits from HormonomicsDB were then exported as a CSV, duplicate hits were removed, yielding a list of putatively identified metabolites. This list was then compared to the putatively identified analytes from Brown et al. 2012 to determine if ‘HormonomicsDB’ has any major bugs which cause issues in querying. The data in Brown et al. 2012 was collected on a time of flight (TOF) mass spectrometer, which typically has a mass error of 3 to 5 ppm. Meta-analysis of previous metabolomics studies To demonstrate the utility of the HormonomicsDB webtool, we performed untargeted hormonomics analysis on all LC-MS the plant studies present on Metabolomics Workbench ( Figure 3 ). 9 First, studies with the study organism “PLANT” were selected, which as of June 2022 returned 58 studies. From these, studies which incorrectly returned a plant species, or used nuclear magnetic resonance (NMR), gas chromatography mass spectrometry (GC-MS), separation techniques such as hydrophilic layer interaction chromatography (HILIC), or reversed phase LC techniques with detection methods other than high resolution MS were excluded, leaving 34 studies. Of these, a number of studies had named peak tables, incomplete peak tables, or only raw, unaligned data. These were excluded further narrowing the number of studies to 14 ( Table 3 ). There were 13 studies, with 10 unique species, with peak tables acquired in ESI+ mode, and 8 studies with 5 unique species in ESI- mode. All these peak tables were formatted for HormonomicsDB and queued against the ‘M+H’ adduct with a mass tolerance of ± 0.02 Da. The output from HormonomicsDB was sorted by RT match. For studies with the same gradient and column used to construct the in silico RT prediction training set, compounds with an RT match >70% were retained. If the gradient and column were different compounds with a match >50% were retained. For studies where the gradient was not provided, RTs >1 minute and before column re-equilibration were retained. If direct injection was used, all compounds were selected. Duplicate compound hits were then removed and the compounds were binned by class. Figure 3. Overview of the steps in the meta-analysis of plant metabolomics studies from Metabolomics Workbench. Table 3. Summary of the 14 datasets archived on the Metabolomics Workbench explored in the meta-analysis of plant metabolomics studies. Study ID Study title Species Detection Ionization mode ST000240 Global LC-MS of Ozone Stress in Maize: GLCMS Maize OrbiTrap ESI +/- ST000289 PPDK RNAi effects in endosperm metabolite pools Maize OrbiTrap ESI +/- ST000290 2014 Biotron Experiment Metabolites Maize OrbiTrap ESI +/- ST000886 Mechanism Behind Stay Green Trait in Bread Wheat (Triticum aestivum L.) Wheat OrbiTrap ESI +/- ST001095 Data resource for fully 13C labelled and non-labelled plant tissues (part-I) Arabidopsis thaliana QTOF ESI +/- ST001096 Arabidopsis thaliana 25 accessions Arabidopsis thaliana QTOF ESI +/- ST001194 Flavonoid study of Ginkgo leaves facing to different elevation and plant age Ginkgo biloba TripleTOF ESI - ST001296 Metabolomics and Hormonomics to Crack the Code of Filbert Growth Corylus americana QTOF ESI + ST001330 Multi-omics of OsGF14b-mediated innate immunity against panicle blast in rice Rice OrbiTrap ESI +/- ST001371 Untargeted metabolomics of Quercus ilex acorns Holly oak QTOF ESI + ST001374 Untargeted Metabolomics for fruit juice authentication Apple TripleTOF ESI + ST001634 A combinatorial action of GmMYB176 and bZIP controls isoflavonoid biosynthesis in soybean. Soybean OrbiTrap ESI + ST001854 Metabolic profiling of Rafflesia-infected Tetrastigma and applications for propagation Woody vine QTOF ESI + ST002062 Endophytic bacteria are key players in the modulation of the secondary metabolome of Lithospermum officinale L. Common gromwell OrbiTrap ESI + Results and discussion HormonomicsDB web-tool functionality and interface The HormonomicsDB web-tool is an open source web tool developed using RShiny allowing users to perform compound annotation of untargeted metabolomics datasets using retention time and accurate mass matching ( Figure 1 ). The database includes 249 hormones which were originally assembled from the plant science perspective. In addition to matching to monoisotopic mass the database allows for matching to common adducts as well as predicted metabolites through the synthetic biotransformations approach ( Figure 2 ; Table 1 ). Data is uploaded in.csv format and results can be viewed either on the web or downloaded as a .csv file. The search functionality may also be used to search any two datasets given they contain m/z.RT data. By comparing the putatively identified phytohormones from Brown et al. 2012 to the output of HormonomicsDB we determined the tool was fit for purpose. 15 The match rate was 104.5%, and was considered acceptable as our algorithm matches first on m/z then on RT, therefore, two or more isobaric phytohormones may return for a given m/z ( Table 4 ). Table 4. Top 10 synthetic biotransformations by total signal intensity as output from HormonomicsDB found in the dataset published by Brown et al. 2012. 15 Compound Name Biotransformation Actual m/z Experimental m/z RT (min) 5-(3’-carboxy-3’-oxopropyl)-4,6-dihydroxypicolinate M-NH 2 +C 6 H 12 O 6 419.08 419.10 2.68 glucobrassicin M+NH 3 465.09 465.10 3.50 IAA aspartate M-C 6 H 12 O 6 +OH 287.07 287.05 2.63 7,8-dihydroxykynurenate M-NH 2 +C 6 H 12 O 6 385.08 385.06 1.38 2-methylthio-cis-zeatin riboside M+C 6 H 12 O 6 577.21 577.20 3.45 IAA glutamate M-C 6 H 12 O 6 +OH 301.08 301.70 2.92 4,6-dihydroxyquinoline M+C 6 H 12 O 6 341.11 341.10 3.62 4,6-dihydroxyquinoline M-CH 3 +H 147.03 147.04 3.61 4,6-dihydroxyquinoline M-NH 2 +H 2 147.04 147.04 3.61 IAA glutamate M-C 6 H 12 O 6 +OH 301.083 301.07 2.77 Additionally, the “HormonomicsDB custom search” function is a novel feature within HormonomicsDB which allows users to search their peak table against their own database of metabolites. This is the first such report of a feature that allows users to queue with their own database. We hope to continue growing this function to allow users to queue against other databases by accessing them through an application programming interface (API) in the HormonomicsDB environment. Development of the standardized protocol In order to facilitate high confidence compound identification, a standardized and easily adapted LC-MS method was developed that accounts for the low concentration, labile nature of hormones and also accounts for the differential polarity of some phytohormones ( Figure 2 ). The method is derived from established protocols and uses equipment and solvents already present in most biology, chemistry and analytical labs and is outlined in Figure 2 . 13 , 18 , 14 Special consideration was applied to extraction conditions as phytohormones represent unique challenges as analytes. First, in sample preparation, keeping samples on ice in a low light environment helps to prevent the degradation of labile phytohormones such as melatonin and auxin. 13 , 19 , 20 Typically, degradation of analytes during sample preparation is negligible for quantitative work, however, hormones often occur at levels approaches detection limits, particularly in untargeted studies making extraction losses a significant concern. Another concern is the potential for reactions during the extraction process which may lead to modification of structures and potentially loss of the biologically relevant forms or bias in the forms observed in the dataset. The use of methanol and water in the extraction solution encourages the extraction of both polar and non-polar analytes. Acidification of the extraction buffer with acetic acid or trichloroacetic (TCA) acid helps to acidify the solution to increase the solubility of phytohormones and protonation increase ionization efficiency in ESI+. TCA also precipitates proteins, and provides ion paring to reduce ion suppression in the mass analyzer. 21 Database curation The databased includes 249 metabolites which are established hormones or precursors or metabolites thereof. Classes of hormones include both naturally occurring and synthetic hormones with broad class coverage of: catecholamines, indolamines, auxins, jasmonates, salicylates, cytokinins, gibberellins, polyamines, butenolids (karrikins and strigolactones), steroids and abscisic acid. While development of the initial database has been from a plant hormone perspective, it also represents good coverage of the overall hormone landscape across Kingdoms. Only known metabolites have been included in the database, though the capacity to predict novel metabolites is built into the predictive biotransformations functionality. Inclusion of molecular formula, SMILES and InChI terms facilitates interoperability between database search results and classification tools such as MetaboAnalyst, ChemRich or ClassyFire. Accurate mass and molecular formula are available for all database entries, predicted retention time is also included for all entries and was predicted for the standardized method using the Retip App 17 to allow for compound identification to MSI Level 3 as the presence of isobars within the database leads to the possibility for non-unique matches even with integration of retention time. 2 The complete database is available in .csv format in Supplementary File 1. Retention time prediction The advent of machine learning algorithms has led to several important tools which facilitate compound identification. We have applied the ReTip app to allow for retention time prediction within the database, given users have uploaded data generated from the standard separation protocol or one similar. The random forest model for retention time prediction showed the best fit to the training data with an R2 = 0.92 ( Table 5 ). Both the standard error (1.1 min) and the 95% confidence interval (± 1.17 min) were lowest of the models tested and were considered acceptable for the purpose. Manual plotting of predicted vs experimental retention time showed a highly linear relationship with R 2 > 0.9 and slope of 1.39. We anticipate that the predictions will be robust for LC-MS based systems running the standard separation protocol. While RT predictions help to increase confidence in putative identification, it is important to note that differences in gradient, column, or solvents can impact the RT of analytes. The users should place more emphasis on the accurate mass matching and use RT prediction results to confirm if the elution pattern or order is as expected and elution of the analyte occurs at a reasonable time within the gradient. Table 5. Accuracy of machine learning models used for retention time prediction. BRNN; Bidirectional recurrent neural networks. CI; Confidence interval. Root Mean Standard Error R2 Mean Absolute Error 95% CI ( ± min) Random Forest 1.04 0.92 0.8 1.17 BRNN 1.26 0.58 0.95 2.00 Synthetic biotransformations approach for hypothesis generation One of the fundamental challenges which exists within the field of metabolomics is the scale of unknown unknowns within datasets. The average plant leaf has been estimated to contain >70,000 metabolites and with only a fraction of these having been characterized this leaves a vast chemical space for compound discovery as well as a significant challenge. 10 One advantage to living systems is that metabolites are generally not independent and are the result of enzymatic reactions, meaning there are a finite number of reactions that can occur. 10 While the vast number of potential novel metabolites is almost infinite, the number of basic reactions is more finite. In the synthetic biotransformations or logical algorithms approach developed in our group we use common chemical reactions such as (de) methylation, oxidation, reduction, (de) hydroxylation, (de) glycosylation, (de) carboxylation and apply these to a select subset of metabolites of interest to predict new pathways and metabolites in a sample based on a known starting point. 4 , 6 , 11 , 10 This approach uses the predicted change in monoisotopic mass of a specific metabolite by the addition or removal of a common moiety which can then be mined in the metabolomics dataset ( Figure 4 ). Figure 4. Overview of HormonomicsDB functionality. The synthetic biotransformations approach can also be used for the annotation of unknown knowns in a sample. This approach is particularly relevant for hormones as due to their biological activity at low concentrations, a common strategy is activation/deactivation of metabolites through simple reactions. It is possible that the active form is present at levels well below detection limits but a storage or deactivated form for transport is present at detectable levels and may still provide interesting biological context. Similarly, as the compounds are generally labile, a biologically active form of a hormone may be absent in a sample due to degradation during sample preparation or ionization but a modified form may be present. One of the best described examples of this is the classical phytohormone auxin which may be stored/deactivated/transported through methylation, glycosylation, and conjugation to amino acids among for example. 8 , 22 , 23 Phytohormones activity in some instances may also be enhanced or modified through conjugation or biotransformation as is the case for jasmonic acid, where the active form is jasmonic acid isoleucine, 24 or serotonin where phenolic conjugates such as feruloylserotonin are important in response to wounding, pathogen challenge and insect feeding. 25 , 26 A proof of concept of the application of synthetic biotransformations was performed on the pathway responsible for melatonin biosynthesis in plants using known conjugates ( Figure 5 ). In this proof of concept, two glycosylated metabolites are present, tryptophan-N-glycoside, and serotonin 5-O- β -glycoside. 27 These glycosylated forms may serve as inactive storage or transport forms of their parent molecule. Furthermore, the serotonin conjugates N-coumaroyl-serotonin and N-feruloyl-serotonin ( Figure 5 , Table 6 ) have been found in several plant species where they serve important functions as defensive molecules. 28 There are potentially many more conjugates in this pathway that are yet to be identified, such as melatonin glycosides or N-coumaroyl-melatonin. The logic can also be performed in reverse, in the absence of a match for the parent compound melatonin the presence of for example while feruloyl-serotonin is not identified in the example cranberry dataset both a hydroxylated version and an aminated version are possible ( Table 6 ). Figure 5. The pathway responsible for the biosynthesis of melatonin in plants starting from tryptophan (a) through to tryptamine (b) serotonin (c) and melatonin (d). The molecules in blue represent conjugates of these main metabolites in the pathway; (e) tryptophan-N-glucoside, (f) tryptamine-N-glucoside, (g) N-Coumaroyl serotonin, and (h) N-feruloylserotonin. Table 6. Synthetic biotransformations for which the parent compound is absent in Brown et al. 2012 dataset but which indicate presence of the parent molecule. 15 Note that while the web-tool provides a predicted retention time this is for the parent compound not the transformed metabolite. Compound name Biotransformation Actual m/z Experimental m/z Experimental RT Predicted RT 7-hydroxy-ABA M-OH+NH 3 280.1549 280.1545 2.3782 5.58 7-hydroxy-ABA M-OH+CH 3 278.1518 278.161 5.7316 5.58 9-hydroxy-ABA M-OH+CH 3 278.1518 278.161 5.7316 5.49 Abscisic acid (ABA) M-OH+CH 3 262.1569 262.1596 3.6688 5.56 Abscisic acid (ABA) M-OH+NH 3 264.16 264.1576 2.478 5.56 Abscisic acid (ABA) M-OH+CH 3 262.1569 262.1458 3.8963 5.56 Abscisic acid (ABA) M-OH+CH 3 262.1569 262.1724 5.2207 5.56 9-hydroxy-ABA M-OH+CH 3 278.1518 278.1693 4.6964 5.49 7-hydroxy-ABA M-OH+CH 3 278.1518 278.1693 4.6964 5.58 Abscisic acid (ABA) M-H+NH 2 279.1471 279.1603 2.4673 5.56 2-methylthio-cis-zeatin riboside M-H+2OH 430.1396 430.1473 5.12 4.13 Zeatin riboside-O-glucoside M+CH 3 528.2306 528.216 3.4882 4.05 2-methylthio-cis-zeatin M-NH 2 +OH 266.0837 266.0744 5.4249 4.52 Melatonin (MEL) M-CH 3 +OH 234.1004 234.1195 5.7546 4.88 Feruloyl serotonin M+OH 369.145 369.1448 3.4826 3.83 Feruloyl serotonin M-OH+NH 3 352.1661 352.1854 3.9573 3.83 6-hydroxymelatonin M-OH+NH 3 248.1399 248.1329 2.4123 5.02 Melatonin (MEL) M-H+OH 248.1161 248.1329 2.4123 4.88 Melatonin (MEL) M.NH 2 248.1399 248.1329 2.4123 4.88 Neophaseic acid M-OH+NH 3 280.1549 280.1545 2.3782 6.01 4-hydroxymelatonin M-CH 3 +H 234.1004 234.1195 5.7546 4.97 N-sinapoyl Melatonin M+CH 3 453.2026 453.2179 5.3808 3.54 2-hydroxymelatonin M-OH+CH 3 248.1525 248.1329 2.4123 5.07 4-hydroxymelatonin M-OH+NH 3 248.1399 248.1329 2.4123 4.97 2-formylamino-benzaldehyde M-OH+C 6 H 12 O 6 284.1134 284.1037 5.8617 5.23 2,3-dihydroxyindole M+C 6 H 12 O 6 329.1111 329.1023 5.8638 4.98 N-Acetylserotonin M.NH 2 234.1243 234.1195 5.7546 4.63 N-Acetylserotonin M-H+OH 234.1004 234.1195 5.7546 4.63 6-hydroxy-kynurenate M-NH 2 +COOH 234.0164 233.9979 5.705 3.95 2,3-dihydroxyindole M+C 6 H 12 O 6 329.1111 329.1299 3.4602 4.98 2,3-dihydroxyindole M+C 6 H 12 O 6 329.1111 329.1299 6.098 4.98 2,3-dihydroxyindole M+C 6 H 12 O 6 329.1111 329.1163 4.876 4.98 2,3-dihydroxyindole M+C 6 H 12 O 6 329.1111 329.1212 5.5453 4.98 Meta-analysis of previous studies Tryptophan metabolism had the most hits of all the classes, across both ionization modes. This is not unexpected as tryptophan is involved in both primary and secondary metabolism, and tryptophan metabolites also make up the largest class in HormonomicsDB, with 75 tryptophan metabolites catalogued in HormonomicsDB ( Figure 6 ). Cytokinins and melatonin conjugates are the next two most abundant classes, respectively, however unlike tryptophan metabolism where the abundance is high across the species and experiments, these classes have a varying range in abundance across species. This demonstrates the sensitive nature of plant hormones, particularly with melatonin conjugates which are prone to degradation under light and oxidative conditions. 18 Figure 6. Number of compounds returned in each class for each of the species in the meta-analysis of data from Metabolomics Workbench, with the total number of compounds per class in HormonomicsDB given in the left most column. (a) Electrospray ionization (ESI) positive peak tables, and (b) ESI negative peak tables. In species where there is an increase in tryptophan metabolism metabolites, an increase in melatonin conjugates and cytokinins is observed ( Figure 6 ). Increases in tryptophan have been observed to increase auxin and indolamine levels in Hypericum perforatum L. 29 Additionally, there is evidence suggesting auxin mediates indolamine biosynthesis in plants. 