Search of sequence databases with uninterpreted high-energy collision-induced dissociation spectra of peptides View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

1996-11-01

AUTHORS

John R. Yates, Jimmy K. Eng, Karl R. Clauser, Alma L. Burlingame

ABSTRACT

We have broadened the utility of the SEQUEST computer algorithms to permit correlation of uninterpreted high-energy collision-induced dissociation spectra of peptides with all sequences in a database. SEQUEST now allows for the additional fragment ion types observed under high-energy conditions. We analyzed spectra from peptides isolated following trypsin digestion of 13 proteins. SEQUEST ranked the correct sequence first for 90% (18/20) of the spectra in searches of the OWL database, without constraint by enzyme cleavage specificity or species of origin. All false-positives were flagged by the scoring system. SEQUEST searches databases for sequences that correspond to the precursor ion mass ±0.5 u. Preliminary ranking of the top 500 candidates is done by calculation of fragment ion masses for each sequence, and comparison to the measured ion masses on the basis of ion series continuity, summed ion intensity, and immonium ion presence. Final ranking is done by construction of model spectra for the 500 candidates and constructing/performing of a cross-correlation analysis with the actual spectrum. Given the need to relate mounting genome sequence information with corresponding suites of proteins that comprise the cellular molecular machinery, tandem mass spectrometry appears destined to play the leading role in accelerating protein identification on the large scale required. More... »

PAGES

1089-1098

References to SciGraph publications

  • 1993-11-01. Low-mass ions produced from peptides by high-energy collision-induced dissociation in tandem mass spectrometry in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 1996-02. Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry in NATURE
  • 1995-10-01. Peptide sequence determination from high-energy collision-induced dissociation spectra using artificial neural networks in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 1996-01-01. Peptide sequence determination by matrix-assisted laser desorption ionization employing a tandem double focusing magnetic—Orthogonal acceleration time-of-flight mass spectrometer in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 1995-09-01. A comparison of the peptide fragmentation obtained from a reflector matrix-assisted laser desorption-ionization time-of-flight and a tandem four sector mass spectrometer in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 1992-05-01. Pattern-based algorithm for peptide sequencing from tandem high energy collision-induced dissociation mass spectra in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 1994-11-01. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 1991-04-01. A computer program (COMPOST) for predicting mass spectrometric information from known amino acid sequences in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1016/s1044-0305(96)00079-7

    DOI

    http://dx.doi.org/10.1016/s1044-0305(96)00079-7

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1014248919

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/24203070


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