Scientific Publications

Modification site localization scoring: strategies and performance.

Publication TypeJournal Article
AuthorsChalkley, RJ, and Clauser KR
AbstractUsing 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.
Year of Publication2012
JournalMolecular & cellular proteomics : MCP
Volume11
Issue5
Pages3-14
Date Published (YYYY/MM/DD)2012/05/01
ISSN Number1535-9476
DOI10.1074/mcp.R111.015305
PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/22328712?dopt=Abstract