29 These mechanisms are not yet well understood and require further investigation. These empirical observations of increased tryptophan, auxin, and melatonin conjugate biosynthesis through the HormonomicsDB meta-analysis reveals the usefulness of the HormonomicsDB approach and how it could be applied to better understand how auxins interact with indolamine biosynthesis in plants. Unlike the other -omics fields, particularly transcriptomics and genomics, variation between metabolomics experimental conditions, including extraction conditions, column chemistry, mobile phase composition, and ionization voltages makes meta-analyses challenging the data is not easily normalized and aligned (Supplementary File 2). 30 Our demonstration of a metabolomics meta-analysis through HormonomicsDB demonstrates the utility of having a standardized untargeted hormonomics protocol, which not only allows for the HormonomicsDB web-tool to be utilized for putative identification, but permits other researchers to analyze multiple metabolomics datasets without the need to account for variation between experiments. Conclusions Phytohormones are an important class of metabolites as they regulate most physiological responses in plants, including reproduction, growth and development, stress response, and secondary metabolism. Our goal was to develop a tool that can putatively identify phytohormones from untargeted metabolomics datasets, as well as predicted phytohormone conjugates, to assist in the development of novel hypotheses about plant physiology. The putative identification of phytohormones from untargeted LC-MS metabolomics experiments provides valuable insight into plant physiology. We developed an easy to use and freely available webtool which allows users to mine their untargeted metabolomics data for phytohormones and potential conjugates. The web tool and accompanying standardized LC-MS protocol is unique in its specific focus on phytohormones and allows for compound identification up to MSI level 3 through incorporation of RT prediction. The discovery of new hormone derived metabolites can generate novel hypotheses about plant physiology and signalling mechanisms. The synthetic biotransformations approach which is integrated into the tool could be applied to future studies to discover new bioactive secondary metabolites to explore how plants metabolize synthetic compounds including pesticides. 4 , 10 It is important to recognize that while the biotransformations approaches has significant power in annotation of unknowns it also has significant limitations and it should be used as a hypothesis generating tool rather than a confirmatory tool. For example, searching the same cranberry dataset 15 finds dozens of potential biotransformations which must be critically assessed for plausibility and feasibility, for example a compound which is not glycosylated cannot lose a sugar moiety. Additionally, as the biotransformations are predicted features, retention time prediction is not feasible for these compounds emphasizing the low confidence as a compound identification strategy alone. The ability to generate novel hypotheses for metabolite metabolism is also the strength of this approach. While some computational work and development is still necessary to implement this at larger scale, at the single metabolite or pathway level it can be a powerful approach to investigate and predict novel medicinal compounds, 10 , 12 understand metabolism of synthetic herbicides, 6 investigate regulation of morphogenesis 4 , 31 or microbiome interactions. 32 Additionally, our meta-analysis of 14 plant metabolomics experiments highlights the utility of using standardized metabolomics protocols, which allows for more comprehensive metabolomics meta-analyses. Although this approach was designed to study phytohormones, there is significant overlap between phytohormones and endogenous human hormones. This approach can be used to explore small molecule hormones in animal samples as well, including in human tissues and bodily fluids. There is significant overlap between phytohormones and endogenous human hormones. As an example, serotonin, melatonin, and IAA are both phytohormones and endogenously produced hormones in humans. Aside from the role melatonin plays in regulating circadian rhythm in humans, it has been investigated for its role in reducing the impact that coronavirus disease 2019 (COVID-19) plays in supressing the damage caused by the virus SARS-CoV-2. 33 , 34 Serotonin metabolism is also altered in breast cancer cells leading to resistance in serotonin induced apoptosis and the serotonin conjugate, N-(p-coumaroyl) serotonin has been observed to induce apoptosis in breast cancer cells. 35 , 36 This highlights the multidisciplinary functionality of this approach to explore hormone biosynthesis in humans, plants and beyond. Author contributions RTG: Conceptualization, Data curation, formal analysis, investigation, methodology, software, validation, visualization, writing original draft, writing review and editing, formal analysis; LAEE: Conceptualization, Data curation, visualization, writing original draft, writing review and editing, methodology; SJM: Conceptualization, data curation, funding acquisition, supervision, writing review and editing. Data and software availability HormonomicsDB is free to use and accessible at HormonomicsDB.com . The code used to develop HormonomicsDB is available at https://github.com/plantSMART-UBC/HormonomicsDB . Formatting instructions, sample data, and output descriptions are available at HormonomicsDB.com and in the GitHub repository. Borealis. Supporting information for “HormonomicsDB: A novel workflow for the untargeted analysis of plant growth regulators and hormones”. DOI: https://doi.org/10.5683/SP3/SIGTUN . 37 This project contains the following underlying data: - Supporting information, consisting of a list of all phytohormones catalogued in HormonomicsDB and their accompanying chemical information (Supplementary File 1) and additional information regarding the studies assessed in the meta-analyses (Supplementary File 2). Extended data Borealis. Supporting information for “HormonomicsDB: A novel workflow for the untargeted analysis of plant growth regulators and hormones”. DOI: https://doi.org/10.5683/SP3/SIGTUN . 37 - The PDF “Supporting Information for HormonomicsDB” contains background information discussing appropriate mass accuracy selection based on the mass detector used. Data are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication). Acknowledgements We are grateful to Olivier Dube (Research Computing, University of British Columbia, Canada) for his assistance in setting up the HormonomicsDB server. References 1. Misra BB: New software tools, databases, and resources in metabolomics: Updates from 2020. Metabolomics. 2021; 17 (5): 1–24. 2. Blaženović I, Kind T, Ji J, et al. : Software tools and approaches for compound identification of lc-ms/ms data in metabolomics. Meta. 8 (2): 31–2018. 3. Reisdorph NA, Walmsley S, Reisdorph R: A perspective and framework for developing sample type specific databases for lc/ms-based clinical metabolomics. Meta. 2019; 10 (1): 8. Publisher Full Text 4. Erland LAE, Turi CE, Saxena PK, et al. : Metabolomics and hormonomics to crack the code of filbert growth. Metabolomics. 2020; 16 (5): 1–15. Publisher Full Text 5. Šimura J, Antoniadi I, Široká J, et al. : Plant hormonomics: multiple phytohormone profiling by targeted metabolomics. Plant Physiol. 2018; 177 (2): 476–489. 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Giebelhaus R, Erland L, Murch S: “Supporting information for “HormonomicsDB: A novel workflow for the untargeted analysis of plant growth regulators and hormones””,[dataset].2022. Borealis, V1, UNF:6:3zWc0kOHv3aEilUA2UbrAQ== [fileUNF]. Publisher Full Text Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 18 Oct 2022 ADD YOUR COMMENT Comment Author details Author details 1 Chemistry, University of British Columbia, Kelowna, British Columbia, V1V1V7, Canada 2 Agriculture, University of the Fraser Valley, Chilliwack, British Columbia, V2R 0N3, Canada Ryland T. Giebelhaus Roles: Data Curation, Formal Analysis, Methodology, Resources, Software, Writing – Original Draft Preparation, Writing – Review & Editing Lauren A.E. Erland Roles: Conceptualization, Data Curation, Formal Analysis, Methodology, Software, Supervision, Validation, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing Susan J. Murch Roles: Conceptualization, Data Curation, Funding Acquisition, Methodology, Project Administration, Supervision, Validation, Writing – Original Draft Preparation, Writing – Review & Editing Competing interests No competing interests were disclosed. Grant information Financial support was provided by the Natural Sciences and Engineering Research Council of Canada. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Article Versions (2) version 2 Revised Published: 08 Apr 2024, 11:1191 https://doi.org/10.12688/f1000research.124194.2 version 1 Published: 18 Oct 2022, 11:1191 https://doi.org/10.12688/f1000research.124194.1 Copyright © 2024 Giebelhaus RT et al . This is an open access article distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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Key to Reviewer Statuses VIEW HIDE Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Version 2 VERSION 2 PUBLISHED 08 Apr 2024 Revised Views 0 Cite How to cite this report: Wang JY. Reviewer Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.161276.r264124 ) The direct URL for this report is: https://f1000research.com/articles/11-1191/v2#referee-response-264124 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 30 Aug 2024 Jian You Wang , King Abdullah University of Science and Technology, Thuwal, Makkah Province, Saudi Arabia Approved VIEWS 0 https://doi.org/10.5256/f1000research.161276.r264124 The authors have addressed my comments in a rational way. ... Continue reading READ ALL The authors have addressed my comments in a rational way. Hope the improved MS version will come in the future. Competing Interests: No competing interests were disclosed. Reviewer Expertise: Analytical biochemistry, Plant hormones, Strigolactones, Plant growth regulators I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Wang JY. Reviewer Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.161276.r264124 ) The direct URL for this report is: https://f1000research.com/articles/11-1191/v2#referee-response-264124 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Emery RJN and Lewis A. Reviewer Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.161276.r264123 ) The direct URL for this report is: https://f1000research.com/articles/11-1191/v2#referee-response-264123 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 13 May 2024 R.J. Neil Emery , Department of Biology, Trent University, Peterborough, ON, Canada Ainsely Lewis , Trent University, Peterborough, ON, Canada Approved VIEWS 0 https://doi.org/10.5256/f1000research.161276.r264123 The author has ... Continue reading READ ALL The author has included all the suggestions. Competing Interests: No competing interests were disclosed. Reviewer Expertise: Mass spectrometry-based metabolomics, phytohormone profiling, chemometrics We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Emery RJN and Lewis A. Reviewer Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.161276.r264123 ) The direct URL for this report is: https://f1000research.com/articles/11-1191/v2#referee-response-264123 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Respond or Comment COMMENT ON THIS REPORT Version 1 VERSION 1 PUBLISHED 18 Oct 2022 Views 0 Cite How to cite this report: Wang JY. Reviewer Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.136376.r174935 ) The direct URL for this report is: https://f1000research.com/articles/11-1191/v1#referee-response-174935 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 12 Jun 2023 Jian You Wang , King Abdullah University of Science and Technology, Thuwal, Makkah Province, Saudi Arabia Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.136376.r174935 HormonomicsDB is definitely required for the plant metabolomics field and it provides many advantages to identify compounds. While the paper is well written and clearly demonstrates how to use this platform, I have a few comments to, hopefully, improve the ... Continue reading READ ALL HormonomicsDB is definitely required for the plant metabolomics field and it provides many advantages to identify compounds. While the paper is well written and clearly demonstrates how to use this platform, I have a few comments to, hopefully, improve the content. What is the maximum mass tolerance (in Da and ppm) when identifying metabolites? Also, natural components usually contain isomers/isoforms, how to distinguish or interpret them by using HormonomicsDB? It would be necessary to guild users on how to transform Da to ppm. Please include the explanations of the PGR Monoisotopic, PGR M+H, and so on to junior users. It is a bit confusing between Table 4 and Table 5 in the m/z, what are the minimum decimal numbers of accurate mass (default setting) of particular metabolites in HormonomicsDB? In the above two cases, what was the mass tolerance (or acceptable error) to identify the compounds? As a researcher in strigolactone (SL) biology, the methanol extraction would lead to the fast degradation of SLs. Could the author pay attention to this? In addition, the unarguable identification of a particular SL requires MS/MS (not only accurate mass). Therefore, if there would be MS/MS database in HormonomicsDB for advanced non-targeted metabolomics, it would be greatly helpful. What is the minimum intensity (e3 or e4?) of peaks to be considered as metabolites instead of noise? Is the rationale for developing the new software tool clearly explained? Yes Is the description of the software tool technically sound? Partly Are sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes Is sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly Are the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Analytical biochemistry, Plant hormones, Strigolactones, Plant growth regulators I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Wang JY. Reviewer Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.136376.r174935 ) The direct URL for this report is: https://f1000research.com/articles/11-1191/v1#referee-response-174935 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 08 Apr 2024 Susan Murch , Chemistry, University of British Columbia, Kelowna, V1V1V7, Canada 08 Apr 2024 Author Response We thank reviewer 2 for reviewing our manuscript and for their appreciation of the need for untargeted metabolomics workflows for exploring phytohormones. Below, we have provided responses to each of ... Continue reading We thank reviewer 2 for reviewing our manuscript and for their appreciation of the need for untargeted metabolomics workflows for exploring phytohormones. Below, we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: HormonomicsDB is definitely required for the plant metabolomics field and it provides many advantages to identify compounds. While the paper is well written and clearly demonstrates how to use this platform, I have a few comments to, hopefully, improve the content. Author Response to Comment: We appreciate that reviewer #2 has also identified the need for metabolomics approaches specifically tailored to the identification of phytohormones, specifically due to their labile and sensitive nature, as addressed in our manuscript. Comment #2: What is the maximum mass tolerance (in Da and ppm) when identifying metabolites? Also, natural components usually contain isomers/isoforms, how to distinguish or interpret them by using HormonomicsDB? It would be necessary to guild users on how to transform Da to ppm. Author Response to Comment: This was a comment also brought up by reviewer #1, and we have revised the manuscript to address this concern. Regarding mass tolerance, we updated HormonomicsDB to include an option to use ppm for mass tolerance. We have also added the following to the supplemental information: “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1. For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below ( https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass ). