Empirical Multidimensional Space for Scoring Peptide Spectrum Matches in Shotgun Proteomics

Empirical Multidimensional Space for Scoring Peptide Spectrum Matches in Shotgun Proteomics

Data-dependent tandem mass spectrometry (MS/MS) is one of the main techniques for protein identification in shotgun proteomics. In a typical LC–MS/MS workflow, peptide product ion mass spectra (MS/MS spectra) are compared with those derived theoretically from a protein sequence database. Scoring of...

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Veröffentlicht in:Journal of proteome research 2014-04, Vol.13 (4), p.1911-1920
Hauptverfasser: Ivanov, Mark V, Levitsky, Lev I, Lobas, Anna A, Panic, Tanja, Laskay, Ünige A, Mitulovic, Goran, Schmid, Rainer, Pridatchenko, Marina L, Tsybin, Yury O, Gorshkov, Mikhail V
Format: Artikel
Sprache:eng
Schlagworte:
Peptide Mapping - methods
Peptides - analysis
Peptides - chemistry
Peptides - classification
Proteomics - methods
Reproducibility of Results
Tandem Mass Spectrometry - methods
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Zusammenfassung:Data-dependent tandem mass spectrometry (MS/MS) is one of the main techniques for protein identification in shotgun proteomics. In a typical LC–MS/MS workflow, peptide product ion mass spectra (MS/MS spectra) are compared with those derived theoretically from a protein sequence database. Scoring of these matches results in peptide identifications. A set of peptide identifications is characterized by false discovery rate (FDR), which determines the fraction of false identifications in the set. The total number of peptides targeted for fragmentation is in the range of 10 000 to 20 000 for a several-hour LC–MS/MS run. Typically,
ISSN:1535-3893
1535-3907
DOI:10.1021/pr401026y