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A new approach that allows identification of intron‐split peptides from mass spectrometric data in genomic databases
Author(s) -
Allmer Jens,
Markert Christine,
Stauber Einar J.,
Hippler Michael
Publication year - 2004
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/s0014-5793(04)00212-1
Subject(s) - intron , fragmentation (computing) , sequence (biology) , peptide sequence , chemistry , computational biology , peptide , mass spectrometry , amino acid , database , biology , gene , computer science , biochemistry , chromatography , ecology
We present a new approach that allows the identification of intron‐split peptides from mass spectrometric data in genomic databases. Our algorithm uses small regions of peptide sequence information which are automatically deduced from de novo amino acid sequence predictions together with the molecular mass information of the precursor ion. The sequence predictions are based on selected collision‐induced mass spectrometric fragmentation spectra. Fragments of the predicted amino acid sequence are aligned with each of the six frames of the translated genome and the precursor mass information is used to assemble the corresponding tryptic peptides using the sequence as a matrix. Hereby, intron‐split peptides can be gathered and in turn verified by mass spectrometric data interpretation tools such as Sequest.