A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics

Journal Article · Fri Jul 15 04:00:00 EDT 2011 · Analytical Chemistry, 83(16):6135-6140

DOI:https://doi.org/10.1021/ac2009806· OSTI ID:1023112

Stanley, Jeffrey R; Adkins, Joshua N; Slysz, Gordon W; Monroe, Matthew E; Purvine, Samuel O; Karpievitch, Yuliya V; Anderson, Gordon A; Smith, Richard D; Dabney, Alan R

High-throughput proteomics is rapidly evolving to require high mass measurement accuracy for a variety of different applications. Increased mass measurement accuracy in bottom-up proteomics specifically allows for an improved ability to distinguish and characterize detected MS features, which may in turn be identified by, e.g., matching to entries in a database for both precursor and fragmentation mass identification methods. Many tools exist with which to score the identification of peptides from LC-MS/MS measurements or to assess matches to an accurate mass and time (AMT) tag database, but these two calculations remain distinctly unrelated. Here we present a statistical method, Statistical Tools for AMT tag Confidence (STAC), which extends our previous work incorporating prior probabilities of correct sequence identification from LC-MS/MS, as well as the quality with which LC-MS features match AMT tags, to evaluate peptide identification confidence. Compared to existing tools, we are able to obtain significantly more high-confidence peptide identifications at a given false discovery rate and additionally assign confidence estimates to individual peptide identifications. Freely available software implementations of STAC are available in both command line and as a Windows graphical application.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1023112
• Report Number(s): PNNL-SA-72379; 34708; KP1601010
• Journal Information: Analytical Chemistry, 83(16):6135-6140, Journal Name: Analytical Chemistry, 83(16):6135-6140 Journal Issue: 16 Vol. 83
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
ACCURACY
Accurate Mass and TIme (AMT) tag
Environmental Molecular Sciences Laboratory
FRAGMENTATION
PEPTIDES
PRECURSOR
Statistical Tools for AMT tag Confidence (STAC)
confidence
false discovery rate (FDR)
peptide identification