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 Scopus citations


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
Issue number1
StatePublished - Jan 1 2008


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

ASJC Scopus subject areas

  • Biochemistry
  • Chemistry(all)

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  • Cite this

    Tanner, S., Payne, S. H., Dasari, S., Shen, Z., Wilmarth, P. A., David, L. L., Loomis, W. F., Briggs, S. P., & Bafna, V. (2008). Accurate annotation of peptide modifications through unrestrictive database search. Journal of Proteome Research, 7(1), 170-181.