Expediting the Development of Targeted SRM Assays: Using Data from Shotgun Proteomics to Automate Method Development
Open accessAbstract
Selected reaction monitoring (SRM) is a powerful tandem mass spectrometry method that can be used to monitor target peptides within a complex protein digest. The specificity and sensitivity of the approach, as well as its capability to multiplex the measurement of many analytes in parallel, has made it a technology of particular promise for hypothesis driven proteomics. An underappreciated step in the development of an assay to measure many peptides in parallel is the time and effort necessary to establish a usable assay. Here we report the use of shotgun proteomics data to expedite the selection of SRM transitions for target peptides of interest. The use of tandem mass spectrometry data acquired on an LTQ ion trap mass spectrometer can accurately predict which fragment ions will produce the greatest signal in an SRM assay using a triple quadrupole mass spectrometer. Furthermore, we present a scoring routine that can compare the targeted SRM chromatogram data with an MS/MS spectrum acquired by data-dependent acquisition and stored in a library. This scoring routine is invaluable in determining which signal in the chromatogram from a complex mixture best represents the target peptide. These algorithmic developments have been implemented in a software package that is available from the authors upon request.
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Targeted MS quantification using selected reaction monitoring was recently applied to investigate the transmission of a plant virus.
“For example, the targeted MS quantification method based on selected reaction monitoring [132–134] was recently implemented to understanding the transmission of a plant virus.”
From Proteomic approaches to uncovering virus–host protein interactions during the progression of viral infection (2016) · cites this paper as [134]
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- Authors
- Prakash, A., Tomazela, D. M., Frewen, B., MacLean, B., Merrihew, G., Peterman, S., & MacCoss, M. J.
- Affiliations
- University of Washington (US)
- Corresponding author
- Peterman, Scott
- MacCoss, Michael J.
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2009-04-30
- Volume
- 8
- Issue
- 6
- Pages
- 2733-2739
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC2743471
- OpenAlex
- W2126869418
- Cited by
- 147
- References
- 24
- Citations by year
- 2026: 4 · 2025: 2 · 2024: 1 · 2023: 2 · 2021: 2 · 2020: 3 · 2019: 2 · 2018: 4 · 2017: 3 · 2016: 13 · 2015: 9 · 2014: 9 · 2013: 15 · 2012: 30
- FWCI
- 11.01
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Cancer Institute (U24CA126479)
- National Institute of General Medical Sciences (P41GM103533)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK069386)
- National Center for Research Resources (P41RR011823)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Metabolomics and Mass Spectrometry Studies
- Keywords
- multiple reaction monitoring, shotgun proteomics, triple quadrupole, data-dependent acquisition, targeted quantification
- MeSH terms
- Algorithms, Animals, Data Interpretation, Statistical, Peptide Fragments, Software, Mass Spectrometry, Peptide Library, Caenorhabditis elegans Proteins, Escherichia coli Proteins, Databases, Protein, Proteomics
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