A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence

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McPherson" }, { "@type": "Person", "name": "Carl Laflamme" }, { "@type": "Person", "name": "NeuroSGC/YCharOS/EDDU collaborative group" }, { "@type": "Person", "name": "ABIF consortium" } ], "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": "Rab1 is a highly conserved small GTPase that exists in humans as two isoforms: Rab1A and Rab1B, sharing 92% sequence identity. These proteins regulate vesicle trafficking between the endoplasmic reticulum (ER) and Golgi and within the Golgi stacks. Rab1A and Rab1B may be oncogenes, as they are frequently dysregulated in various human cancers. Moreover, they contribute to the progression of Parkinson’s disease. The availability of high-quality antibodies specific for Rab1A or Rab1B is essential to understand the distinct functions of these Rab1 proteins in both health and diseaseand to enhance the reproducibility of research involving these proteins. In this study, we characterized seven antibodies targeting Rab1A and five antibodies targeting Rab1B for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a much larger, collaborative initiative seeking to address the antibody reproducibility issue by characterizing commercially available antibodies for human proteins and publishing the results openly as a valuable resource for the scientific community. While uses of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs." } { "@context": "http://schema.org", "@type": "BreadcrumbList", "itemListElement": [ { "@type": "ListItem", "position": "1", "item": { "@id": "https://f1000research.com/", "name": "Home" } }, { "@type": "ListItem", "position": "2", "item": { "@id": "https://f1000research.com/browse/articles", "name": "Browse" } }, { "@type": "ListItem", "position": "3", "item": { "@id": "https://f1000research.com/articles/12-1578", "name": "A guide to selecting high-performing antibodies for Rab1A and Rab1B..." } } ] } Home Browse A guide to selecting high-performing antibodies for Rab1A and Rab1B... ALL Metrics - Views Downloads Get PDF Get XML Cite How to cite this article Ruíz Moleón V, Alende C, Fotouhi M et al. A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 3; peer review: 2 approved] . F1000Research 2025, 12 :1578 ( https://doi.org/10.12688/f1000research.143928.3 ) 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 ▬ ✚ Data Note Revised A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 3; peer review: 2 approved] Vera Ruíz Moleón https://orcid.org/0000-0003-3728-3158 1 , Charles Alende https://orcid.org/0009-0005-4611-6134 1 , Maryam Fotouhi 1 , [...] Riham Ayoubi 1 , Sara González Bolívar https://orcid.org/0000-0002-4299-8281 1 , Kathleen Southern https://orcid.org/0000-0002-4125-3608 1 , Peter S. McPherson 1 , Carl Laflamme https://orcid.org/0000-0001-5906-025X 1 , NeuroSGC/YCharOS/EDDU collaborative group , ABIF consortium Vera Ruíz Moleón https://orcid.org/0000-0003-3728-3158 1 , Charles Alende https://orcid.org/0009-0005-4611-6134 1 , [...] Maryam Fotouhi 1 , Riham Ayoubi 1 , Sara González Bolívar https://orcid.org/0000-0002-4299-8281 1 , Kathleen Southern https://orcid.org/0000-0002-4125-3608 1 , Peter S. McPherson 1 , Carl Laflamme https://orcid.org/0000-0001-5906-025X 1 , NeuroSGC/YCharOS/EDDU collaborative group , ABIF consortium PUBLISHED 07 Mar 2025 Author details Author details 1 Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Québec, H3A 2B4, Canada Vera Ruíz Moleón Roles: Investigation, Writing – Review & Editing Charles Alende Roles: Formal Analysis, Investigation, Writing – Review & Editing Maryam Fotouhi Roles: Investigation, Methodology, Writing – Review & Editing Riham Ayoubi Roles: Investigation, Methodology, Validation, Visualization, Writing – Review & Editing Sara González Bolívar Roles: Investigation, Writing – Review & Editing Kathleen Southern Roles: Writing – Original Draft Preparation, Writing – Review & Editing Peter S. McPherson Roles: Conceptualization, Funding Acquisition, Resources, Supervision, Writing – Review & Editing Carl Laflamme Roles: Conceptualization, Formal Analysis, Funding Acquisition, Methodology, Project Administration, Resources, Supervision, Writing – Review & Editing OPEN PEER REVIEW DETAILS REVIEWER STATUS This article is included in the YCharOS (Antibody Characterization through Open Science) gateway. Abstract Rab1 is a highly conserved small GTPase that exists in humans as two isoforms: Rab1A and Rab1B, sharing 92% sequence identity. These proteins regulate vesicle trafficking between the endoplasmic reticulum (ER) and Golgi and within the Golgi stacks. Rab1A and Rab1B may be oncogenes, as they are frequently dysregulated in various human cancers. Moreover, they contribute to the progression of Parkinson’s disease. The availability of high-quality antibodies specific for Rab1A or Rab1B is essential to understand the distinct functions of these Rab1 proteins in both health and diseaseand to enhance the reproducibility of research involving these proteins. In this study, we characterized seven antibodies targeting Rab1A and five