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Free computational resources for designing selected reaction monitoring transitions
Author(s) -
Cham Mead Jennifer A.,
Bianco Luca,
Bessant Conrad
Publication year - 2010
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200900396
Subject(s) - peptide , proteome , chemistry , mass spectrometry , tandem mass spectrometry , triple quadrupole mass spectrometer , computer science , quantitative proteomics , selected reaction monitoring , proteomics , database search engine , product (mathematics) , combinatorial chemistry , ion , biological system , chromatography , analytical chemistry (journal) , search engine , biology , biochemistry , mathematics , geometry , information retrieval , gene , organic chemistry
Selected reaction monitoring (SRM) is a technique for quantifying specific proteins using triple quadrupole MS. Proteins are digested into peptides and fed into MS following HPLC separation. The stream of ionized peptides is filtered by m/z ratio so only specific peptide targets enter the collision cell, where they are fragmented into product ions. A specific product ion is then filtered from the cell and its intensity measured. By spiking an isotopically labeled version of each target peptide into a sample, both native and surrogate peptides enter MS, pass the filters and transition into product ions in tandem; thus the quantity of the native peptide may be calculated by examining the relative intensities of the native and surrogate signals. The choice of precursor‐to‐product ion transitions is critical for SRM, but predicting the best candidates is challenging and time‐consuming. To alleviate this problem, software tools for designing and optimizing transitions have recently emerged, predominantly driven by data from public proteomics repositories, such as the Global Proteome Machine and PeptideAtlas. In this review, we provide an overview of the state‐of‐the‐art in automated SRM transition design tools in the public domain, explaining how the systems work and how to use them.