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Regarding isomers/isoforms, it is often challenging in LC-MS to separate isomers as they can have relatively similar retention times. Additionally, MS/MS fragmentation often struggles to differentiate isomers. Ion mobility spectrometry – mass spectrometry (IMS-MS) is a relatively new technique which has been deployed to separate isomers in time based on their collisional cross section (CCS). This is an emerging technology and we expect that IMS will play an important role in future hormonomics studies. However, in silico CCS predictions are still in their infancy and IMS-MS capable instruments are still fairly inaccessible. Given these hurdles we cannot include IMS-MS in this current version of HormonomicsDB, however as these technologies become more accessible we will work toward including IMS-MS data in HormonomicsDB. Comment #3: Please include the explanations of the PGR Monoisotopic, PGR M+H, and so on to junior users. Author Response to Comment: To address any ambiguity to these terms we have added the following to the Methods section “Plant growth regulators”: “PGR Monoisotopic contains the monoisotopic mass for each phytohormone, the PGR M+H contains the m/z of each phytohormone as an M+H adduct, the PGR adducts contains the m/z of 7 common adducts (Table 1), and PGR biotransformations contains 27 common biotransformations (Table 1) as M+H adducts.” Comment #4: It is a bit confusing between Table 4 and Table 5 in the m/z, what are the minimum decimal numbers of accurate mass (default setting) of particular metabolites in HormonomicsDB? In the above two cases, what was the mass tolerance (or acceptable error) to identify the compounds? Author Response to Comment: We have updated table 4 and 6 to include more decimal points for both the experimental and library match m/z. Additionally, we have included the ppm difference, as HormonomicsDB now computes this. The data in Brown et al. was acquired on a TOF, therefore an uncertainty of 3-5 ppm is expected. We have added the following to the methods section discussing this: “The data in Brown et al. 2012 was collected on a time of flight (TOF) mass spectrometer, which typically has a mass error of 3 to 5 ppm.” Comment #5: As a researcher in strigolactone (SL) biology, the methanol extraction would lead to the fast degradation of SLs. Could the author pay attention to this? In addition, the unarguable identification of a particular SL requires MS/MS (not only accurate mass). Therefore, if there would be MS/MS database in HormonomicsDB for advanced non-targeted metabolomics, it would be greatly helpful. Author Response to Comment: We understand that MS/MS is an important tool for discovering and identifying phytohormones in untargeted studies, however, we found that current tools for in silico prediction of low energy MS/MS spectra often provide incorrect predictions, we felt it would be inappropriate to add MS/MS to HormonomicsDB in this publication. But, as in silico MS/MS prediction tools improve and more phytohormone standards become accessible, we hope to release another version of HormonomicsDB with MS/MS searching capabilities. Comment #5: What is the minimum intensity (e3 or e4?) of peaks to be considered as metabolites instead of noise? Author Response to Comment: Since HormonomicsDB takes aligned peak tables, the signal to noise (S/N) cut-off would have been determined during the alignment process, as this is the most common approach vendor software currently use for selecting chemical features prior to alignment. Additionally, some software outputs the aligned peak table with relative intensities. To address this concern we added the following to the Methods: “HormonomicsDB makes no assumptions about signal to noise (S/N) or other sensitivity figures of merit as these are typically made during this peak alignment step.” We thank reviewer 2 for reviewing our manuscript and for their appreciation of the need for untargeted metabolomics workflows for exploring phytohormones. Below, we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: HormonomicsDB is definitely required for the plant metabolomics field and it provides many advantages to identify compounds. While the paper is well written and clearly demonstrates how to use this platform, I have a few comments to, hopefully, improve the content. Author Response to Comment: We appreciate that reviewer #2 has also identified the need for metabolomics approaches specifically tailored to the identification of phytohormones, specifically due to their labile and sensitive nature, as addressed in our manuscript. Comment #2: What is the maximum mass tolerance (in Da and ppm) when identifying metabolites? Also, natural components usually contain isomers/isoforms, how to distinguish or interpret them by using HormonomicsDB? It would be necessary to guild users on how to transform Da to ppm. Author Response to Comment: This was a comment also brought up by reviewer #1, and we have revised the manuscript to address this concern. Regarding mass tolerance, we updated HormonomicsDB to include an option to use ppm for mass tolerance. We have also added the following to the supplemental information: “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1. For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below ( https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass ). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Regarding isomers/isoforms, it is often challenging in LC-MS to separate isomers as they can have relatively similar retention times. Additionally, MS/MS fragmentation often struggles to differentiate isomers. Ion mobility spectrometry – mass spectrometry (IMS-MS) is a relatively new technique which has been deployed to separate isomers in time based on their collisional cross section (CCS). This is an emerging technology and we expect that IMS will play an important role in future hormonomics studies. However, in silico CCS predictions are still in their infancy and IMS-MS capable instruments are still fairly inaccessible. Given these hurdles we cannot include IMS-MS in this current version of HormonomicsDB, however as these technologies become more accessible we will work toward including IMS-MS data in HormonomicsDB. Comment #3: Please include the explanations of the PGR Monoisotopic, PGR M+H, and so on to junior users. Author Response to Comment: To address any ambiguity to these terms we have added the following to the Methods section “Plant growth regulators”: “PGR Monoisotopic contains the monoisotopic mass for each phytohormone, the PGR M+H contains the m/z of each phytohormone as an M+H adduct, the PGR adducts contains the m/z of 7 common adducts (Table 1), and PGR biotransformations contains 27 common biotransformations (Table 1) as M+H adducts.” Comment #4: It is a bit confusing between Table 4 and Table 5 in the m/z, what are the minimum decimal numbers of accurate mass (default setting) of particular metabolites in HormonomicsDB? In the above two cases, what was the mass tolerance (or acceptable error) to identify the compounds? Author Response to Comment: We have updated table 4 and 6 to include more decimal points for both the experimental and library match m/z. Additionally, we have included the ppm difference, as HormonomicsDB now computes this. The data in Brown et al. was acquired on a TOF, therefore an uncertainty of 3-5 ppm is expected. We have added the following to the methods section discussing this: “The data in Brown et al. 2012 was collected on a time of flight (TOF) mass spectrometer, which typically has a mass error of 3 to 5 ppm.” Comment #5: As a researcher in strigolactone (SL) biology, the methanol extraction would lead to the fast degradation of SLs. Could the author pay attention to this? In addition, the unarguable identification of a particular SL requires MS/MS (not only accurate mass). Therefore, if there would be MS/MS database in HormonomicsDB for advanced non-targeted metabolomics, it would be greatly helpful. Author Response to Comment: We understand that MS/MS is an important tool for discovering and identifying phytohormones in untargeted studies, however, we found that current tools for in silico prediction of low energy MS/MS spectra often provide incorrect predictions, we felt it would be inappropriate to add MS/MS to HormonomicsDB in this publication. But, as in silico MS/MS prediction tools improve and more phytohormone standards become accessible, we hope to release another version of HormonomicsDB with MS/MS searching capabilities. Comment #5: What is the minimum intensity (e3 or e4?) of peaks to be considered as metabolites instead of noise? Author Response to Comment: Since HormonomicsDB takes aligned peak tables, the signal to noise (S/N) cut-off would have been determined during the alignment process, as this is the most common approach vendor software currently use for selecting chemical features prior to alignment. Additionally, some software outputs the aligned peak table with relative intensities. To address this concern we added the following to the Methods: “HormonomicsDB makes no assumptions about signal to noise (S/N) or other sensitivity figures of merit as these are typically made during this peak alignment step.” Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 08 Apr 2024 Susan Murch , Chemistry, University of British Columbia, Kelowna, V1V1V7, Canada 08 Apr 2024 Author Response We thank reviewer 2 for reviewing our manuscript and for their appreciation of the need for untargeted metabolomics workflows for exploring phytohormones. Below, we have provided responses to each of ... Continue reading We thank reviewer 2 for reviewing our manuscript and for their appreciation of the need for untargeted metabolomics workflows for exploring phytohormones. Below, we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: HormonomicsDB is definitely required for the plant metabolomics field and it provides many advantages to identify compounds. While the paper is well written and clearly demonstrates how to use this platform, I have a few comments to, hopefully, improve the content. Author Response to Comment: We appreciate that reviewer #2 has also identified the need for metabolomics approaches specifically tailored to the identification of phytohormones, specifically due to their labile and sensitive nature, as addressed in our manuscript. Comment #2: What is the maximum mass tolerance (in Da and ppm) when identifying metabolites? Also, natural components usually contain isomers/isoforms, how to distinguish or interpret them by using HormonomicsDB? It would be necessary to guild users on how to transform Da to ppm. Author Response to Comment: This was a comment also brought up by reviewer #1, and we have revised the manuscript to address this concern. Regarding mass tolerance, we updated HormonomicsDB to include an option to use ppm for mass tolerance. We have also added the following to the supplemental information: “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1. For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below ( https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass ). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Regarding isomers/isoforms, it is often challenging in LC-MS to separate isomers as they can have relatively similar retention times. Additionally, MS/MS fragmentation often struggles to differentiate isomers. Ion mobility spectrometry – mass spectrometry (IMS-MS) is a relatively new technique which has been deployed to separate isomers in time based on their collisional cross section (CCS). This is an emerging technology and we expect that IMS will play an important role in future hormonomics studies. However, in silico CCS predictions are still in their infancy and IMS-MS capable instruments are still fairly inaccessible. Given these hurdles we cannot include IMS-MS in this current version of HormonomicsDB, however as these technologies become more accessible we will work toward including IMS-MS data in HormonomicsDB. Comment #3: Please include the explanations of the PGR Monoisotopic, PGR M+H, and so on to junior users. Author Response to Comment: To address any ambiguity to these terms we have added the following to the Methods section “Plant growth regulators”: “PGR Monoisotopic contains the monoisotopic mass for each phytohormone, the PGR M+H contains the m/z of each phytohormone as an M+H adduct, the PGR adducts contains the m/z of 7 common adducts (Table 1), and PGR biotransformations contains 27 common biotransformations (Table 1) as M+H adducts.” Comment #4: It is a bit confusing between Table 4 and Table 5 in the m/z, what are the minimum decimal numbers of accurate mass (default setting) of particular metabolites in HormonomicsDB? In the above two cases, what was the mass tolerance (or acceptable error) to identify the compounds? Author Response to Comment: We have updated table 4 and 6 to include more decimal points for both the experimental and library match m/z. Additionally, we have included the ppm difference, as HormonomicsDB now computes this. The data in Brown et al. was acquired on a TOF, therefore an uncertainty of 3-5 ppm is expected. We have added the following to the methods section discussing this: “The data in Brown et al. 2012 was collected on a time of flight (TOF) mass spectrometer, which typically has a mass error of 3 to 5 ppm.” Comment #5: As a researcher in strigolactone (SL) biology, the methanol extraction would lead to the fast degradation of SLs. Could the author pay attention to this? In addition, the unarguable identification of a particular SL requires MS/MS (not only accurate mass). Therefore, if there would be MS/MS database in HormonomicsDB for advanced non-targeted metabolomics, it would be greatly helpful. Author Response to Comment: We understand that MS/MS is an important tool for discovering and identifying phytohormones in untargeted studies, however, we found that current tools for in silico prediction of low energy MS/MS spectra often provide incorrect predictions, we felt it would be inappropriate to add MS/MS to HormonomicsDB in this publication. But, as in silico MS/MS prediction tools improve and more phytohormone standards become accessible, we hope to release another version of HormonomicsDB with MS/MS searching capabilities. Comment #5: What is the minimum intensity (e3 or e4?) of peaks to be considered as metabolites instead of noise? Author Response to Comment: Since HormonomicsDB takes aligned peak tables, the signal to noise (S/N) cut-off would have been determined during the alignment process, as this is the most common approach vendor software currently use for selecting chemical features prior to alignment. Additionally, some software outputs the aligned peak table with relative intensities. To address this concern we added the following to the Methods: “HormonomicsDB makes no assumptions about signal to noise (S/N) or other sensitivity figures of merit as these are typically made during this peak alignment step.” We thank reviewer 2 for reviewing our manuscript and for their appreciation of the need for untargeted metabolomics workflows for exploring phytohormones. Below, we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: HormonomicsDB is definitely required for the plant metabolomics field and it provides many advantages to identify compounds. While the paper is well written and clearly demonstrates how to use this platform, I have a few comments to, hopefully, improve the content. Author Response to Comment: We appreciate that reviewer #2 has also identified the need for metabolomics approaches specifically tailored to the identification of phytohormones, specifically due to their labile and sensitive nature, as addressed in our manuscript. Comment #2: What is the maximum mass tolerance (in Da and ppm) when identifying metabolites? Also, natural components usually contain isomers/isoforms, how to distinguish or interpret them by using HormonomicsDB? It would be necessary to guild users on how to transform Da to ppm. Author Response to Comment: This was a comment also brought up by reviewer #1, and we have revised the manuscript to address this concern. Regarding mass tolerance, we updated HormonomicsDB to include an option to use ppm for mass tolerance. We have also added the following to the supplemental information: “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1. For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below ( https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass ). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Regarding isomers/isoforms, it is often challenging in LC-MS to separate isomers as they can have relatively similar retention times. Additionally, MS/MS fragmentation often struggles to differentiate isomers. Ion mobility spectrometry – mass spectrometry (IMS-MS) is a relatively new technique which has been deployed to separate isomers in time based on their collisional cross section (CCS). This is an emerging technology and we expect that IMS will play an important role in future hormonomics studies. However, in silico CCS predictions are still in their infancy and IMS-MS capable instruments are still fairly inaccessible. Given these hurdles we cannot include IMS-MS in this current version of HormonomicsDB, however as these technologies become more accessible we will work toward including IMS-MS data in HormonomicsDB. Comment #3: Please include the explanations of the PGR Monoisotopic, PGR M+H, and so on to junior users. Author Response to Comment: To address any ambiguity to these terms we have added the following to the Methods section “Plant growth regulators”: “PGR Monoisotopic contains the monoisotopic mass for each phytohormone, the PGR M+H contains the m/z of each phytohormone as an M+H adduct, the PGR adducts contains the m/z of 7 common adducts (Table 1), and PGR biotransformations contains 27 common biotransformations (Table 1) as M+H adducts.” Comment #4: It is a bit confusing between Table 4 and Table 5 in the m/z, what are the minimum decimal numbers of accurate mass (default setting) of particular metabolites in HormonomicsDB? In the above two cases, what was the mass tolerance (or acceptable error) to identify the compounds? Author Response to Comment: We have updated table 4 and 6 to include more decimal points for both the experimental and library match m/z. Additionally, we have included the ppm difference, as HormonomicsDB now computes this. The data in Brown et al. was acquired on a TOF, therefore an uncertainty of 3-5 ppm is expected. We have added the following to the methods section discussing this: “The data in Brown et al. 2012 was collected on a time of flight (TOF) mass spectrometer, which typically has a mass error of 3 to 5 ppm.” Comment #5: As a researcher in strigolactone (SL) biology, the methanol extraction would lead to the fast degradation of SLs. Could the author pay attention to this? In addition, the unarguable identification of a particular SL requires MS/MS (not only accurate mass). Therefore, if there would be MS/MS database in HormonomicsDB for advanced non-targeted metabolomics, it would be greatly helpful. Author Response to Comment: We understand that MS/MS is an important tool for discovering and identifying phytohormones in untargeted studies, however, we found that current tools for in silico prediction of low energy MS/MS spectra often provide incorrect predictions, we felt it would be inappropriate to add MS/MS to HormonomicsDB in this publication. But, as in silico MS/MS prediction tools improve and more phytohormone standards become accessible, we hope to release another version of HormonomicsDB with MS/MS searching capabilities. Comment #5: What is the minimum intensity (e3 or e4?) of peaks to be considered as metabolites instead of noise? Author Response to Comment: Since HormonomicsDB takes aligned peak tables, the signal to noise (S/N) cut-off would have been determined during the alignment process, as this is the most common approach vendor software currently use for selecting chemical features prior to alignment. Additionally, some software outputs the aligned peak table with relative intensities. To address this concern we added the following to the Methods: “HormonomicsDB makes no assumptions about signal to noise (S/N) or other sensitivity figures of merit as these are typically made during this peak alignment step.” Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Views 0 Cite How to cite this report: Lewis A and Emery RJN. Reviewer Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.136376.r153643 ) The direct URL for this report is: https://f1000research.com/articles/11-1191/v1#referee-response-153643 NOTE: it is important to ensure the information in square brackets after the title is included in this citation. Close Copy Citation Details Reviewer Report 08 Nov 2022 Ainsely Lewis , Trent University, Peterborough, ON, Canada R.J. Neil Emery , Department of Biology, Trent University, Peterborough, ON, Canada Approved with Reservations VIEWS 0 https://doi.org/10.5256/f1000research.136376.r153643 Review by Ainsely Lewis, Ph.D., and Professor RJ Neil Emery Good points/Strengths of article: HormonomicsDB undoubtedly is a needed comprehensive tool to screen metabolites/phytohormones and plant growth regulators putatively. This tool ... Continue reading READ ALL Review by Ainsely Lewis, Ph.D., and Professor RJ Neil Emery Good points/Strengths of article: HormonomicsDB undoubtedly is a needed comprehensive tool to screen metabolites/phytohormones and plant growth regulators putatively. This tool is no doubt a novel tool that will aid researchers using mass spectrometry-based metabolomics for hormones in either plant or animal systems. Making choices of what classes or types of compounds to search for is particularly difficult. Therefore, this is a particularly helpful tool for narrowing metabolomics studies into a search for signaling molecules. It offers a focused study on a higher level in that it can uncover important compounds that have wider reaching or pleiotropic effects. This is especially good for screening for these hormones especially if they are not known to be present in a given system of study. Knowing putative compounds in an extraction procedure with various factors (extraction buffer used, solvents, using SPE or not), can really aid in targeted analysis, or to help develop a method to maximize extraction of hormones/phytohormones of interest. This manuscript is quite an undertaking! This is a well written and well-done manuscript, that is scientifically sound. Introduction was well done and nicely sets the pace for readers. Methodology was thorough and straightforward. Results and discussion section was thorough. Liked the COVID angle in the conclusions. The grammar and word choices used in the manuscript was good as well. Approved with reservations. Minor adjustments/revisions needed. Minor suggestions - Things for clarification for other users/readers with commentary. These are suggestions that we believe can aid in improving the manuscript: Not everyone is aware of the relationship with Dalton (Da) and parts per million (ppm). This is speaking about mass tolerance, especially looking on m/z values near the theoretical values of phytohormones/plant growth regulators. Conversion from Da to ppm is dependent on the m/z examined as you are aware. I think it is important for users to be aware of this, as not everyone may have an intense Chemistry background. We suggest that either adding this in the text (supplemental or otherwise) would really aid the manuscript and users new to mass spectrometry-based metabolomics. Additionally, you could mention that for the data that is downloaded from HormonomicsDB, that to know the ppm error used, that they use the formula: observed mass – theoretical mass/theoretical mass * 10 ^6 to know what error in ppm. The default for HormonomicsDB is ±0.01 Da. How much Daltons error wise do you recommend people using? In other words, if you have an ion mass of 1000.1356, and you want a desired ppm error of 5, how much would it be in daltons, or how much deviation can you expect? Using this formula (i.e., deviation in daltons with a given ion mass), especially, would clear up some ambiguity using either ppm or daltons, as well as to guide users/readers. We suggest that you should mention that the acceptable error limits that would be dependent on the mass spectrometer of question. For example, using 20 ppm on a high-resolution mass spectrometry instrument especially with MS1 data is not kindly looked on some individuals in the mass spectrometry world. For example, 5-10 ppm error or less for Orbitrap is acceptable. This is not necessarily needed in the main text, but can be put in the supplemental, as this is not the main message of the manuscript. This was mentioned as studies you screened are from the Orbitrap and Q-TOF instruments. Having being users of HormonomicsDB, we think it is important to mention on the HormonomicsDB website the LC gradient that was used for the study. You mention it in the manuscript, which is good, but having it on the website somewhere will let the user be reminded that the LC gradient used in the paper may not be like theirs. Too much reliance on RTs may result in false negatives or positives. Even among different labs, the same machine, same columns, and mobile phase gradients can result in significantly different Rt’s. The readers should be more in tune to the elution points of compounds relative to others or external standards. Although the note about RT match is dependent on machine learning (which is a nice and novel approach by the way), we suggest that the authors should emphasize more to the reader that they should stick with exact mass (m/z) within a certain error margin, should they use another LC gradient, with various run times (solvents, columns, etc). In the supplemental information, especially supplemental file 1, although for the table of phytohormones M+H was used, we suggest that the masses from the [M-H] - ionization mode should be added as well. We also suggest that the synthetic compounds should not be grouped with the plant growth regulators or their precursor compounds and/or intermediates. Rather, separate them into different sheets. For example: predicted metabolites (Table 1), training standards (Table 2), and synthetic compounds (Table 3). Many people won’t care about glyphosate or thidiazuron as much as other compounds that are endogenous such as Spermidine, Indoleacetate (IAA), or Gibberellins (GAs). While it is still good to know if glyphosate was used in the plant organism of interest, for the supplemental, maybe put glyphosate and other synthetic compounds to themselves. That way, the focus can be on phytohormones/plant growth regulators and other related compounds from Tryptophan metabolism. If the readers want, they can consider the other synthetic ones just to see. Putting them in different tables also helps in reading. We tested HormonomicsDB with XCMS Online results from untargeted metabolomics data and it (i.e., HormonomicsDB) works! Targeting Gibberellins via extraction can be a challenge, but they were putatively identified in negative mode data extracted using XCMS Online! I think it would aid the manuscript to mention that XCMS Online data can be formatted for use in HormonomicsDB! It gives surprising results! Although XCMS Online is a tool used for aligning peaks/mass features, we still must check the actual retention time in the processing software that comes with the mass spectrometer to make sure that the peak is a good one. It is wonderful that you mentioned MetaboAnalyst but think about XCMS Online or other peak/feature aligning methods as well. XCMS Online and MetaboAnalyst can be used in tandem to make meaningful information. One that readers can try is a recent peak/feature aligning server/software: Metaboseek (published this year). You did mention Misra et al . 2021’s comprehensive review! We suggest that you should mention other open-source tools that can be used to preprocess data that could be used with HormonomicsDB. It would bolster the strength of HormonomicsDB as being more versatile than just a standalone tool. While not the pivot of the study, the custom database output does not get enough credit in this paper. We tried primary metabolites with XCMS Online data and found compounds based on m/z values! We did not consider the RT as a factor as our lab method is 1/3 rd the length of the lab method mentioned in this manuscript. But this goes to show that users can use a subset of hormones and other key metabolites they are only interested in to get an output, for more targeted analyses later. We believe that this is another strength of using HormonomicsDB custom database that should be emphasized more. When do you use biotransformations? In using the software, it can be confusing. Can you clarify this part a bit? Letting the user know what the ups and downs or advantages and disadvantages of each function (i.e., PGR monoisotopic, PGR M-H or M+H, PGR Adducts, PGR Biotransformations) would be helpful. What have you found using these? Some commentary about how to use these functions alone, or in support of each other would be quite helpful. Is the rationale for developing the new software tool clearly explained? Yes Is the description of the software tool technically sound? Yes Are sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes Is sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes Are the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Mass spectrometry-based metabolomics, phytohormone profiling, chemometrics We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above. Close READ LESS CITE CITE HOW TO CITE THIS REPORT Lewis A and Emery RJN. Reviewer Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.136376.r153643 ) The direct URL for this report is: https://f1000research.com/articles/11-1191/v1#referee-response-153643 NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS Report a concern Author Response 08 Apr 2024 Susan Murch , Chemistry, University of British Columbia, Kelowna, V1V1V7, Canada 08 Apr 2024 Author Response We thank reviewer 1 for pointing out what they identified as strengths within our article and ultimately in our novel metabolomics tool/workflow. We appreciate their helpful feedback and comments which ... Continue reading We thank reviewer 1 for pointing out what they identified as strengths within our article and ultimately in our novel metabolomics tool/workflow. We appreciate their helpful feedback and comments which we believe will strengthen our manuscript and metabolomics tool. Below we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: Not everyone is aware of the relationship with Dalton (Da) and parts per million (ppm). This is speaking about mass tolerance, especially looking on m/z values near the theoretical values of phytohormones/plant growth regulators. Conversion from Da to ppm is dependent on the m/z examined as you are aware. I think it is important for users to be aware of this, as not everyone may have an intense Chemistry background. We suggest that either adding this in the text (supplemental or otherwise) would really aid the manuscript and users new to mass spectrometry-based metabolomics. Additionally, you could mention that for the data that is downloaded from HormonomicsDB, that to know the ppm error used, that they use the formula: observed mass – theoretical mass/theoretical mass * 10^6 to know what error in ppm. The default for HormonomicsDB is ±0.01 Da. How much Daltons error wise do you recommend people using? In other words, if you have an ion mass of 1000.1356, and you want a desired ppm error of 5, how much would it be in daltons, or how much deviation can you expect? Using this formula (i.e., deviation in daltons with a given ion mass), especially, would clear up some ambiguity using either ppm or daltons, as well as to guide users/readers. Comment #2: We suggest that you should mention that the acceptable error limits that would be dependent on the mass spectrometer of question. For example, using 20 ppm on a highresolution mass spectrometry instrument especially with MS1 data is not kindly looked on some individuals in the mass spectrometry world. For example, 5-10 ppm error or less for Orbitrap is acceptable. This is not necessarily needed in the main text, but can be put in the supplemental, as this is not the main message of the manuscript. This was mentioned as studies you screened are from the Orbitrap and Q-TOF instruments. Author Response to Comment: We have chosen to address comment #1 and #2 together since they are closely related. We have added a Supplemental Information (SI) file to address this issue regarding mass tolerance in Da and ppm. We have added the following to the SI under the heading “Selecting Mass Tolerance”. Reference has been made to this section in the SI on page 4 in the manuscript under the section “Data inputs and outputs”: We have also updated HormonomicsDB to include an option to use ppm for mass tolerance. “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1 . For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below ( https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass ). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Comment #3: Having being users of HormonomicsDB, we think it is important to mention on the HormonomicsDB website the LC gradient that was used for the study. You mention it in the manuscript, which is good, but having it on the website somewhere will let the user be reminded that the LC gradient used in the paper may not be like theirs. Too much reliance on RTs may result in false negatives or positives. Even among different labs, the same machine, same columns, and mobile phase gradients can result in significantly different Rt’s. The readers should be more in tune to the elution points of compounds relative to others or external standards. Comment #4: Although the note about RT match is dependent on machine learning (which is a nice and novel approach by the way), we suggest that the authors should emphasize more to the reader that they should stick with exact mass (m/z) within a certain error margin, should they use another LC gradient, with various run times (solvents, columns, etc). Author Response to Comment: We are going to address comments #3 and #4 together as they discuss similar concerns. We will add a mention of the RT and gradient used on the landing page for HormonomicsDB. Additionally, we will add a link to this manuscript there so users can refer to the paper before using the tool. We feel that this should address the concerns in comment #3. We have added the following statement to the manuscript to the section “Retention time prediction” in the Result and discussion: “While RT predictions help to increase confidence in putative identification, it is important to note that differences in gradient, column, or solvents can impact the RT of analytes. The users should place more emphasis on the accurate mass matching and use RT prediction results to confirm if the elution pattern or order is as expected and elution of the analyte occurs at a reasonable time within the gradient”. Comment #5: In the supplemental information, especially supplemental file 1, although for the table of phytohormones M+H was used, we suggest that the masses from the [M-H]- ionization mode should be added as well. We also suggest that the synthetic compounds should not be grouped with the plant growth regulators or their precursor compounds and/or intermediates. Rather, separate them into different sheets. For example: predicted metabolites (Table 1), training standards (Table 2), and synthetic compounds (Table 3). Many people won’t care about glyphosate or thidiazuron as much as other compounds that are endogenous such as Spermidine, Indoleacetate (IAA), or Gibberellins (GAs). While it is still good to know if glyphosate was used in the plant organism of interest, for the supplemental, maybe put glyphosate and other synthetic compounds to themselves. That way, the focus can be on phytohormones/plant growth regulators and other related compounds from Tryptophan metabolism. If the readers want, they can consider the other synthetic ones just to see. Putting them in different tables also helps in reading. Author Response to Comment: We appreciate these great suggestions for the database content. The synthetic compounds provide some useful and comparatively inexpensive standards to train the chromatography model and are useful for the analytical method but not necessarily the biological question. We are working on software updates will incorporate a tool to distinguish between synthetics and naturally occurring compounds in a future version. Comment #6: We tested HormonomicsDB with XCMS Online results from untargeted metabolomics data and it (i.e., HormonomicsDB) works! Targeting Gibberellins via extraction can be a challenge, but they were putatively identified in negative mode data extracted using XCMS Online! I think it would aid the manuscript to mention that XCMS Online data can be formatted for use in HormonomicsDB! It gives surprising results! Although XCMS Online is a tool used for aligning peaks/mass features, we still must check the actual retention time in the processing software that comes with the mass spectrometer to make sure that the peak is a good one. It is wonderful that you mentioned MetaboAnalyst but think about XCMS Online or other peak/feature aligning methods as well. XCMS Online and MetaboAnalyst can be used in tandem to make meaningful information. One that readers can try is a recent peak/feature aligning server/software: Metaboseek (published this year). You did mention Misra et al. 2021’s comprehensive review! We suggest that you should mention other opensource tools that can be used to preprocess data that could be used with HormonomicsDB. It would bolster the strength of HormonomicsDB as being more versatile than just a standalone tool. Author Response to Comment: This is an important point that is often understated in the literature, since many analysts do not consider how raw data files are converted into a peak table, or the “X” block for putative ID or statistical analysis. To address this, we added the following to the section “Data input and output”: “Users can generate peak tables for upload to HormonomicsDB a number of ways, including with vendor software, or open source packages. These software take raw data files collected from individual chromatographic runs, and align the peaks to generate a single peak table which describes all the samples in the metabolomics experiment. These open source tools include XCMS (xcmsonline.scripps.edu), MetaboAnalyst (metaboanalyst.com), mzMine (mzmine.github.io), and Metaboseek (metaboseek.com).” Comment #7: While not the pivot of the study, the custom database output does not get enough credit in this paper. We tried primary metabolites with XCMS Online data and found compounds based on m/z values! We