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Mol Cell Proteomics. 2012 May;11(5):3-14. doi: 10.1074/mcp.R111.015305. Epub 2012 Feb 11.

Modification site localization scoring: strategies and performance.

Author information

  • 1University of California San Francisco, 600 16th Street, Genentech Hall N-474A, San Francisco, California 94158, USA. chalkley@cgl.ucsf.edu

Abstract

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.

PMID:
22328712
[PubMed - indexed for MEDLINE]
PMCID:
PMC3418845
Free PMC Article

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