Accurate annotation of peptide modifications through unrestrictive database search

Stephen Tanner, Samuel H. Payne, Surendra Dasari, Zhouxin Shen, Phillip A. Wilmarth, Larry L. David, William F. Loomis, Steven P. Briggs, Vineet Bafna

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

Proteins are extensively modified after translation due to cellular regulation, signal transduction, or chemical damage. Peptide tandem mass spectrometry can discover post-translational modifications, as well as sequence polymorphisms. Recent efforts have studied modifications at the proteomic scale. In this context, it becomes crucial to assess the accuracy of modification discovery. We discuss methods to quantify the false discovery rate from a search and demonstrate how several features can be used to distinguish valid modifications from search artifacts. We present a tool, PTMFinder, which implements these methods. We summarize the corpus of post-translational modifications identified on large data sets. Thousands of known and novel modification sites are identified, including site-specific modifications conserved over vast evolutionary distances.

Original languageEnglish (US)
Pages (from-to)170-181
Number of pages12
JournalJournal of Proteome Research
Volume7
Issue number1
DOIs
StatePublished - Jan 2008
Externally publishedYes

Fingerprint

Signal transduction
Post Translational Protein Processing
Polymorphism
Mass spectrometry
Databases
Peptides
Tandem Mass Spectrometry
Proteomics
Artifacts
Signal Transduction
Proteins
Datasets

Keywords

  • Crystallin
  • Dictyostelium
  • Human lens
  • Lens proteins
  • Mass spectrometry
  • Post-translational modifications

ASJC Scopus subject areas

  • Genetics
  • Biotechnology
  • Biochemistry

Cite this

Tanner, S., Payne, S. H., Dasari, S., Shen, Z., Wilmarth, P. A., David, L. L., ... Bafna, V. (2008). Accurate annotation of peptide modifications through unrestrictive database search. Journal of Proteome Research, 7(1), 170-181. https://doi.org/10.1021/pr070444v

Accurate annotation of peptide modifications through unrestrictive database search. / Tanner, Stephen; Payne, Samuel H.; Dasari, Surendra; Shen, Zhouxin; Wilmarth, Phillip A.; David, Larry L.; Loomis, William F.; Briggs, Steven P.; Bafna, Vineet.

In: Journal of Proteome Research, Vol. 7, No. 1, 01.2008, p. 170-181.

Research output: Contribution to journalArticle

Tanner, S, Payne, SH, Dasari, S, Shen, Z, Wilmarth, PA, David, LL, Loomis, WF, Briggs, SP & Bafna, V 2008, 'Accurate annotation of peptide modifications through unrestrictive database search', Journal of Proteome Research, vol. 7, no. 1, pp. 170-181. https://doi.org/10.1021/pr070444v
Tanner, Stephen ; Payne, Samuel H. ; Dasari, Surendra ; Shen, Zhouxin ; Wilmarth, Phillip A. ; David, Larry L. ; Loomis, William F. ; Briggs, Steven P. ; Bafna, Vineet. / Accurate annotation of peptide modifications through unrestrictive database search. In: Journal of Proteome Research. 2008 ; Vol. 7, No. 1. pp. 170-181.
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