did not consider the RT as a factor as our lab method is 1/3rd the length of the lab method mentioned in this manuscript. But this goes to show that users can use a subset of hormones and other key metabolites they are only interested in to get an output, for more targeted analyses later. We believe that this is another strength of using HormonomicsDB custom database that should be emphasized more. Author Response to Comment: To emphasize the utility of the HormonomicsDB custom search function we have changed this section from a sub section to its own section in the manuscript (in the methods), and discussed the utility of this function by adding the following to the Results and discussion section “HormonomicsDB web-tool functionality and interface”: “Additionally, the “HormonomicsDB custom search” function is a novel feature within HormonomicsDB which allows users to search their peak table against their own database of metabolites. This is the first such report of a feature that allows users to queue with their own database. We hope to continue growing this function to allow users to queue against other databases by accessing them through an application programming interface (API) in the HormonomicsDB environment.” Comment #8: When do you use biotransformations? In using the software, it can be confusing. Can you clarify this part a bit? Comment #9: Letting the user know what the ups and downs or advantages and disadvantages of each function (i.e., PGR monoisotopic, PGR M-H or M+H, PGR Adducts, PGR Biotransformations) would be helpful. What have you found using these? Some commentary about how to use these functions alone, or in support of each other would be quite helpful. Author Response to Comment: Comments #8 and #9 are related, so we will address them together. We added the following to the end of the section in methods “Data input and output”: “The databases queued against depend on the structure of the input data and the users hypothesis. Certain software, particularly for Fourier transform mass spectrometry (FT-MS) data, convert ion masses to monoisotopic mass before exporting a peak table. If this is the case, the user can queue against the “PGR Monoisotopic” database. In ESI-LC-MS, the most common adduct is M+H in ESI positive mode and M-H in ESI negative mode. To queue for molecular ions only in the untargeted dataset, users should select the “PGR M+H” or “PGR M-H” databases, depending on their ionization mode. Adducts are often encountered in ESI-LC-MS, especially in ESI positive mode, as metal ions tend to form cations in aqueous solution. If the intensity for a particular PGR is decreased, or the PGR is absent when searching for molecular ion, the user can search for the common adducts of the PGRs in HormonomicsDB by queueing against the “PGR Adducts” database. Searching for the molecular ion and adducts at the same time is permissible in HormonomicsDB and allows the user to detect PGRs present in both forms. Biotransformations allow the user to search for modified forms of PGRs in their metabolomics dataset. This is useful when the goal is to identify conjugates and metabolites of PGRs in plants. The “PGR Biotransformations” database can be searched concurrently with the “PGR M+H” database, to identify PGRs in their native state and as conjugates. This approach can lead to the generation of new hypotheses in plant physiology and metabolism.” We thank reviewer 1 for pointing out what they identified as strengths within our article and ultimately in our novel metabolomics tool/workflow. We appreciate their helpful feedback and comments which we believe will strengthen our manuscript and metabolomics tool. Below we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: Not everyone is aware of the relationship with Dalton (Da) and parts per million (ppm). This is speaking about mass tolerance, especially looking on m/z values near the theoretical values of phytohormones/plant growth regulators. Conversion from Da to ppm is dependent on the m/z examined as you are aware. I think it is important for users to be aware of this, as not everyone may have an intense Chemistry background. We suggest that either adding this in the text (supplemental or otherwise) would really aid the manuscript and users new to mass spectrometry-based metabolomics. Additionally, you could mention that for the data that is downloaded from HormonomicsDB, that to know the ppm error used, that they use the formula: observed mass – theoretical mass/theoretical mass * 10^6 to know what error in ppm. The default for HormonomicsDB is ±0.01 Da. How much Daltons error wise do you recommend people using? In other words, if you have an ion mass of 1000.1356, and you want a desired ppm error of 5, how much would it be in daltons, or how much deviation can you expect? Using this formula (i.e., deviation in daltons with a given ion mass), especially, would clear up some ambiguity using either ppm or daltons, as well as to guide users/readers. Comment #2: We suggest that you should mention that the acceptable error limits that would be dependent on the mass spectrometer of question. For example, using 20 ppm on a highresolution mass spectrometry instrument especially with MS1 data is not kindly looked on some individuals in the mass spectrometry world. For example, 5-10 ppm error or less for Orbitrap is acceptable. This is not necessarily needed in the main text, but can be put in the supplemental, as this is not the main message of the manuscript. This was mentioned as studies you screened are from the Orbitrap and Q-TOF instruments. Author Response to Comment: We have chosen to address comment #1 and #2 together since they are closely related. We have added a Supplemental Information (SI) file to address this issue regarding mass tolerance in Da and ppm. We have added the following to the SI under the heading “Selecting Mass Tolerance”. Reference has been made to this section in the SI on page 4 in the manuscript under the section “Data inputs and outputs”: We have also updated HormonomicsDB to include an option to use ppm for mass tolerance. “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1 . For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below ( https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass ). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Comment #3: Having being users of HormonomicsDB, we think it is important to mention on the HormonomicsDB website the LC gradient that was used for the study. You mention it in the manuscript, which is good, but having it on the website somewhere will let the user be reminded that the LC gradient used in the paper may not be like theirs. Too much reliance on RTs may result in false negatives or positives. Even among different labs, the same machine, same columns, and mobile phase gradients can result in significantly different Rt’s. The readers should be more in tune to the elution points of compounds relative to others or external standards. Comment #4: Although the note about RT match is dependent on machine learning (which is a nice and novel approach by the way), we suggest that the authors should emphasize more to the reader that they should stick with exact mass (m/z) within a certain error margin, should they use another LC gradient, with various run times (solvents, columns, etc). Author Response to Comment: We are going to address comments #3 and #4 together as they discuss similar concerns. We will add a mention of the RT and gradient used on the landing page for HormonomicsDB. Additionally, we will add a link to this manuscript there so users can refer to the paper before using the tool. We feel that this should address the concerns in comment #3. We have added the following statement to the manuscript to the section “Retention time prediction” in the Result and discussion: “While RT predictions help to increase confidence in putative identification, it is important to note that differences in gradient, column, or solvents can impact the RT of analytes. The users should place more emphasis on the accurate mass matching and use RT prediction results to confirm if the elution pattern or order is as expected and elution of the analyte occurs at a reasonable time within the gradient”. Comment #5: In the supplemental information, especially supplemental file 1, although for the table of phytohormones M+H was used, we suggest that the masses from the [M-H]- ionization mode should be added as well. We also suggest that the synthetic compounds should not be grouped with the plant growth regulators or their precursor compounds and/or intermediates. Rather, separate them into different sheets. For example: predicted metabolites (Table 1), training standards (Table 2), and synthetic compounds (Table 3). Many people won’t care about glyphosate or thidiazuron as much as other compounds that are endogenous such as Spermidine, Indoleacetate (IAA), or Gibberellins (GAs). While it is still good to know if glyphosate was used in the plant organism of interest, for the supplemental, maybe put glyphosate and other synthetic compounds to themselves. That way, the focus can be on phytohormones/plant growth regulators and other related compounds from Tryptophan metabolism. If the readers want, they can consider the other synthetic ones just to see. Putting them in different tables also helps in reading. Author Response to Comment: We appreciate these great suggestions for the database content. The synthetic compounds provide some useful and comparatively inexpensive standards to train the chromatography model and are useful for the analytical method but not necessarily the biological question. We are working on software updates will incorporate a tool to distinguish between synthetics and naturally occurring compounds in a future version. Comment #6: We tested HormonomicsDB with XCMS Online results from untargeted metabolomics data and it (i.e., HormonomicsDB) works! Targeting Gibberellins via extraction can be a challenge, but they were putatively identified in negative mode data extracted using XCMS Online! I think it would aid the manuscript to mention that XCMS Online data can be formatted for use in HormonomicsDB! It gives surprising results! Although XCMS Online is a tool used for aligning peaks/mass features, we still must check the actual retention time in the processing software that comes with the mass spectrometer to make sure that the peak is a good one. It is wonderful that you mentioned MetaboAnalyst but think about XCMS Online or other peak/feature aligning methods as well. XCMS Online and MetaboAnalyst can be used in tandem to make meaningful information. One that readers can try is a recent peak/feature aligning server/software: Metaboseek (published this year). You did mention Misra et al. 2021’s comprehensive review! We suggest that you should mention other opensource tools that can be used to preprocess data that could be used with HormonomicsDB. It would bolster the strength of HormonomicsDB as being more versatile than just a standalone tool. Author Response to Comment: This is an important point that is often understated in the literature, since many analysts do not consider how raw data files are converted into a peak table, or the “X” block for putative ID or statistical analysis. To address this, we added the following to the section “Data input and output”: “Users can generate peak tables for upload to HormonomicsDB a number of ways, including with vendor software, or open source packages. These software take raw data files collected from individual chromatographic runs, and align the peaks to generate a single peak table which describes all the samples in the metabolomics experiment. These open source tools include XCMS (xcmsonline.scripps.edu), MetaboAnalyst (metaboanalyst.com), mzMine (mzmine.github.io), and Metaboseek (metaboseek.com).” Comment #7: While not the pivot of the study, the custom database output does not get enough credit in this paper. We tried primary metabolites with XCMS Online data and found compounds based on m/z values! We did not consider the RT as a factor as our lab method is 1/3rd the length of the lab method mentioned in this manuscript. But this goes to show that users can use a subset of hormones and other key metabolites they are only interested in to get an output, for more targeted analyses later. We believe that this is another strength of using HormonomicsDB custom database that should be emphasized more. Author Response to Comment: To emphasize the utility of the HormonomicsDB custom search function we have changed this section from a sub section to its own section in the manuscript (in the methods), and discussed the utility of this function by adding the following to the Results and discussion section “HormonomicsDB web-tool functionality and interface”: “Additionally, the “HormonomicsDB custom search” function is a novel feature within HormonomicsDB which allows users to search their peak table against their own database of metabolites. This is the first such report of a feature that allows users to queue with their own database. We hope to continue growing this function to allow users to queue against other databases by accessing them through an application programming interface (API) in the HormonomicsDB environment.” Comment #8: When do you use biotransformations? In using the software, it can be confusing. Can you clarify this part a bit? Comment #9: Letting the user know what the ups and downs or advantages and disadvantages of each function (i.e., PGR monoisotopic, PGR M-H or M+H, PGR Adducts, PGR Biotransformations) would be helpful. What have you found using these? Some commentary about how to use these functions alone, or in support of each other would be quite helpful. Author Response to Comment: Comments #8 and #9 are related, so we will address them together. We added the following to the end of the section in methods “Data input and output”: “The databases queued against depend on the structure of the input data and the users hypothesis. Certain software, particularly for Fourier transform mass spectrometry (FT-MS) data, convert ion masses to monoisotopic mass before exporting a peak table. If this is the case, the user can queue against the “PGR Monoisotopic” database. In ESI-LC-MS, the most common adduct is M+H in ESI positive mode and M-H in ESI negative mode. To queue for molecular ions only in the untargeted dataset, users should select the “PGR M+H” or “PGR M-H” databases, depending on their ionization mode. Adducts are often encountered in ESI-LC-MS, especially in ESI positive mode, as metal ions tend to form cations in aqueous solution. If the intensity for a particular PGR is decreased, or the PGR is absent when searching for molecular ion, the user can search for the common adducts of the PGRs in HormonomicsDB by queueing against the “PGR Adducts” database. Searching for the molecular ion and adducts at the same time is permissible in HormonomicsDB and allows the user to detect PGRs present in both forms. Biotransformations allow the user to search for modified forms of PGRs in their metabolomics dataset. This is useful when the goal is to identify conjugates and metabolites of PGRs in plants. The “PGR Biotransformations” database can be searched concurrently with the “PGR M+H” database, to identify PGRs in their native state and as conjugates. This approach can lead to the generation of new hypotheses in plant physiology and metabolism.” Competing Interests: No competing interests were disclosed. Close Report a concern Respond or Comment COMMENTS ON THIS REPORT Author Response 08 Apr 2024 Susan Murch , Chemistry, University of British Columbia, Kelowna, V1V1V7, Canada 08 Apr 2024 Author Response We thank reviewer 1 for pointing out what they identified as strengths within our article and ultimately in our novel metabolomics tool/workflow. We appreciate their helpful feedback and comments which ... Continue reading We thank reviewer 1 for pointing out what they identified as strengths within our article and ultimately in our novel metabolomics tool/workflow. We appreciate their helpful feedback and comments which we believe will strengthen our manuscript and metabolomics tool. Below we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: Not everyone is aware of the relationship with Dalton (Da) and parts per million (ppm). This is speaking about mass tolerance, especially looking on m/z values near the theoretical values of phytohormones/plant growth regulators. Conversion from Da to ppm is dependent on the m/z examined as you are aware. I think it is important for users to be aware of this, as not everyone may have an intense Chemistry background. We suggest that either adding this in the text (supplemental or otherwise) would really aid the manuscript and users new to mass spectrometry-based metabolomics. Additionally, you could mention that for the data that is downloaded from HormonomicsDB, that to know the ppm error used, that they use the formula: observed mass – theoretical mass/theoretical mass * 10^6 to know what error in ppm. The default for HormonomicsDB is ±0.01 Da. How much Daltons error wise do you recommend people using? In other words, if you have an ion mass of 1000.1356, and you want a desired ppm error of 5, how much would it be in daltons, or how much deviation can you expect? Using this formula (i.e., deviation in daltons with a given ion mass), especially, would clear up some ambiguity using either ppm or daltons, as well as to guide users/readers. Comment #2: We suggest that you should mention that the acceptable error limits that would be dependent on the mass spectrometer of question. For example, using 20 ppm on a highresolution mass spectrometry instrument especially with MS1 data is not kindly looked on some individuals in the mass spectrometry world. For example, 5-10 ppm error or less for Orbitrap is acceptable. This is not necessarily needed in the main text, but can be put in the supplemental, as this is not the main message of the manuscript. This was mentioned as studies you screened are from the Orbitrap and Q-TOF instruments. Author Response to Comment: We have chosen to address comment #1 and #2 together since they are closely related. We have added a Supplemental Information (SI) file to address this issue regarding mass tolerance in Da and ppm. We have added the following to the SI under the heading “Selecting Mass Tolerance”. Reference has been made to this section in the SI on page 4 in the manuscript under the section “Data inputs and outputs”: We have also updated HormonomicsDB to include an option to use ppm for mass tolerance. “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1 . For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below ( https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass ). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Comment #3: Having being users of HormonomicsDB, we think it is important to mention on the HormonomicsDB website the LC gradient that was used for the study. You mention it in the manuscript, which is good, but having it on the website somewhere will let the user be reminded that the LC gradient used in the paper may not be like theirs. Too much reliance on RTs may result in false negatives or positives. Even among different labs, the same machine, same columns, and mobile phase gradients can result in significantly different Rt’s. The readers should be more in tune to the elution points of compounds relative to others or external standards. Comment #4: Although the note about RT match is dependent on machine learning (which is a nice and novel approach by the way), we suggest that the authors should emphasize more to the reader that they should stick with exact mass (m/z) within a certain error margin, should they use another LC gradient, with various run times (solvents, columns, etc). Author Response to Comment: We are going to address comments #3 and #4 together as they discuss similar concerns. We will add a mention of the RT and gradient used on the landing page for HormonomicsDB. Additionally, we will add a link to this manuscript there so users can refer to the paper before using the tool. We feel that this should address the concerns in comment #3. We have added the following statement to the manuscript to the section “Retention time prediction” in the Result and discussion: “While RT predictions help to increase confidence in putative identification, it is important to note that differences in gradient, column, or solvents can impact the RT of analytes. The users should place more emphasis on the accurate mass matching and use RT prediction results to confirm if the elution pattern or order is as expected and elution of the analyte occurs at a reasonable time within the gradient”. Comment #5: In the supplemental information, especially supplemental file 1, although for the table of phytohormones M+H was used, we suggest that the masses from the [M-H]- ionization mode should be added as well. We also suggest that the synthetic compounds should not be grouped with the plant growth regulators or their precursor compounds and/or intermediates. Rather, separate them into different sheets. For example: predicted metabolites (Table 1), training standards (Table 2), and synthetic compounds (Table 3). Many people won’t care about glyphosate or thidiazuron as much as other compounds that are endogenous such as Spermidine, Indoleacetate (IAA), or Gibberellins (GAs). While it is still good to know if glyphosate was used in the plant organism of interest, for the supplemental, maybe put glyphosate and other synthetic compounds to themselves. That way, the focus can be on phytohormones/plant growth regulators and other related compounds from Tryptophan metabolism. If the readers want, they can consider the other synthetic ones just to see. Putting them in different tables also helps in reading. Author Response to Comment: We appreciate these great suggestions for the database content. The synthetic compounds provide some useful and comparatively inexpensive standards to train the chromatography model and are useful for the analytical method but not necessarily the biological question. We are working on software updates will incorporate a tool to distinguish between synthetics and naturally occurring compounds in a future version. Comment #6: We tested HormonomicsDB with XCMS Online results from untargeted metabolomics data and it (i.e., HormonomicsDB) works! Targeting Gibberellins via extraction can be a challenge, but they were putatively identified in negative mode data extracted using XCMS Online! I think it would aid the manuscript to mention that XCMS Online data can be formatted for use in HormonomicsDB! It gives surprising results! Although XCMS Online is a tool used for aligning peaks/mass features, we still must check the actual retention time in the processing software that comes with the mass spectrometer to make sure that the peak is a good one. It is wonderful that you mentioned MetaboAnalyst but think about XCMS Online or other peak/feature aligning methods as well. XCMS Online and MetaboAnalyst can be used in tandem to make meaningful information. One that readers can try is a recent peak/feature aligning server/software: Metaboseek (published this year). You did mention Misra et al. 2021’s comprehensive review! We suggest that you should mention other opensource tools that can be used to preprocess data that could be used with HormonomicsDB. It would bolster the strength of HormonomicsDB as being more versatile than just a standalone tool. Author Response to Comment: This is an important point that is often understated in the literature, since many analysts do not consider how raw data files are converted into a peak table, or the “X” block for putative ID or statistical analysis. To address this, we added the following to the section “Data input and output”: “Users can generate peak tables for upload to HormonomicsDB a number of ways, including with vendor software, or open source packages. These software take raw data files collected from individual chromatographic runs, and align the peaks to generate a single peak table which describes all the samples in the metabolomics experiment. These open source tools include XCMS (xcmsonline.scripps.edu), MetaboAnalyst (metaboanalyst.com), mzMine (mzmine.github.io), and Metaboseek (metaboseek.com).” Comment #7: While not the pivot of the study, the custom database output does not get enough credit in this paper. We tried primary metabolites with XCMS Online data and found compounds based on m/z values! We did not consider the RT as a factor as our lab method is 1/3rd the length of the lab method mentioned in this manuscript. But this goes to show that users can use a subset of hormones and other key metabolites they are only interested in to get an output, for more targeted analyses later. We believe that this is another strength of using HormonomicsDB custom database that should be emphasized more. Author Response to Comment: To emphasize the utility of the HormonomicsDB custom search function we have changed this section from a sub section to its own section in the manuscript (in the methods), and discussed the utility of this function by adding the following to the Results and discussion section “HormonomicsDB web-tool functionality and interface”: “Additionally, the “HormonomicsDB custom search” function is a novel feature within HormonomicsDB which allows users to search their peak table against their own database of metabolites. This is the first such report of a feature that allows users to queue with their own database. We hope to continue growing this function to allow users to queue against other databases by accessing them through an application programming interface (API) in the HormonomicsDB environment.” Comment #8: When do you use biotransformations? In using the software, it can be confusing. Can you clarify this part a bit? Comment #9: Letting the user know what the ups and downs or advantages and disadvantages of each function (i.e., PGR monoisotopic, PGR M-H or M+H, PGR Adducts, PGR Biotransformations) would be helpful. What have you found using these? Some commentary about how to use these functions alone, or in support of each other would be quite helpful. Author Response to Comment: Comments #8 and #9 are related, so we will address them together. We added the following to the end of the section in methods “Data input and output”: “The databases queued against depend on the structure of the input data and the users hypothesis. Certain software, particularly for Fourier transform mass spectrometry (FT-MS) data, convert ion masses to monoisotopic mass before exporting a peak table. If this is the case, the user can queue against the “PGR Monoisotopic” database. In ESI-LC-MS, the most common adduct is M+H in ESI positive mode and M-H in ESI negative mode. To queue for molecular ions only in the untargeted dataset, users should select the “PGR M+H” or “PGR M-H” databases, depending on their ionization mode. Adducts are often encountered in ESI-LC-MS, especially in ESI positive mode, as metal ions tend to form cations in aqueous solution. If the intensity for a particular PGR is decreased, or the PGR is absent when searching for molecular ion, the user can search for the common adducts of the PGRs in HormonomicsDB by queueing against the “PGR Adducts” database. Searching for the molecular ion and adducts at the same time is permissible in HormonomicsDB and allows the user to detect PGRs present in both forms. Biotransformations allow the user to search for modified forms of PGRs in their metabolomics dataset. This is useful when the goal is to identify conjugates and metabolites of PGRs in plants. The “PGR Biotransformations” database can be searched concurrently with the “PGR M+H” database, to identify PGRs in their native state and as conjugates. This approach can lead to the generation of new hypotheses in plant physiology and metabolism.” We thank reviewer 1 for pointing out what they identified as strengths within our article and ultimately in our novel metabolomics tool/workflow. We appreciate their helpful feedback and comments which we believe will strengthen our manuscript and metabolomics tool. Below we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: Not everyone is aware of the relationship with Dalton (Da) and parts per million (ppm). This is speaking about mass tolerance, especially looking on m/z values near the theoretical values of phytohormones/plant growth regulators. Conversion from Da to ppm is dependent on the m/z examined as you are aware. I think it is important for users to be aware of this, as not everyone may have an intense Chemistry background. We suggest that either adding this in the text (supplemental or otherwise) would really aid the manuscript and users new to mass spectrometry-based metabolomics. Additionally, you could mention that for the data that is downloaded from HormonomicsDB, that to know the ppm error used, that they use the formula: observed mass – theoretical mass/theoretical mass * 10^6 to know what error in ppm. The default for HormonomicsDB is ±0.01 Da. How much Daltons error wise do you recommend people using? In other words, if you have an ion mass of 1000.1356, and you want a desired ppm error of 5, how much would it be in daltons, or how much deviation can you expect? Using this formula (i.e., deviation in daltons with a given ion mass), especially, would clear up some ambiguity using either ppm or daltons, as well as to guide users/readers. Comment #2: We suggest that you should mention that the acceptable error limits that would be dependent on the mass spectrometer of question. For example, using 20 ppm on a highresolution mass spectrometry instrument especially with MS1 data is not kindly looked on some individuals in the mass spectrometry world. For example, 5-10 ppm error or less for Orbitrap is acceptable. This is not necessarily needed in the main text, but can be put in the supplemental, as this is not the main message of the manuscript. This was mentioned as studies you screened are from the Orbitrap and Q-TOF instruments. Author Response to Comment: We have chosen to address comment #1 and #2 together since they are closely related. We have added a Supplemental Information (SI) file to address this issue regarding mass tolerance in Da and ppm. We have added the following to the SI under the heading “Selecting Mass Tolerance”. Reference has been made to this section in the SI on page 4 in the manuscript under the section “Data inputs and outputs”: We have also updated HormonomicsDB to include an option to use ppm for mass tolerance. “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1 . For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below ( https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass ). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Comment #3: Having being users of HormonomicsDB, we think it is important to mention on the HormonomicsDB website the LC gradient that was used for the study. You mention it in the manuscript, which is good, but having it on the website somewhere will let the user be reminded that the LC gradient used in the paper may not be like theirs. Too much reliance on RTs may result in false negatives or positives. Even among different labs, the same machine, same columns, and mobile phase gradients can result in significantly different Rt’s. The readers should be more in tune to the elution points of compounds relative to others or external standards. Comment #4: Although the note about RT match is dependent on machine learning (which is a nice and novel approach by the way), we suggest that the authors should emphasize more to the reader that they should stick with exact mass (m/z) within a certain error margin, should they use another LC gradient, with various run times (solvents, columns, etc). Author Response to Comment: We are going to address comments #3 and #4 together as they discuss similar concerns. We will add a mention of the RT and gradient used on the landing page for HormonomicsDB. Additionally, we will add a link to this manuscript there so users can refer to the paper before using the tool. We feel that this should address the concerns in comment #3. We have added the following statement to the manuscript to the section “Retention time prediction” in the Result and discussion: “While RT predictions help to increase confidence in putative identification, it is important to note that differences in gradient, column, or solvents can impact the RT of analytes. The users should place more emphasis on the accurate mass matching and use RT prediction results to confirm if the elution pattern or order is as expected and elution of the analyte occurs at a reasonable time within the gradient”. Comment #5: In the supplemental information, especially supplemental file 1, although for the table of phytohormones M+H was used, we suggest that the masses from the [M-H]- ionization mode should be added as well. We also suggest that the synthetic compounds should not be grouped with the plant growth regulators or their precursor compounds and/or intermediates. Rather, separate them into different sheets. For example: predicted metabolites (Table 1), training standards (Table 2), and synthetic compounds (Table 3). Many people won’t care about glyphosate or thidiazuron as much as other compounds that are endogenous such as Spermidine, Indoleacetate (IAA), or Gibberellins (GAs). While it is still good to know if glyphosate was used in the plant organism of interest, for the supplemental, maybe put glyphosate and other synthetic compounds to themselves. That way, the focus can be on phytohormones/plant growth regulators and other related compounds from Tryptophan metabolism. If the readers want, they can consider the other synthetic ones just to see. Putting them in different tables also helps in reading. Author Response to Comment: We appreciate these great suggestions for the database content. The synthetic compounds provide some useful and comparatively inexpensive standards to train the chromatography model and are useful for the analytical method but not necessarily the biological question. We are working on software updates will incorporate a tool to distinguish between synthetics and naturally occurring compounds in a future version. Comment #6: We tested HormonomicsDB with XCMS Online results from untargeted metabolomics data and it (i.e., HormonomicsDB) works! Targeting Gibberellins via extraction can be a challenge, but they were putatively identified in negative mode data extracted using XCMS Online! I think it would aid the manuscript to mention that XCMS Online data can be formatted for use in HormonomicsDB! It gives surprising results! Although XCMS Online is a tool used for aligning peaks/mass features, we still must check the actual retention time in the processing software that comes with the mass spectrometer to make sure that the peak is a good one. It is wonderful that you mentioned MetaboAnalyst but think about XCMS Online or other peak/feature aligning methods as well. XCMS Online and MetaboAnalyst can be used in tandem to make meaningful information. One that readers can try is a recent peak/feature aligning server/software: Metaboseek (published this year). You did mention Misra et al. 2021’s comprehensive review! We suggest that you should mention other opensource tools that can be used to preprocess data that could be used with HormonomicsDB. It would bolster the strength of HormonomicsDB as being more versatile than just a standalone tool. Author Response to Comment: This is an important point that is often understated in the literature, since many analysts do not consider how raw data files are converted into a peak table, or the “X” block for putative ID or statistical analysis. To address this, we added the following to the section “Data input and output”: “Users can generate peak tables for upload to HormonomicsDB a number of ways, including with vendor software, or open source packages. These software take raw data files collected from individual chromatographic runs, and align the peaks to generate a single peak table which describes all the samples in the metabolomics experiment. These open source tools include XCMS (xcmsonline.scripps.edu), MetaboAnalyst (metaboanalyst.com), mzMine (mzmine.github.io), and Metaboseek (metaboseek.com).” Comment #7: While not the pivot of the study, the custom database output does not get enough credit in this paper. We tried primary metabolites with XCMS Online data and found compounds based on m/z values! We did not consider the RT as a factor as our lab method is 1/3rd the length of the lab method mentioned in this manuscript. But this goes to show that users can use a subset of hormones and other key metabolites they are only interested in to get an output, for more targeted analyses later. We believe that this is another strength of using HormonomicsDB custom database that should be emphasized more. Author Response to Comment: To emphasize the utility of the HormonomicsDB custom search function we have changed this section from a sub section to its own section in the manuscript (in the methods), and discussed the utility of this function by adding the following to the Results and discussion section “HormonomicsDB web-tool functionality and interface”: “Additionally, the “HormonomicsDB custom search” function is a novel feature within HormonomicsDB which allows users to search their peak table against their own database of metabolites. This is the first such report of a feature that allows users to queue with their own database. We hope to continue growing this function to allow users to queue against other databases by accessing them through an application programming interface (API) in the HormonomicsDB environment.” Comment #8: When do you use biotransformations? In using the software, it can be confusing. Can you clarify this part a bit? Comment #9: Letting the user know what the ups and downs or advantages and disadvantages of each function (i.e., PGR monoisotopic, PGR M-H or M+H, PGR Adducts, PGR Biotransformations) would be helpful. What have you found using these? Some commentary about how to use these functions alone, or in support of each other would be quite helpful. Author Response to Comment: Comments #8 and #9 are related, so we will address them together. We added the following to the end of the section in methods “Data input and output”: “The databases queued against depend on the structure of the input data and the users hypothesis. Certain software, particularly for Fourier transform mass spectrometry (FT-MS) data, convert ion masses to monoisotopic mass before exporting a peak table. If this is the case, the user can queue against the “PGR Monoisotopic” database. In ESI-LC-MS, the most common adduct is M+H in ESI positive mode and M-H in ESI negative mode. To queue for molecular ions only in the untargeted dataset, users should select the “PGR M+H” or “PGR M-H” databases, depending on their ionization mode. Adducts are often encountered in ESI-LC-MS, especially in ESI positive mode, as metal ions tend to form cations in aqueous solution. If the intensity for a particular PGR is decreased, or the PGR is absent when searching for molecular ion, the user can search for the common adducts of the PGRs in HormonomicsDB by queueing against the “PGR Adducts” database. Searching for the molecular ion and adducts at the same time is permissible in HormonomicsDB and allows the user to detect PGRs present in both forms. Biotransformations allow the user to search for modified forms of PGRs in their metabolomics dataset. This is useful when the goal is to identify conjugates and metabolites of PGRs in plants. The “PGR Biotransformations” database can be searched concurrently with the “PGR M+H” database, to identify PGRs in their native state and as conjugates. This approach can lead to the generation of new hypotheses in plant physiology and metabolism.” Competing Interests: No competing interests were disclosed. Close Report a concern COMMENT ON THIS REPORT Comments on this article Comments (0) Version 2 VERSION 2 PUBLISHED 18 Oct 2022 ADD YOUR COMMENT Comment keyboard_arrow_left keyboard_arrow_right Open Peer Review Reviewer Status info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Reviewer Reports Invited Reviewers 1 2 Version 2 (revision) 08 Apr 24 read read Version 1 18 Oct 22 read read Ainsely Lewis , Trent University, Peterborough, Canada R.J. Neil Emery , Trent University, Peterborough, Canada Jian You Wang , King Abdullah University of Science and Technology, Thuwal, Saudi Arabia Comments on this article All Comments (0) Add a comment Sign up for content alerts Sign Up You are now signed up to receive this alert Browse by related subjects keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Wang J. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 30 Aug 2024 | for Version 2 Jian You Wang , King Abdullah University of Science and Technology, Thuwal, Makkah Province, Saudi Arabia 0 Views copyright © 2024 Wang J. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions The authors have addressed my comments in a rational way. Hope the improved MS version will come in the future. Competing Interests No competing interests were disclosed. Reviewer Expertise Analytical biochemistry, Plant hormones, Strigolactones, Plant growth regulators I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. reply Respond to this report Responses (0) Wang JY. Peer Review Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.161276.r264124) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/11-1191/v2#referee-response-264124 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Emery R et al. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 13 May 2024 | for Version 2 R.J. Neil Emery , Department of Biology, Trent University, Peterborough, ON, Canada Ainsely Lewis , Trent University, Peterborough, ON, Canada 0 Views copyright © 2024 Emery R et al. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (0) Approved info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions The author has included all the suggestions. Competing Interests No competing interests were disclosed. Reviewer Expertise Mass spectrometry-based metabolomics, phytohormone profiling, chemometrics We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. reply Respond to this report Responses (0) Emery RJN and Lewis A. Peer Review Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.161276.r264123) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/11-1191/v2#referee-response-264123 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2023 Wang J. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 12 Jun 2023 | for Version 1 Jian You Wang , King Abdullah University of Science and Technology, Thuwal, Makkah Province, Saudi Arabia 0 Views copyright © 2023 Wang J. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (1) Approved With Reservations info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions HormonomicsDB is definitely required for the plant metabolomics field and it provides many advantages to identify compounds. While the paper is well written and clearly demonstrates how to use this platform, I have a few comments to, hopefully, improve the content. What is the maximum mass tolerance (in Da and ppm) when identifying metabolites? Also, natural components usually contain isomers/isoforms, how to distinguish or interpret them by using HormonomicsDB? It would be necessary to guild users on how to transform Da to ppm. Please include the explanations of the PGR Monoisotopic, PGR M+H, and so on to junior users. It is a bit confusing between Table 4 and Table 5 in the m/z, what are the minimum decimal numbers of accurate mass (default setting) of particular metabolites in HormonomicsDB? In the above two cases, what was the mass tolerance (or acceptable error) to identify the compounds? As a researcher in strigolactone (SL) biology, the methanol extraction would lead to the fast degradation of SLs. Could the author pay attention to this? In addition, the unarguable identification of a particular SL requires MS/MS (not only accurate mass). Therefore, if there would be MS/MS database in HormonomicsDB for advanced non-targeted metabolomics, it would be greatly helpful. What is the minimum intensity (e3 or e4?) of peaks to be considered as metabolites instead of noise? Is the rationale for developing the new software tool clearly explained? Yes Is the description of the software tool technically sound? Partly Are sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes Is sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly Are the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Analytical biochemistry, Plant hormones, Strigolactones, Plant growth regulators I confirm that I have read this submission and believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however I have significant reservations, as outlined above. reply Respond to this report Responses (1) Author Response 08 Apr 2024 Susan Murch, Chemistry, University of British Columbia, Kelowna, V1V1V7, Canada We thank reviewer 2 for reviewing our manuscript and for their appreciation of the need for untargeted metabolomics workflows for exploring phytohormones. Below, we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: HormonomicsDB is definitely required for the plant metabolomics field and it provides many advantages to identify compounds. While the paper is well written and clearly demonstrates how to use this platform, I have a few comments to, hopefully, improve the content. Author Response to Comment: We appreciate that reviewer #2 has also identified the need for metabolomics approaches specifically tailored to the identification of phytohormones, specifically due to their labile and sensitive nature, as addressed in our manuscript. Comment #2: What is the maximum mass tolerance (in Da and ppm) when identifying metabolites? Also, natural components usually contain isomers/isoforms, how to distinguish or interpret them by using HormonomicsDB? It would be necessary to guild users on how to transform Da to ppm. Author Response to Comment: This was a comment also brought up by reviewer #1, and we have revised the manuscript to address this concern. Regarding mass tolerance, we updated HormonomicsDB to include an option to use ppm for mass tolerance. We have also added the following to the supplemental information: “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1. For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below ( https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass ). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Regarding isomers/isoforms, it is often challenging in LC-MS to separate isomers as they can have relatively similar retention times. Additionally, MS/MS fragmentation often struggles to differentiate isomers. Ion mobility spectrometry – mass spectrometry (IMS-MS) is a relatively new technique which has been deployed to separate isomers in time based on their collisional cross section (CCS). This is an emerging technology and we expect that IMS will play an important role in future hormonomics studies. However, in silico CCS predictions are still in their infancy and IMS-MS capable instruments are still fairly inaccessible. Given these hurdles we cannot include IMS-MS in this current version of HormonomicsDB, however as these technologies become more accessible we will work toward including IMS-MS data in HormonomicsDB. Comment #3: Please include the explanations of the PGR Monoisotopic, PGR M+H, and so on to junior users. Author Response to Comment: To address any ambiguity to these terms we have added the following to the Methods section “Plant growth regulators”: “PGR Monoisotopic contains the monoisotopic mass for each phytohormone, the PGR M+H contains the m/z of each phytohormone as an M+H adduct, the PGR adducts contains the m/z of 7 common adducts (Table 1), and PGR biotransformations contains 27 common biotransformations (Table 1) as M+H adducts.” Comment #4: It is a bit confusing between Table 4 and Table 5 in the m/z, what are the minimum decimal numbers of accurate mass (default setting) of particular metabolites in HormonomicsDB? In the above two cases, what was the mass tolerance (or acceptable error) to identify the compounds? Author Response to Comment: We have updated table 4 and 6 to include more decimal points for both the experimental and library match m/z. Additionally, we have included the ppm difference, as HormonomicsDB now computes this. The data in Brown et al. was acquired on a TOF, therefore an uncertainty of 3-5 ppm is expected. We have added the following to the methods section discussing this: “The data in Brown et al. 2012 was collected on a time of flight (TOF) mass spectrometer, which typically has a mass error of 3 to 5 ppm.” Comment #5: As a researcher in strigolactone (SL) biology, the methanol extraction would lead to the fast degradation of SLs. Could the author pay attention to this? In addition, the unarguable identification of a particular SL requires MS/MS (not only accurate mass). Therefore, if there would be MS/MS database in HormonomicsDB for advanced non-targeted metabolomics, it would be greatly helpful. Author Response to Comment: We understand that MS/MS is an important tool for discovering and identifying phytohormones in untargeted studies, however, we found that current tools for in silico prediction of low energy MS/MS spectra often provide incorrect predictions, we felt it would be inappropriate to add MS/MS to HormonomicsDB in this publication. But, as in silico MS/MS prediction tools improve and more phytohormone standards become accessible, we hope to release another version of HormonomicsDB with MS/MS searching capabilities. Comment #5: What is the minimum intensity (e3 or e4?) of peaks to be considered as metabolites instead of noise? Author Response to Comment: Since HormonomicsDB takes aligned peak tables, the signal to noise (S/N) cut-off would have been determined during the alignment process, as this is the most common approach vendor software currently use for selecting chemical features prior to alignment. Additionally, some software outputs the aligned peak table with relative intensities. To address this concern we added the following to the Methods: “HormonomicsDB makes no assumptions about signal to noise (S/N) or other sensitivity figures of merit as these are typically made during this peak alignment step.” View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Wang JY. Peer Review Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.136376.r174935) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. The direct URL for this report is: https://f1000research.com/articles/11-1191/v1#referee-response-174935 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2022 Emery R et al. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 08 Nov 2022 | for Version 1 Ainsely Lewis , Trent University, Peterborough, ON, Canada R.J. Neil Emery , Department of Biology, Trent University, Peterborough, ON, Canada 0 Views copyright © 2022 Emery R et al. This is an open access peer review report distributed under the terms of the Creative Commons Attribution License , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. format_quote Cite this report speaker_notes Responses (1) Approved With Reservations info_outline Alongside their report, reviewers assign a status to the article: Approved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit. Not approved Fundamental flaws in the paper seriously undermine the findings and conclusions Review by Ainsely Lewis, Ph.D., and Professor RJ Neil Emery Good points/Strengths of article: HormonomicsDB undoubtedly is a needed comprehensive tool to screen metabolites/phytohormones and plant growth regulators putatively. This tool is no doubt a novel tool that will aid researchers using mass spectrometry-based metabolomics for hormones in either plant or animal systems. Making choices of what classes or types of compounds to search for is particularly difficult. Therefore, this is a particularly helpful tool for narrowing metabolomics studies into a search for signaling molecules. It offers a focused study on a higher level in that it can uncover important compounds that have wider reaching or pleiotropic effects. This is especially good for screening for these hormones especially if they are not known to be present in a given system of study. Knowing putative compounds in an extraction procedure with various factors (extraction buffer used, solvents, using SPE or not), can really aid in targeted analysis, or to help develop a method to maximize extraction of hormones/phytohormones of interest. This manuscript is quite an undertaking! This is a well written and well-done manuscript, that is scientifically sound. Introduction was well done and nicely sets the pace for readers. Methodology was thorough and straightforward. Results and discussion section was thorough. Liked the COVID angle in the conclusions. The grammar and word choices used in the manuscript was good as well. Approved with reservations. Minor adjustments/revisions needed. Minor suggestions - Things for clarification for other users/readers with commentary. These are suggestions that we believe can aid in improving the manuscript: Not everyone is aware of the relationship with Dalton (Da) and parts per million (ppm). This is speaking about mass tolerance, especially looking on m/z values near the theoretical values of phytohormones/plant growth regulators. Conversion from Da to ppm is dependent on the m/z examined as you are aware. I think it is important for users to be aware of this, as not everyone may have an intense Chemistry background. We suggest that either adding this in the text (supplemental or otherwise) would really aid the manuscript and users new to mass spectrometry-based metabolomics. Additionally, you could mention that for the data that is downloaded from HormonomicsDB, that to know the ppm error used, that they use the formula: observed mass – theoretical mass/theoretical mass * 10 ^6 to know what error in ppm. The default for HormonomicsDB is ±0.01 Da. How much Daltons error wise do you recommend people using? In other words, if you have an ion mass of 1000.1356, and you want a desired ppm error of 5, how much would it be in daltons, or how much deviation can you expect? Using this formula (i.e., deviation in daltons with a given ion mass), especially, would clear up some ambiguity using either ppm or daltons, as well as to guide users/readers. We suggest that you should mention that the acceptable error limits that would be dependent on the mass spectrometer of question. For example, using 20 ppm on a high-resolution mass spectrometry instrument especially with MS1 data is not kindly looked on some individuals in the mass spectrometry world. For example, 5-10 ppm error or less for Orbitrap is acceptable. This is not necessarily needed in the main text, but can be put in the supplemental, as this is not the main message of the manuscript. This was mentioned as studies you screened are from the Orbitrap and Q-TOF instruments. Having being users of HormonomicsDB, we think it is important to mention on the HormonomicsDB website the LC gradient that was used for the study. You mention it in the manuscript, which is good, but having it on the website somewhere will let the user be reminded that the LC gradient used in the paper may not be like theirs. Too much reliance on RTs may result in false negatives or positives. Even among different labs, the same machine, same columns, and mobile phase gradients can result in significantly different Rt’s. The readers should be more in tune to the elution points of compounds relative to others or external standards. Although the note about RT match is dependent on machine learning (which is a nice and novel approach by the way), we suggest that the authors should emphasize more to the reader that they should stick with exact mass (m/z) within a certain error margin, should they use another LC gradient, with various run times (solvents, columns, etc). In the supplemental information, especially supplemental file 1, although for the table of phytohormones M+H was used, we suggest that the masses from the [M-H] - ionization mode should be added as well. We also suggest that the synthetic compounds should not be grouped with the plant growth regulators or their precursor compounds and/or intermediates. Rather, separate them into different sheets. For example: predicted metabolites (Table 1), training standards (Table 2), and synthetic compounds (Table 3). Many people won’t care about glyphosate or thidiazuron as much as other compounds that are endogenous such as Spermidine, Indoleacetate (IAA), or Gibberellins (GAs). While it is still good to know if glyphosate was used in the plant organism of interest, for the supplemental, maybe put glyphosate and other synthetic compounds to themselves. That way, the focus can be on phytohormones/plant growth regulators and other related compounds from Tryptophan metabolism. If the readers want, they can consider the other synthetic ones just to see. Putting them in different tables also helps in reading. We tested HormonomicsDB with XCMS Online results from untargeted metabolomics data and it (i.e., HormonomicsDB) works! Targeting Gibberellins via extraction can be a challenge, but they were putatively identified in negative mode data extracted using XCMS Online! I think it would aid the manuscript to mention that XCMS Online data can be formatted for use in HormonomicsDB! It gives surprising results! Although XCMS Online is a tool used for aligning peaks/mass features, we still must check the actual retention time in the processing software that comes with the mass spectrometer to make sure that the peak is a good one. It is wonderful that you mentioned MetaboAnalyst but think about XCMS Online or other peak/feature aligning methods as well. XCMS Online and MetaboAnalyst can be used in tandem to make meaningful information. One that readers can try is a recent peak/feature aligning server/software: Metaboseek (published this year). You did mention Misra et al . 