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Mol Cell Proteomics DOI:10.1074/mcp.R111.015305

Modification site localization scoring: strategies and performance.

Publication TypeJournal Article
Year of Publication2012
AuthorsChalkley, RJ, Clauser, KR
JournalMol Cell Proteomics
Date Published2012 May
KeywordsAmino Acid Motifs, Computer Simulation, Humans, Models, Molecular, Molecular Sequence Annotation, Protein Processing, Post-Translational, Proteome, Proteomics, Sequence Analysis, Protein, Software, Tandem Mass Spectrometry

Using enrichment strategies many research groups are routinely producing large data sets of post-translationally modified peptides for proteomic analysis using tandem mass spectrometry. Although search engines are relatively effective at identifying these peptides with a defined measure of reliability, their localization of site/s of modification is often arbitrary and unreliable. The field continues to be in need of a widely accepted metric for false localization rate that accurately describes the certainty of site localization in published data sets and allows for consistent measurement of differences in performance of emerging scoring algorithms. In this article are discussed the main strategies currently used by software for modification site localization and ways of assessing the performance of these different tools. Methods for representing ambiguity are reviewed and a discussion of how the approaches transfer to different data types and modifications is presented.


Alternate JournalMol. Cell Proteomics
PubMed ID22328712
PubMed Central IDPMC3418845
Grant ListU24CA126476 / CA / NCI NIH HHS / United States
P41RR001614 / RR / NCRR NIH HHS / United States
HHSN268201000033C / / PHS HHS / United States
P41M103481 / / PHS HHS / United States
HHSN268201000033C / HL / NHLBI NIH HHS / United States
U24 CA126476 / CA / NCI NIH HHS / United States
P41 RR001614 / RR / NCRR NIH HHS / United States