High Resolution Multi-Pass Astral Analyzer Quantification Enables Highly Multiplexed 35-Plex Tandem Mass Tag Proteomics

ABSTRACT Tandem mass tags (TMT) allow highly multiplexed and thus high-throughput, precisely quantitative proteomic analysis. Incorporation of additional deuterated reporter channels has near-doubled the multiplexation achieved with Thermo Scientific™ TMTpro reagents from 18 to 35-plex but requires extremely high ∼100k analyzer resolving power at m/z 128 to differentiate and quantify reporter ion channels, far beyond any single reflection time-of-flight analyzer, and exceeding the multi-reflection Thermo Scientific™ Astral™ analyzer in its standard operation. A multi-pass mode of Astral operation has been developed for the Thermo Scientific™ Orbitrap™ Astral™ Zoom mass spectrometer that triples the ion path to 90 m, more than doubling resolving power for a narrow m/z range. This “TMT HR mode” has been integrated into a new method of TMT proteomic analysis that splits regular MS2 analysis of labeled peptides into paired measurements comprising wide mass range scans for peptide identification, and TMT HR mode scans for reporter ion quantification. The method has been shown to accurately quantify 32-plex labeled HeLa protein lysate and provide far greater depth of analysis as state-of-the-art Orbitrap-only methods, while analysis of 11-plex labeled yeast showed no analytical depth sacrificed vs regular Orbitrap Astral TMT analysis. Further comparative measurements of a 2-cell line 35-plex sample demonstrated greater analytical depth, and similar quantitative precision, to “gold standard” Orbitrap MS3 methods. Competing Interest Statement The authors declare the following competing financial interest(s): HS, CR, JK, MZ, TNA, BH, ED, RO, DG, JP, DN, PC, FB, BD, MW, AW, RB, DCF, ED, AM, VZ and CH are employees of, and SPG a consultant for, Thermo Fisher Scientific, the manufacturer of instrumentation used in this research.