on 12-11-201805:39 AM - edited on 10-15-202110:54 AM by AnalyteGuru
Christopher M. Rose1, Brian K. Erickson2 , Devin K. Schweppe2 , Rosa Viner3 , Jae Choi4 , John Rogers4 , Ryan Bomgarden4 , Steven P. Gygi2 , Donald S. Kirkpatrick J Proteome Res. 2018 Dec 3. doi: 10.1021/acs.jproteome.8b00767 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.
https://pubs.acs.org/doi/10.1021/acs.jproteome.8b00767 1. Department of Microchemistry, Proteomics and Lipidomics, Genentech, South San Francisco, CA 94080, United States.
2. Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States.
3. Thermo Fisher Scientific, San Jose, CA 95134, United States
4. Thermo Fisher Scientific, Rockford, Illinois 61101, United States