A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry

Changyu Shen, Zhiping Wang, Ganesh Shankar, Xiang Zhang, Lang Li

Research output: Contribution to journalArticle

30 Citations (Scopus)

Abstract

Motivation: Statistical evaluation of the confidence of peptide and protein identifications made by tandem mass spectrometry is a critical component for appropriately interpreting the experimental data and conducting downstream analysis. Although many approaches have been developed to assign confidence measure from different perspectives, a unified statistical framework that integrates the uncertainty of peptides and proteins is still missing. Results: We developed a hierarchical statistical model (HSM) that jointly models the uncertainty of the identified peptides and proteins and can be applied to any scoring system. With data sets of a standard mixture and the yeast proteome, we demonstrate that the HSM offers a reliable or at least conservative false discovery rate (FDR) estimate for peptide and protein identifications. The probability measure of HSM also offers a powerful discriminating score for peptide identification.

Original languageEnglish
Pages (from-to)202-208
Number of pages7
JournalBioinformatics
Volume24
Issue number2
DOIs
StatePublished - Jan 15 2008

Fingerprint

Mass Spectrometry
Statistical Models
Hierarchical Model
Tandem Mass Spectrometry
Peptides
Statistical Model
Confidence
Mass spectrometry
Proteins
Protein
Uncertainty
Confidence Measure
Proteome
Scoring
Yeast
Probability Measure
Assign
Yeasts
Integrate
Experimental Data

ASJC Scopus subject areas

  • Clinical Biochemistry
  • Computer Science Applications
  • Computational Theory and Mathematics

Cite this

A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry. / Shen, Changyu; Wang, Zhiping; Shankar, Ganesh; Zhang, Xiang; Li, Lang.

In: Bioinformatics, Vol. 24, No. 2, 15.01.2008, p. 202-208.

Research output: Contribution to journalArticle

Shen, Changyu ; Wang, Zhiping ; Shankar, Ganesh ; Zhang, Xiang ; Li, Lang. / A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry. In: Bioinformatics. 2008 ; Vol. 24, No. 2. pp. 202-208.
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