antibodies targeting Rab1B for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a much larger, collaborative initiative seeking to address the antibody reproducibility issue by characterizing commercially available antibodies for human proteins and publishing the results openly as a valuable resource for the scientific community. While uses of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs. READ ALL READ LESS Keywords Uniprot ID P62820 (Rab1A), Q9H0U4 (Rab1B), RAB1A and RAB1B, Rab1A, Rab1B, antibody characterization, antibody validation, Western Blot, immunoprecipitation, immunofluorescence Corresponding Author(s) Carl Laflamme ( [email protected] ) Close Corresponding author: Carl Laflamme Competing interests: For this project, the laboratory of Peter McPherson developed partnerships with high-quality antibody manufacturers and knockout cell line providers. The partners provide antibodies and knockout cell lines to the McPherson laboratory at no cost. These partners include: - Abcam-Aviva Systems Biology -Bio Techne -Cell Signalling Technology -Developmental Studies Hybridoma Bank -GeneTex – Horizon Discovery – Proteintech – Synaptic Systems –Thermo Fisher Scientific. Grant information: The grant was from a Canadian Institutes of Health Research Foundation (grant no. FDN154305) and by the Government of Canada through Genome Canada, Genome Quebec and Ontario Genomics (OGI-210). RA is supported by a Mitacs fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Copyright: © 2025 Ruíz Moleón V 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: Ruíz Moleón V, Alende C, Fotouhi M et al. A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 3; peer review: 2 approved] . F1000Research 2025, 12 :1578 ( https://doi.org/10.12688/f1000research.143928.3 ) First published: 11 Dec 2023, 12 :1578 ( https://doi.org/10.12688/f1000research.143928.1 ) Latest published: 07 Mar 2025, 12 :1578 ( https://doi.org/10.12688/f1000research.143928.3 ) Revised Amendments from Version 2 A co-author was added. A co-author was added. To read any peer review reports and author responses for this article, follow the "read" links in the Open Peer Review table. READ REVIEWER RESPONSES Introduction Multiple steps in membrane trafficking are coordinated by Rab proteins, a family of small guanosine triphosphatases (GTPase). 1 Rab GTPases undergo a dynamic cycle, alternating between an active GTP-bound state, catalyzed by guanine exchange factors (GEF), and an inactive GDP-bound state, achieved through GTP hydrolysis, stimulated by a GTPase-activating protein (GAP). 1 – 3 When activated, Rab proteins partake in crosstalk through shared effector proteins or through Rab activators to ensure vesicle traffic is spatiotemporally regulated. 1 Homologous to YTP1 in yeast, the Rab1 human proteins play key roles in regulating ER-Golgi and intra-Golgi transport. They exist as two isoforms in humans, Rab1A and Rab1B. While Rab1A and Rab1B share 92% amino acid identity, understanding their specific roles in membrane trafficking is a matter of ongoing investigation. 4 – 6 Rab1B has been proposed to function in the initial stages of the secretory pathways, serving to assemble and disassemble machinery required for vesicle fission and fusion, 4 whereas Rab1A exhibits unique functions such as its involvement in cell adhesion and migration, and plays a role in facilitating autophagosome formation, an early step in the autophagy pathway 7 , 8 Elevated expression of R AB1A and RAB1B genes have implications in various cancer types, including colorectal cancer, 9 hepatocellular cancer, 10 gliomas, 11 tongue carcinomas, prostate cancer 12 for RAB1A and colorectal cancer, 13 hepatocellular cancer, 14 and prostate cancer 12 for RAB1B. Rab1A in human cancer is highly studied in comparison to Rab1B as abnormal expression of Rab1A activates mTORC1 signalling, promoting tumour growth, invasion and ultimately cancer progression. 9 Rab1 proteins are also involved in the pathogenesis of Parkinson’s disease, characterized by accumulation of α-synuclein. Inhibition of ER-Golgi traffic has been reported to trigger α-synuclein aggregation, suggesting that an increase in production of Rab1 proteins can potentially rescue this α-synuclein toxic phenotype. 15 Further research is required to understand the role of Rab1A and Rab1B in various diseased states and their potential as therapeutic targets to slow the progression of cancer and neurodegeneration. In-depth mechanistic investigations would significantly benefit from the accessibility of high-performing antibodies, which can help elucidate the underlying processes and pathways involving Rab1A and Rab1B. An editorial by Biddle et al . can provide valuable insights on how to interpret the antibody characterization data found in this article. 