ABRF-PRG05: De novo peptide sequence determination

Arnold M. Falick, Jeffrey A. Kowalak, William S. Lane, Brett S. Phinney, Christoph W. Turck, Susan T. Weintraub, Karen A. West, Thomas A. Neubert

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

A common request of proteomics core facilities is protein identification. However, in some instances primary sequence information for the protein in question is not present in public databases. In other cases, the amino acid sequence of a protein may differ in some way from the sequence predicted from the gene sequence in a database as a result of gene mutation, gene splicing, and/or multiple posttranslational modifications. Thus, it may be necessary to determine the sequence of one or more peptides de novo in order to identify and/or adequately characterize the protein of interest. The primary goal of this study was to give participating labora- tories an opportunity to evaluate their proficiency in sequencing unknown peptides that are not included in any published database. Samples containing 3-6 pmol each of five synthetic peptides with amino acid sequences that were not present in public databases were sent to 106 laboratories. One nonstandard amino acid was present in one of the peptides. From a comparison of the results obtained by different strategies, participating laboratories will be able to gauge their own capabilities and establish realistic expectations for the approaches that can be used for this determination.

Original languageEnglish (US)
Pages (from-to)251-257
Number of pages7
JournalJournal of Biomolecular Techniques
Volume19
Issue number4
StatePublished - Sep 1 2008

Keywords

  • De novo peptide sequencing
  • Edman sequencing
  • Mass spectrometry
  • Post-translational modification

ASJC Scopus subject areas

  • Molecular Biology

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