Doubling down on phosphorylation as a variable peptide modification. Issue 18 (23rd June 2016)

• Record Type: Journal Article
• Authors: Cooper, Bret
• Other Names: Haynes Paul A. guestEditor.; Stein Stephen E. guestEditor.; Washburn Michael P. guestEditor.
• Is Part Of: Proteomics. Volume 16:Issue 18(2016)
• Page Start: 2444
• Page End: 2447
• Publication Date: 2016-06-23
• Subjects: Bioinformatics -- Mass spectrometry -- Peptide spectrum matching -- Variable modification; Proteins -- Separation -- Periodicals; Bioinformatics -- Periodicals; Proteomics -- Periodicals; Genomes -- Periodicals; Molecular genetics -- Periodicals; 572.605
• DOI: 10.1002/pmic.201500440
• Languages: English
• ISSNs: 1615-9853

Abstract

Abstract : Some mass spectrometrists believe that searching for variable PTMs like phosphorylation of serine or threonine when using database‐search algorithms to interpret peptide tandem mass spectra will increase false‐positive matching. The basis for this is the premise that the algorithm compares a spectrum to both a nonphosphorylated peptide candidate and a phosphorylated candidate, which is double the number of candidates compared to a search with no possible phosphorylation. Hence, if the search space doubles, false‐positive matching could increase accordingly as the algorithm considers more candidates to which false matches could be made. In this study, it is shown that the search for variable phosphoserine and phosphothreonine modifications does not always double the search space or unduly impinge upon the FDR. A breakdown of how one popular database‐search algorithm deals with variable phosphorylation is presented.