16 This research is part of a broader collaborative initiative in which academics, funders and commercial antibody manufacturers are working together to address antibody reproducibility issues by characterizing commercial antibodies for human proteins using standardized protocols, and openly sharing the data. 17 – 19 Here, twelve commercially available antibodies that target either Rab1A or Rab1B were tested in Western Blot, immunoprecipitation and immunofluorescence applications using a knockout-based validation approach. This article serves as a valuable guide to help researchers select high-quality antibodies for their specific needs, facilitating the biochemical and cellular assessment of Rab1A and Rab1B properties and function. Results and discussion Our standard protocol involves comparing readouts from wild-type (WT) and knockout (KO) cells. 20 , 21 The first step was to identify a cell line(s) that expresses sufficient endogenous levels of a given protein to generate a measurable signal. To this end, we examined the DepMap transcriptomics database to identify all cell lines that express the Rab1 isoforms at levels greater than 2.5 log 2 (transcripts per million “TPM” + 1), which we have found to be a suitable cut-off (Cancer Dependency Map Portal, RRID:SCR_017655). Commercially available HAP1 cells express Rab1A and Rab1B transcripts at RNA levels above the average range of cancer cells analyzed. Parental and RAB1A and RAB1B KO HAP1 cells were obtained from Horizon Discovery ( Table 1 ). Table 1. Summary of the cell lines used. Institution Catalog number RRID (Cellosaurus) Cell line Genotype Horizon Discovery C631 CVCL_Y019 HAP1 WT Horizon Discovery HZGHC007227c012 CVCL_B5KT HAP1 RAB1A KO Horizon Discovery HZGHC001225c011 CVCL_TI00 HAP1 RAB1B KO For Western Blot experiments, we resolved proteins from WT and RAB1A and RAB1B KO cell extracts and probed them side-by-side with all antibodies in parallel ( Figure 1 ). 21 Figure 1 indicates which antibodies are intended for Rab1A (A) or Rab1B (B) . In the results, it was observed that Rab1A antibodies, namely ab302545**, NBP3-11042*, NBP3-11043*, 13075** and 11671-1-AP immunodetected their target, Rab1A protein as a ~23 kDa band in the HAP1 WT lysate while the levels of Rab1A increased by ~2-3 fold in the lysates of Rab1B KO cells. Similarly, Rab1B antibodies 17824-1-AP and PA5-77240 detect Rab1B at ~23 kDa in the HAP1 WT lysate, and revealed a similar ~2-3 fold increase in Rab1B protein level in the Rab1A KO lysate. These results demonstrated that a compensatory mechanism exists to ensure that overall Rab1 protein levels remain balanced. Figure 1. Rab1A and Rab1B antibody screening by Western Blot. Lysates of HAP1 (WT and RAB1A and RAB1B KO) were prepared and 30 μg of protein were processed for Western Blot with the indicated Rab1A and Rab1B antibodies. Figure 1A represents the findings from the Western Blot experiments for antibodies intended to bind to Rab1A while Figure 1B represents the Western Blots for antibodies intended to bind Rab1B. The Ponceau stained transfers of each Blot are presented to show equal loading of WT and KO lysates and protein transfer efficiency from the acrylamide gels to the nitrocellulose membrane. Antibody dilutions were chosen according to the recommendations of the antibody supplier. Exceptions were given for antibodies ab302545**, NBP3-11042*, 13075**, 11671-1-AP, PA5-104066, 17824-1-AP, PA5-104067 and PA5-77240, which were titrated to the corresponding dilutions found below, as the signals were too weak when following the supplier’s recommendations. Antibody dilution used: ab302545** at 1/200, NBP3-11042* at 1/500, NBP3-11043* at 1/500, 13075** at 1/200, 11671-1-AP at 1/500, PA5-44578 at 1/500, PA5-104066 at 1/500, NBP3-18251 at 1/200, 17824-1-AP at 1/500, MA5-31880* at 1/500, PA5-104067 at 1/200, PA5-77240 at 1/200. Predicted band size: 22 kDa. *Monoclonal antibody, **Recombinant antibody. As per our standard procedure, we next used the antibodies to immunoprecipitateRab1A and Rab1B from HAP1 cell extracts. The performance of each antibody was evaluated by detecting the Rab1A and Rab1B protein in extracts, in the immunodepleted extracts and in the immunoprecipitates using an antibdy that was validated by Western Blot ( Figure 2 ). 21 Figure 2. Rab1A and Rab1B antibody screening by immunoprecipitation. HAP1 lysates were prepared, and IP was performed using 2.0 μg of the indicated Rab1A and Rab1B antibodies pre-coupled to Dynabeads protein A or protein G. Samples were washed and processed for Western Blot with the indicated Rab1A and Rab1B antibodies. Figure 2A represents the IP results for antibodies intended to immunodetect Rab1A while Figure 2B represents the results for antibodies intended to immunodetect Rab1B. For Rab1A Western Blots ( A ), ab302545** was used at 1/200. For Rab1B Western Blots ( B ), 17824-1-AP was used at 1/500. The Ponceau stained transfers of each Blot are shown. SM=4% starting material; UB=4% unbound fraction; IP=immunoprecipitate; LC=antibody light chain. *Monoclonal antibody, **Recombinant antibody. For immunofluorescence, antibodies were screened using a mosaic strategy, as per our standard procedure. First, the HAP1 WT and RAB1A KO cells were plated together in the same tissue culture wells, using different colour fluorescent dyes to distinguish the two cell lines, and the seven Rab1A antibodies were tested. Then, HAP1 WT and RAB1B KO cells were plated together