Use of theoretical peptide distributions in phosphoproteome analysis

Mridul Kalita, Takhar Kasumov, Allan R. Brasier, Rovshan G. Sadygov

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


The high mass accuracy and resolution of modern mass spectrometers provides new opportunities to employ theoretical peptide distributions in large-scale proteomic studies. We used theoretical distributions to study noise filtering and mass measurement errors and to examine mass-based differentiation of phosphorylated and nonphosphorylated peptides. Only the monoisotopic mass of the experimental precursor ion was necessary for this analysis. We found that peak deviations can be used to characterize the modification states of peptides in a sample. When applied to large-scale proteomic data sets, the peak deviation distribution can be used to filter chemical/electronic noise for singly charged species. Using peak deviation distributions, it is possible to separate the phosphorylated peptides from the nonphosphorylated peptides, enabling evaluation of the phosphoproteome content of a sample. Because this approach is simple, with light computational requirements, the analysis of theoretical peptide distributions has a significant potential for application to phosphoproteome analyses. For our studies we used publicly available data sets from three large-scale proteomic studies.

Original languageEnglish (US)
Pages (from-to)3207-3214
Number of pages8
JournalJournal of Proteome Research
Issue number7
StatePublished - Jul 5 2013


  • high mass accuracy informatics
  • mass defect
  • noise filtering
  • peak deviation
  • phosphopeptides
  • tandem mass spectrometry
  • theoretical peptides
  • theoretical phosphopeptide enrichment

ASJC Scopus subject areas

  • Biochemistry
  • General Chemistry


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