2021’s comprehensive review! We suggest that you should mention other open-source tools that can be used to preprocess data that could be used with HormonomicsDB. It would bolster the strength of HormonomicsDB as being more versatile than just a standalone tool. While not the pivot of the study, the custom database output does not get enough credit in this paper. We tried primary metabolites with XCMS Online data and found compounds based on m/z values! We did not consider the RT as a factor as our lab method is 1/3 rd the length of the lab method mentioned in this manuscript. But this goes to show that users can use a subset of hormones and other key metabolites they are only interested in to get an output, for more targeted analyses later. We believe that this is another strength of using HormonomicsDB custom database that should be emphasized more. When do you use biotransformations? In using the software, it can be confusing. Can you clarify this part a bit? Letting the user know what the ups and downs or advantages and disadvantages of each function (i.e., PGR monoisotopic, PGR M-H or M+H, PGR Adducts, PGR Biotransformations) would be helpful. What have you found using these? Some commentary about how to use these functions alone, or in support of each other would be quite helpful. Is the rationale for developing the new software tool clearly explained? Yes Is the description of the software tool technically sound? Yes Are sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes Is sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes Are the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Mass spectrometry-based metabolomics, phytohormone profiling, chemometrics We confirm that we have read this submission and believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above. reply Respond to this report Responses (1) Author Response 08 Apr 2024 Susan Murch, Chemistry, University of British Columbia, Kelowna, V1V1V7, Canada We thank reviewer 1 for pointing out what they identified as strengths within our article and ultimately in our novel metabolomics tool/workflow. We appreciate their helpful feedback and comments which we believe will strengthen our manuscript and metabolomics tool. Below we have provided responses to each of the reviewer comments and how they were implemented to improve the manuscript. Comment #1: Not everyone is aware of the relationship with Dalton (Da) and parts per million (ppm). This is speaking about mass tolerance, especially looking on m/z values near the theoretical values of phytohormones/plant growth regulators. Conversion from Da to ppm is dependent on the m/z examined as you are aware. I think it is important for users to be aware of this, as not everyone may have an intense Chemistry background. We suggest that either adding this in the text (supplemental or otherwise) would really aid the manuscript and users new to mass spectrometry-based metabolomics. Additionally, you could mention that for the data that is downloaded from HormonomicsDB, that to know the ppm error used, that they use the formula: observed mass – theoretical mass/theoretical mass * 10^6 to know what error in ppm. The default for HormonomicsDB is ±0.01 Da. How much Daltons error wise do you recommend people using? In other words, if you have an ion mass of 1000.1356, and you want a desired ppm error of 5, how much would it be in daltons, or how much deviation can you expect? Using this formula (i.e., deviation in daltons with a given ion mass), especially, would clear up some ambiguity using either ppm or daltons, as well as to guide users/readers. Comment #2: We suggest that you should mention that the acceptable error limits that would be dependent on the mass spectrometer of question. For example, using 20 ppm on a highresolution mass spectrometry instrument especially with MS1 data is not kindly looked on some individuals in the mass spectrometry world. For example, 5-10 ppm error or less for Orbitrap is acceptable. This is not necessarily needed in the main text, but can be put in the supplemental, as this is not the main message of the manuscript. This was mentioned as studies you screened are from the Orbitrap and Q-TOF instruments. Author Response to Comment: We have chosen to address comment #1 and #2 together since they are closely related. We have added a Supplemental Information (SI) file to address this issue regarding mass tolerance in Da and ppm. We have added the following to the SI under the heading “Selecting Mass Tolerance”. Reference has been made to this section in the SI on page 4 in the manuscript under the section “Data inputs and outputs”: We have also updated HormonomicsDB to include an option to use ppm for mass tolerance. “Users can input their desired mass tolerance in Daltons (Da) or parts per million (ppm) in HormonomicsDB. The default mass tolerance is ± 0.01 Da; however, users can adjust this depending on the mass accuracy and resolution of their mass spectrometer. PPM is another common way to report mass tolerances, it is dependent on the value of the mass being measured. The relationship between Da and ppm is described by Equation 1 . For example, a mass of 500 Da, the uncertainty at 1 ppm (calculated with Equation 1) is ± 0.0005 Da, while the mass range for 100 Da is ± 0.0001 Da and ± 0.001 Da for a mass of 1000 Da. For untargeted LC-MS metabolomics workflows, it is strongly suggested that analysts use a mass detector with a high mass accuracy and resolving power, This improves the certainty in putative identification, by ensuring the mass measured is the correct mass and that ions with similar masses can be resolved from each other. Users of HormonomicsDB should consider the mass accuracy of their mass detector before selecting a mass tolerance. The mass accuracy ranges for the five most common mass spectrometers are given below ( https://fiehnlab.ucdavis.edu/projects/seven-golden-rules/accurate-mass ). Supporting Table 1. Mass accuracy ranges for the five most common mass spectrometers, given in parts per million (ppm). Type Mass Accuracy FT-MS 0.1 - 1 ppm Orbitrap 0.5 - 1 ppm TOF-MS 3 - 5 ppm Q-TOF 3 - 5 ppm Triple Quad 3 - 5 ppm Comment #3: Having being users of HormonomicsDB, we think it is important to mention on the HormonomicsDB website the LC gradient that was used for the study. You mention it in the manuscript, which is good, but having it on the website somewhere will let the user be reminded that the LC gradient used in the paper may not be like theirs. Too much reliance on RTs may result in false negatives or positives. Even among different labs, the same machine, same columns, and mobile phase gradients can result in significantly different Rt’s. The readers should be more in tune to the elution points of compounds relative to others or external standards. Comment #4: Although the note about RT match is dependent on machine learning (which is a nice and novel approach by the way), we suggest that the authors should emphasize more to the reader that they should stick with exact mass (m/z) within a certain error margin, should they use another LC gradient, with various run times (solvents, columns, etc). Author Response to Comment: We are going to address comments #3 and #4 together as they discuss similar concerns. We will add a mention of the RT and gradient used on the landing page for HormonomicsDB. Additionally, we will add a link to this manuscript there so users can refer to the paper before using the tool. We feel that this should address the concerns in comment #3. We have added the following statement to the manuscript to the section “Retention time prediction” in the Result and discussion: “While RT predictions help to increase confidence in putative identification, it is important to note that differences in gradient, column, or solvents can impact the RT of analytes. The users should place more emphasis on the accurate mass matching and use RT prediction results to confirm if the elution pattern or order is as expected and elution of the analyte occurs at a reasonable time within the gradient”. Comment #5: In the supplemental information, especially supplemental file 1, although for the table of phytohormones M+H was used, we suggest that the masses from the [M-H]- ionization mode should be added as well. We also suggest that the synthetic compounds should not be grouped with the plant growth regulators or their precursor compounds and/or intermediates. Rather, separate them into different sheets. For example: predicted metabolites (Table 1), training standards (Table 2), and synthetic compounds (Table 3). Many people won’t care about glyphosate or thidiazuron as much as other compounds that are endogenous such as Spermidine, Indoleacetate (IAA), or Gibberellins (GAs). While it is still good to know if glyphosate was used in the plant organism of interest, for the supplemental, maybe put glyphosate and other synthetic compounds to themselves. That way, the focus can be on phytohormones/plant growth regulators and other related compounds from Tryptophan metabolism. If the readers want, they can consider the other synthetic ones just to see. Putting them in different tables also helps in reading. Author Response to Comment: We appreciate these great suggestions for the database content. The synthetic compounds provide some useful and comparatively inexpensive standards to train the chromatography model and are useful for the analytical method but not necessarily the biological question. We are working on software updates will incorporate a tool to distinguish between synthetics and naturally occurring compounds in a future version. Comment #6: We tested HormonomicsDB with XCMS Online results from untargeted metabolomics data and it (i.e., HormonomicsDB) works! Targeting Gibberellins via extraction can be a challenge, but they were putatively identified in negative mode data extracted using XCMS Online! I think it would aid the manuscript to mention that XCMS Online data can be formatted for use in HormonomicsDB! It gives surprising results! Although XCMS Online is a tool used for aligning peaks/mass features, we still must check the actual retention time in the processing software that comes with the mass spectrometer to make sure that the peak is a good one. It is wonderful that you mentioned MetaboAnalyst but think about XCMS Online or other peak/feature aligning methods as well. XCMS Online and MetaboAnalyst can be used in tandem to make meaningful information. One that readers can try is a recent peak/feature aligning server/software: Metaboseek (published this year). You did mention Misra et al. 2021’s comprehensive review! We suggest that you should mention other opensource tools that can be used to preprocess data that could be used with HormonomicsDB. It would bolster the strength of HormonomicsDB as being more versatile than just a standalone tool. Author Response to Comment: This is an important point that is often understated in the literature, since many analysts do not consider how raw data files are converted into a peak table, or the “X” block for putative ID or statistical analysis. To address this, we added the following to the section “Data input and output”: “Users can generate peak tables for upload to HormonomicsDB a number of ways, including with vendor software, or open source packages. These software take raw data files collected from individual chromatographic runs, and align the peaks to generate a single peak table which describes all the samples in the metabolomics experiment. These open source tools include XCMS (xcmsonline.scripps.edu), MetaboAnalyst (metaboanalyst.com), mzMine (mzmine.github.io), and Metaboseek (metaboseek.com).” Comment #7: While not the pivot of the study, the custom database output does not get enough credit in this paper. We tried primary metabolites with XCMS Online data and found compounds based on m/z values! We did not consider the RT as a factor as our lab method is 1/3rd the length of the lab method mentioned in this manuscript. But this goes to show that users can use a subset of hormones and other key metabolites they are only interested in to get an output, for more targeted analyses later. We believe that this is another strength of using HormonomicsDB custom database that should be emphasized more. Author Response to Comment: To emphasize the utility of the HormonomicsDB custom search function we have changed this section from a sub section to its own section in the manuscript (in the methods), and discussed the utility of this function by adding the following to the Results and discussion section “HormonomicsDB web-tool functionality and interface”: “Additionally, the “HormonomicsDB custom search” function is a novel feature within HormonomicsDB which allows users to search their peak table against their own database of metabolites. This is the first such report of a feature that allows users to queue with their own database. We hope to continue growing this function to allow users to queue against other databases by accessing them through an application programming interface (API) in the HormonomicsDB environment.” Comment #8: When do you use biotransformations? In using the software, it can be confusing. Can you clarify this part a bit? Comment #9: Letting the user know what the ups and downs or advantages and disadvantages of each function (i.e., PGR monoisotopic, PGR M-H or M+H, PGR Adducts, PGR Biotransformations) would be helpful. What have you found using these? Some commentary about how to use these functions alone, or in support of each other would be quite helpful. Author Response to Comment: Comments #8 and #9 are related, so we will address them together. We added the following to the end of the section in methods “Data input and output”: “The databases queued against depend on the structure of the input data and the users hypothesis. Certain software, particularly for Fourier transform mass spectrometry (FT-MS) data, convert ion masses to monoisotopic mass before exporting a peak table. If this is the case, the user can queue against the “PGR Monoisotopic” database. In ESI-LC-MS, the most common adduct is M+H in ESI positive mode and M-H in ESI negative mode. To queue for molecular ions only in the untargeted dataset, users should select the “PGR M+H” or “PGR M-H” databases, depending on their ionization mode. Adducts are often encountered in ESI-LC-MS, especially in ESI positive mode, as metal ions tend to form cations in aqueous solution. If the intensity for a particular PGR is decreased, or the PGR is absent when searching for molecular ion, the user can search for the common adducts of the PGRs in HormonomicsDB by queueing against the “PGR Adducts” database. Searching for the molecular ion and adducts at the same time is permissible in HormonomicsDB and allows the user to detect PGRs present in both forms. Biotransformations allow the user to search for modified forms of PGRs in their metabolomics dataset. This is useful when the goal is to identify conjugates and metabolites of PGRs in plants. The “PGR Biotransformations” database can be searched concurrently with the “PGR M+H” database, to identify PGRs in their native state and as conjugates. This approach can lead to the generation of new hypotheses in plant physiology and metabolism.” View more View less Competing Interests No competing interests were disclosed. reply Respond Report a concern Lewis A and Emery RJN. Peer Review Report For: HormonomicsDB: a novel workflow for the untargeted analysis of plant growth regulators and hormones [version 2; peer review: 2 approved] . F1000Research 2024, 11 :1191 ( https://doi.org/10.5256/f1000research.136376.r153643) NOTE: it is important to ensure the information in square brackets after the title is included in this citation. 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