using the same strategy, and the five Rab1B antibodies were tested. Cells were imaged in the same field of view to reduce staining, imaging and image analysis bias ( Figure 3 ). Quantification of immunofluorescence intensity hundreds of WT and KO cells was performedfor each antibody tested. The images presented in Figure 3 are representative of the results of this analysis. Figure 3. Rab1A and Rab1B antibody screening by immunofluorescence. HAP1 WT were labelled with a green fluorescence dye, and HAP1 RAB1A and RAB1B KO cells were labelled with a far-red fluorescent dye. Figure 3A represents WT cells plated together RAB1A KO, while Figure 3B represents WT cells plated with RAB1B KO cells. WT/KO cells are plated to a 1:1 ratio in a 96-well plate with optically clear flat-bottom. In panel (A) , WT and RAB1A KO cells were stained with the antibodies intended to target Rab1A, and the corresponding Alexa-fluor 555 coupled secondary antibody including DAPI. In panel (B) , WT and RAB1B KO cells were stained with the antibodies intended to target Rab1B, and the corresponding Alexa-fluor 555 coupled secondary antibody including DAPI. Acquisition of the blue (nucleus-DAPI), green (identification of WT cells), red (antibody staining) and far-red (identification of KO cells) channels was performed. Representative images of the merged blue and red (grayscale) channels are shown. WT and KO cells are outlined with green and magenta dashed line, respectively. When the concentration was not indicated by the supplier, we tested antibodies at 1/100 or 1/500, which was the case for antibodies NBP3-11042*, NBP3-11043*, PA5-44578, PA5-104066, NBP3-18251 and 17824-1-AP. At these concentrations, the signal from each antibody was in the range of detection of the microscope used. Antibody dilution used: ab302545** at 1/100, NBP3-11042* at 1/100, NBP3-11043* at 1/100, 13075** at 1/800, 11671-1-AP at 1/700, PA5-44578 at 1/500, PA5-104066 at 1/100, NBP3-18251 at 1/100, 17824-1-AP at 1/50, MA5-31880* at 1/1000, PA5-104067 at 1/1000, PA5-77240 at 1/50. Bars = 10 μm. *Monoclonal antibody, **Recombinant antibody. In conclusion, we have screened seven Rab1A and Rab1B commercial antibodies by Western Blot, immunoprecipitation and immunofluorescence. Several high-quality antibodies that selectively detect either Rab1A or Rab1B under the standardized experimental conditions were identified in each of the tested applications. In our efforts to address the antibody reliability and reproducibility challenges in scientific research, the authors recommend the antibodies that demonstrated to be underperforming be removed from the commercial antibody market. However, the authors do not engage in result analysis or offer explicit antibody recommendations. A limitation of this study is the use of universal protocols - any conclusions remain relevant within the confines of the experimental setup and cell line used in this study. Our primary aim is to deliver top-tier data to the scientific community, grounded in Open Science principles. This empowers experts to interpret the characterization data independently, enabling them to make informed choices regarding the most suitable antibodies for their specific experimental needs. The underlying data for this study can be found on Zenodo, an open access repository for which YCharOS has its own community. 22 , 23 Methods Antibodies All Rab1A and Rab1B antibodies are listed in Table 2 , together with their corresponding Research Resource Identifiers, or RRID, to ensure the antibodies are cited properly. 24 Peroxidase-conjugated goat anti-rabbit and anti-mouse antibodies are from Thermo Fisher Scientific (cat. number 65-6120 and 62-6520). Alexa-555-conjugated goat anti-rabbit and anti-mouse secondary antibodies are from Thermo Fisher Scientific (cat. number A21429 and A21424). Table 2. Summary of the Rab1A and Rab1B antibodies tested. Intended Rab-1 target Company Catalog number Lot number RRID (Antibody Registry) Clonality Clone ID Host Concentration (μg/μL) Vendors recommended applications Rab1A Abcam ab302545 ** GR3458765-3 AB_2942108 recombinant-mono EPR27169-83 rabbit 0.502 WB, IP, IF Rab1A Novus Biologicals (a Bio-Techne brand) NBP3-11042 * MR288278 AB_2942092 monoclonal 7H4 mouse 1.000 WB, IP Rab1A Novus Biologicals (a Bio-Techne brand) NBP3-11043 * MR488278 AB_2942109 monoclonal 4G10 mouse 1.000 WB, IP Rab1A Cell Signaling Technology 13075 ** 1 AB_2665537 recombinant-mono D3X9S rabbit 0.200 WB, IF Rab1A Proteintech 11671-1-AP 66720 AB_2173437 polyclonal - rabbit 0.700 WB, IP, IF Rab1A Thermo Fisher Scientific PA5-44578 YA3805788 AB_2608352 polyclonal - rabbit 0.500 WB Rab1A Thermo Fisher Scientific PA5-104066 YA3806218A AB_2853395 polyclonal - rabbit 1.000 WB Rab1B Novus Biologicals (a Bio-Techne brand) NBP3-18251 PR285216 AB_2942110 polyclonal - rabbit 1.000 WB, IF Rab1B Proteintech 17824-1-AP 39221 AB_2237881 polyclonal - rabbit 0.200 WB, IF Rab1B Thermo Fisher Scientific MA5-31880 * YA3806197 AB_2787503 monoclonal 7A12G2 mouse 1.000 WB Rab1B Thermo Fisher Scientific PA5-104067 YA3806219A AB_2853396 polyclonal - rabbit 1.000 WB, IF Rab1B Thermo Fisher Scientific PA5-77240 YA3805998 AB_2720967 polyclonal - rabbit 1.000 WB, IF * Monoclonal antibody, ** Recombinant antibody Cell culture Both HAP1 WT and RAB1A and RAB1B KO cell lines used are listed in Table 1 , together with their corresponding RRID, to ensure the cell lines are cited properly. 