TomahaqCompanion: A Tool for the Creation and Analysis of Isobaric Label Based Multiplexed Targeted Assays.
Triggered by Offset, Multiplexed, Accurate mass, High resolution, and Absolute Quantitation (TOMAHAQ) is a recently introduced targeted proteomics method that combines peptide and sample multiplexing. TOMAHAQ assays enable sensitive and accurate multiplexed quantification by implementing an intricate data collection scheme that comprises multiple MSn scans, mass inclusion lists, and data-driven filters. Consequently, manual creation of TOMAHAQ methods can be time-consuming and error prone, while the resulting TOMAHAQ data may not be compatible with common mass spectrometry analysis pipelines. To address these concerns we introduce TomahaqCompanion, an open-source desktop application that enables rapid creation of TOMAHAQ methods and analysis of TOMAHAQ data. Starting from a list of peptide sequences, a user can perform each step of TOMAHAQ assay development including (1) generation of priming run target list, (2) analysis of priming run data, (3) generation of TOMAHAQ method file, and (4) analysis and export of quantitative TOMAHAQ data. We demonstrate the flexibility of TomahaqCompanion by creating a variety of methods testing TOMAHAQ parameters (e.g., number of SPS notches, run length, etc.). Lastly, we analyze an interference sample comprising heavy yeast peptides, a standard human peptide mixture, TMT11-plex, and super heavy TMT (shTMT) isobaric labels to demonstrate ∼10-200 attomol limit of quantification within a complex background using TOMAHAQ.
['Rose|Christopher M|CM|0000-0002-7502-3368', 'Erickson|Brian K|BK|0000-0002-1150-5042', 'Schweppe|Devin K|DK|0000-0002-3241-6276', 'Viner|Rosa|R|', 'Choi|Jae|J|', 'Rogers|John|J|', 'Bomgarden|Ryan|R|', 'Gygi|Steven P|SP|', 'Kirkpatrick|Donald S|DS|']
D006801:Humans D010455:Peptides D040901:Proteomics D012984:Software D013194:Staining and Labeling D053719:Tandem Mass Spectrometry D013997:Time Factors D014584:User-Computer Interface D015003:Yeasts
isobaric labeling TOMAHAQ targeted proteomics mass spectrometry TMT Orbitrap SPS-MS3 computational analysis open source quantitative proteomics