Determination of partial amino acid composition from tandem mass spectra for use in peptide identification strategies

Ian Shadforth, Kieran Todd, Daniel Crowther, Conrad Bessant (Lead / Corresponding author)

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


We demonstrate a new approach to the determination of amino acid composition from tandem mass spectrometrically fragmented peptides using both experimental and simulated data. The approach has been developed to be used as a search-space filter in a protein identification pipeline with the aim of increased performance above that which could be attained by using immonium ion information. Three automated methods have been developed and tested: one based upon a simple peak traversal, in which all intense ion peaks are treated as being either a b- or y-ion using a wide mass tolerance; a second which uses a much narrower tolerance and does not perform transformations of ion peaks to the complementary type; and the unique fragments method which allows for b- or y-ion type to be inferred and corroborated using a scan of the other ions present in each peptide spectrum. The combination of these methods is shown to provide a high-accuracy set of amino acid predictions using both experimental and simulated data sets. These high quality predictions, with an accuracy of over 85%, may be used to identify peptide fragments that are hard to identify using other methods. The data simulation algorithm is also shown post priori to be a good model of noiseless tandem mass spectrometric peptide data.

Original languageEnglish
Pages (from-to)1787-1796
Number of pages10
Issue number7
Early online date7 Apr 2005
Publication statusPublished - 6 May 2005


  • Database searching
  • De novo sequencing
  • Peptide identification
  • Tandem mass spectrometry

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology


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