25 Cells were cultured in DMEM high-glucose (GE Healthcare cat. number SH30081.01) containing 10% fetal bovine serum (Wisent, cat. number 080450), 2 mM L-glutamate (Wisent cat. number 609065), 100 IU penicillin and 100 μg/mL streptomycin (Wisent cat. number 450201). Antibody screening by Western Blot Western Blots were performed as described in our standard operating procedure. HAP1 WT and the HAP1 RAB1A and RAB1B KO lines (listed in Table 1 ) were collected in RIPA buffer (25 mM Tris-HCl pH 7.6, 150 mM NaCl, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS) from Thermo Fisher Scientific (cat. number 89901) supplemented with 1× protease inhibitor cocktail mix (MilliporeSigma, cat. number P8340). Lysates were sonicated briefly and incubated for 30 min on ice. Lysates were spun at ~110,000 × g for 15 min at 4°C and equal protein aliquots of the supernatants were analyzed by SDS-PAGE and Western Blot. BLUelf prestained protein ladder from GeneDireX (cat. number PM008-0500) was used. Western Blots were performed with a precast midi 10% Bis-Tris polyacrylamide gels from Thermo Fisher Scientific (cat. number WG1201BOX) ran with MES SDS buffer (Thermo Fisher Scientific, cat. number NP000202), loaded in LDS sample buffer (Thermo Fisher Scientific, cat. number NP0008) with 1× sample reducing agent (Thermo Fisher Scientific, cat. number NP0009) and transferred on nitrocellulose membranes. Proteins on the Blots were visualized with Ponceau S staining (Thermo Fisher Scientific, cat. number BP103-10) which is scanned to show together with individual Western Blot. Blots were blocked with 5% milk for 1 hr, and antibodies were incubated overnight at 4°C with 5% milk in TBS with 0.1% Tween 20 (TBST) (Cell Signalling Technology, cat. number 9997). Following three washes with TBST, the peroxidase conjugated secondary antibody was incubated at a dilution of ~0.2 μg/mL in TBST with 5% milk for 1 hr at room temperature followed by three washes with TBST. Membranes were incubated with Pierce ECL from Thermo Fisher Scientific (cat. number 32106) or Clarity Western ECL Substrate from Bio-Rad (cat. number 1705061) prior to detection with the iBright™ CL1500 Imaging System from Thermo Fisher Scientific (cat. number A44240). Membranes incubated with primary antibodies NBP3-11043*, 13075**, PA5-44578, PA5-104066, NBP3-18251 and PA5-104067 were developed with Clarity Western ECL Substrate, and the remaining antibodies with Pierce ECL. Antibody screening by immunoprecipitation Immunoprecipitation was performed as described in our standard operating procedure. Antibody-bead conjugates were prepared by adding 2 μg or 10 μL of antibody NBP3-18251 (unknown concentration) to 500 μL of Pierce IP Lysis Buffer from Thermo Fisher Scientific (cat. number 87788) in a 1.5 mL microcentrifuge tube, together with 30 μL of Dynabeads protein A - (for rabbit antibodies) or protein G - (for mouse antibodies) from Thermo Fisher Scientific (cat. number 10002D and 10004D, respectively). Tubes were rocked for ~1 hr at 4°C followed by two washes to remove unbound antibodies. HAP1 WT were collected in Pierce IP buffer (25 mM Tris-HCl pH 7.4, 150 mM NaCl, 1 mM EDTA, 1% NP-40 and 5% glycerol) supplemented with protease inhibitor. Lysates were rocked for 30 min at 4°C and spun at 110,000 × g for 15 min at 4°C. 0.5 mL aliquots at 2.0 mg/mL of lysate were incubated with an antibody-bead conjugate for ~1 hr at 4°C. The unbound fractions were collected, and beads were subsequently washed three times with 1.0 mL of IP lysis buffer and processed for SDS-PAGE and Western Blot on a precast midi 10% Bis-Tris polyacrylamide gels. Prot-A: HRP (MilliporeSigma, cat. number P8651) was used as a secondary detection system at a concentration of 0.3 μg/mL. Antibody screening by immunofluorescence Immunofluorescence was performed as described in our standard operating procedure. 21 HAP1 WT and the HAP1 RAB1A and RAB1B KO cell lines were labelled with a green and a far-red fluorescence dye, respectively. The fluorescent dyes used are from Thermo Fisher Scientific (cat. number C2925 and C34565). The nuclei were labelled with DAPI (Thermo Fisher Scientific, cat. number D3571) fluorescent stain. WT and KO cells were plated in a 96-well plate with optically clear flat-bottom (Perkin Elmer, cat. number 6055300) as a mosaic and incubated for 24 hrs in a cell culture incubator at 37°C, 5% CO 2 . Cells were fixed in 4% paraformaldehyde (PFA) (Beantown chemical, cat. number 140770-10 ml) in phosphate buffered saline (PBS) (Wisent, cat. number 311-010-CL) for 15 min at room temperature and washed 3 times with PBS. Cells were permeabilized in PBS with 0.1% Triton X-100 (Thermo Fisher Scientific, cat. number BP151-500) for 10 min at room temperature and blocked with PBS with 5% bovine serum albumin (BSA) (Wisent, cat. number 800-095), 5% goat serum (Gibco, cat. number 16210-064) and 0.01% Triton X-100 for 30 min at room temperature. Cells were incubated with IF buffer (PBS, 5% BSA, 0.01% Triton X-100) containing the primary Rab1A and Rab1B antibodies overnight at 4°C. Cells were then washed 3 × 10 min each with IF buffer and incubated with corresponding Alexa Fluor 555-conjugated secondary antibodies in IF buffer at a dilution of 1.0 μg/mL for 1 hr at room temperature with DAPI. Cells were washed 3 × 10 min with IF buffer and once with PBS. Images were acquired on an ImageXpress micro widefield high-content microscopy system (Molecular Devices), using a 20x NA 0.95 water objective lens and scientific CMOS camera (16- bit, 1.97 mm field of view), equipped with 395, 475, 555 and 635 nm solid state LED lights (Lumencor Aura III light engine) and bandpass emission filters (432/36 nm, 520/35 nm, 600/37 nm and 692/40 nm) to excite and capture fluorescence emission for DAPI, CellTracker TM Green, Alexa fluor 555 and CellTracker TM Red, respectively. Images had pixel sizes of 0.68 × 0.68 microns. Exposure time was set with maximal (relevant) pixel intensity ~80% of dynamic range and verified on multiple wells before acquisition. Since the IF staining varied depending on the primary antibody used, the exposure time was set using the most intensely stained well as reference. Frequently, the focal plane varied slightly within a single field of view. To remedy this issue, a stack of three images per channel was acquired at a z-interval of 4 microns per field and best focus projections were generated during the acquisition ( MetaXpress v6.7.1, Molecular Devices). Segmentation was carried out on the projections of CellTracker TM channels using CellPose v1.0 on green (WT) and far-red (KO) channels, using as parameters the ‘cyto’ model to detect whole cells, and using an estimated diameter tested for each cell type, between 15 and 20 microns. 26 Masks were used to generate cell outlines for intensity quantification. Figures were assembled with Adobe Photoshop (version 24.1.2) to adjust contrast then assembled with Adobe Illustrator (version 27.3.1). Data availability Underlying data Zenodo: Antibody Characterization Report for Rab1A and Rab1B, https://doi.org/10.5281/zenodo.8356353 . 22 Zenodo: Dataset for the Rab1A and Rab1B antibody screening study, https://doi.org/10.5281/zenodo.8400619 . 23 Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0) Acknowledgments We would like to thank the NeuroSGC/YCharOS/EDDU collaborative group for their important contribution to the creation of an open scientific ecosystem of antibody manufacturers and knockout cell line suppliers, for the development of community-agreed protocols, and for their shared ideas, resources and collaboration. We would also like to thank the Advanced BioImaging Facility (ABIF) consortium for their image analysis pipeline development and conduction (RRID:SCR_017697). Members of each group can be found below. NeuroSGC/YCharOS/EDDU collaborative group: Thomas M. Durcan, Aled M. Edwards, Chetan Raina and Wolfgang Reintsch. ABIF consortium: Claire M. Brown and Joel Ryan. Thank you to the Structural Genomics Consortium, a registered charity (no. 1097737), for supporting this project. The Structural Genomics Consortium receives funding from Bayer AG, Boehringer Ingelheim, Bristol-Myers Squibb, Genentech, Genome Canada through Ontario Genomics Institute (grant no. OGI-196), the EU and EFPIA through the Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN grant no. 875510), Janssen, Merck KGaA (also known as EMD in Canada and the United States), Pfizer and Takeda. An earlier version of this of this article can be found on Zenodo (doi: 10.5281/zenodo.8356353 ). References 1. Stenmark H: Rab GTPases as coordinators of vesicle traffic. Nat. Rev. Mol. Cell Biol. 2009; 10 (8): 513–525. Publisher Full Text 2. Barr F, Lambright DG: Rab GEFs and GAPs. Curr. Opin. Cell Biol. 2010; 22 (4): 461–470. PubMed Abstract | Publisher Full Text | Free Full Text 3. 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PubMed Abstract | Publisher Full Text Comments on this article Comments (0) Version 3 VERSION 3 PUBLISHED 11 Dec 2023 ADD YOUR COMMENT Comment Author details Author details 1 Department of Neurology and Neurosurgery, Structural Genomics Consortium, The Montreal Neurological Institute, McGill University, Montreal, Québec, H3A 2B4, Canada Vera Ruíz Moleón Roles: Investigation, Writing – Review & Editing Charles Alende Roles: Formal Analysis, Investigation, Writing – Review & Editing Maryam Fotouhi Roles: Investigation, Methodology, Writing – Review & Editing Riham Ayoubi Roles: Investigation, Methodology, Validation, Visualization, Writing – Review & Editing Sara González Bolívar Roles: Investigation, Writing – Review & Editing Kathleen Southern Roles: Writing – Original Draft Preparation, Writing – Review & Editing Peter S. McPherson Roles: Conceptualization, Funding Acquisition, Resources, Supervision, Writing – Review & Editing Carl Laflamme Roles: Conceptualization, Formal Analysis, Funding Acquisition, Methodology, Project Administration, Resources, Supervision, Writing – Review & Editing Competing interests For this project, the laboratory of Peter McPherson developed partnerships with high-quality antibody manufacturers and knockout cell line providers. The partners provide antibodies and knockout cell lines to the McPherson laboratory at no cost. These partners include: - Abcam-Aviva Systems Biology -Bio Techne -Cell Signalling Technology -Developmental Studies Hybridoma Bank -GeneTex – Horizon Discovery – Proteintech – Synaptic Systems –Thermo Fisher Scientific. Grant information The grant was from a Canadian Institutes of Health Research Foundation (grant no. FDN154305) and by the Government of Canada through Genome Canada, Genome Quebec and Ontario Genomics (OGI-210). RA is supported by a Mitacs fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Article Versions (3) version 3 Revised Published: 07 Mar 2025, 12:1578 https://doi.org/10.12688/f1000research.143928.3 version 2 Revised Published: 28 Dec 2023, 12:1578 https://doi.org/10.12688/f1000research.143928.2 version 1 Published: 11 Dec 2023, 12:1578 https://doi.org/10.12688/f1000research.143928.1 Copyright © 2025 Ruíz Moleón V 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. Download Export To Sciwheel Bibtex EndNote ProCite Ref. Manager (RIS) Sente metrics Views Downloads F1000Research - - PubMed Central info_outline Data from PMC are received and updated monthly. - - Citations open_in_new 0 open_in_new 0 open_in_new SEE MORE DETAILS CITE how to cite this article Ruíz Moleón V, Alende C, Fotouhi M et al. A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 3; peer review: 2 approved] . F1000Research 2025, 12 :1578 ( https://doi.org/10.12688/f1000research.143928.3 ) NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article. COPY CITATION DETAILS track receive updates on this article Track an article to receive email alerts on any updates to this article. TRACK THIS ARTICLE Share Open Peer Review Current Reviewer Status: ? 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 28 Dec 2023 Revised Views 0 Cite How to cite this report: Fallini C. Reviewer Report For: A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 3; peer review: 2 approved] . F1000Research 2025, 12 :1578 ( https://doi.org/10.5256/f1000research.160069.r253285 ) The direct URL for this report is: https://f1000research.com/articles/12-1578/v2#referee-response-253285 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 28 Mar 2024 Claudia Fallini , University of Rhode Island, Kingston, Rhode Island, USA Approved VIEWS 0 https://doi.org/10.5256/f1000research.160069.r253285 In this report, Moleon and colleagues characterize several antibodies directed against the human Rab1A or Rab1B proteins. Rab1 proteins are small GTP-binding proteins that participate in vesicle trafficking, among other cellular functions. Interest in these proteins also ... Continue reading READ ALL In this report, Moleon and colleagues characterize several antibodies directed against the human Rab1A or Rab1B proteins. Rab1 proteins are small GTP-binding proteins that participate in vesicle trafficking, among other cellular functions. Interest in these proteins also stems from their potential role as oncogenes, as several cancer types have been shown to upregulate Rab1A or Rab1B. The authors carefully characterized 7 Rab1A and 5 Rab1B antibodies by western blot, immunoprecipitation, and immunofluorescence assays using KO and isogenic parental cell lines. The results are clearly presented, and the methods detailed enough to allow replication. Overall, there are no specific concerns in my view. Only few minor typos were identified such as missing spaces in the abstract ("diseaseand") and on page 5 ("immunoprecipitateRab1A", "antibdy", and "performedfor"). Is the rationale for creating the dataset(s) clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: Cell biology and neuroscience 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 Fallini C. Reviewer Report For: A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 3; peer review: 2 approved] . F1000Research 2025, 12 :1578 ( https://doi.org/10.5256/f1000research.160069.r253285 ) The direct URL for this report is: https://f1000research.com/articles/12-1578/v2#referee-response-253285 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: Niwa S. Reviewer Report For: A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 3; peer review: 2 approved] . F1000Research 2025, 12 :1578 ( https://doi.org/10.5256/f1000research.160069.r246962 ) The direct URL for this report is: https://f1000research.com/articles/12-1578/v2#referee-response-246962 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 26 Feb 2024 Shinsuke Niwa , Tohoku University, Miyagi, Japan Approved VIEWS 0 https://doi.org/10.5256/f1000research.160069.r246962 1. It would be helpful to have a table describing which antibodies are useful and reliable and which are not for each application. 2. A limitation of this study is that the authors analyzed only the human cell ... Continue reading READ ALL 1. It would be helpful to have a table describing which antibodies are useful and reliable and which are not for each application. 2. A limitation of this study is that the authors analyzed only the human cell line HAP1 and not widely used cells such as Hela cells and 293 cells. 3. While "the authors recommend the antibodies that demonstrated to be underperforming be removed from the commercial antibody market", one cannot conclude usefulness of these antibodies in cell lines derived from other species such as mouse, hamster (CHO cells) and rat. Is the rationale for creating the dataset(s) clearly described? Partly Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests: No competing interests were disclosed. Reviewer Expertise: cell biology 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 Niwa S. Reviewer Report For: A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 3; peer review: 2 approved] . F1000Research 2025, 12 :1578 ( https://doi.org/10.5256/f1000research.160069.r246962 ) The direct URL for this report is: https://f1000research.com/articles/12-1578/v2#referee-response-246962 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 Comments on this article Comments (0) Version 3 VERSION 3 PUBLISHED 11 Dec 2023 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 3 (revision) 07 Mar 25 Version 2 (revision) 28 Dec 23 read read Version 1 11 Dec 23 Shinsuke Niwa , Tohoku University, Miyagi, Japan Claudia Fallini , University of Rhode Island, Kingston, USA 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 Fallini C. 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. 28 Mar 2024 | for Version 2 Claudia Fallini , University of Rhode Island, Kingston, Rhode Island, USA 0 Views copyright © 2024 Fallini C. 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 In this report, Moleon and colleagues characterize several antibodies directed against the human Rab1A or Rab1B proteins. Rab1 proteins are small GTP-binding proteins that participate in vesicle trafficking, among other cellular functions. Interest in these proteins also stems from their potential role as oncogenes, as several cancer types have been shown to upregulate Rab1A or Rab1B. The authors carefully characterized 7 Rab1A and 5 Rab1B antibodies by western blot, immunoprecipitation, and immunofluorescence assays using KO and isogenic parental cell lines. The results are clearly presented, and the methods detailed enough to allow replication. Overall, there are no specific concerns in my view. Only few minor typos were identified such as missing spaces in the abstract ("diseaseand") and on page 5 ("immunoprecipitateRab1A", "antibdy", and "performedfor"). Is the rationale for creating the dataset(s) clearly described? Yes Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise Cell biology and neuroscience 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) Fallini C. Peer Review Report For: A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 3; peer review: 2 approved] . F1000Research 2025, 12 :1578 ( https://doi.org/10.5256/f1000research.160069.r253285) 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/12-1578/v2#referee-response-253285 keyboard_arrow_left Back to all reports Reviewer Report 0 Views copyright © 2024 Niwa S. 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. 26 Feb 2024 | for Version 2 Shinsuke Niwa , Tohoku University, Miyagi, Japan 0 Views copyright © 2024 Niwa S. 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 1. It would be helpful to have a table describing which antibodies are useful and reliable and which are not for each application. 2. A limitation of this study is that the authors analyzed only the human cell line HAP1 and not widely used cells such as Hela cells and 293 cells. 3. While "the authors recommend the antibodies that demonstrated to be underperforming be removed from the commercial antibody market", one cannot conclude usefulness of these antibodies in cell lines derived from other species such as mouse, hamster (CHO cells) and rat. Is the rationale for creating the dataset(s) clearly described? Partly Are the protocols appropriate and is the work technically sound? Yes Are sufficient details of methods and materials provided to allow replication by others? Yes Are the datasets clearly presented in a useable and accessible format? Yes Competing Interests No competing interests were disclosed. Reviewer Expertise cell biology 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) Niwa S. Peer Review Report For: A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 3; peer review: 2 approved] . F1000Research 2025, 12 :1578 ( https://doi.org/10.5256/f1000research.160069.r246962) 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/12-1578/v2#referee-response-246962 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 Adjust parameters to alter display View on desktop for interactive features Includes Interactive Elements View on desktop for interactive features Competing Interests Policy Provide sufficient details of any financial or non-financial competing interests to enable users to assess whether your comments might lead a reasonable person to question your impartiality. 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