Precursor ion independent algorithm for top-down shotgun proteomics View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-11

AUTHORS

Yihsuan S. Tsai, Alexander Scherl, Jason L. Shaw, C. Logan MacKay, Scott A. Shaffer, Patrick R. R. Langridge-Smith, David R. Goodlett

ABSTRACT

We present a precursor ion independent top-down algorithm (PIITA) for use in automated assignment of protein identifications from tandem mass spectra of whole proteins. To acquire the data, we utilize data-dependent acquisition to select protein precursor ions eluting from a C4-based HPLC column for collision induced dissociation in the linear ion trap of an LTQ-Orbitrap mass spectrometer. Gas-phase fractionation is used to increase the number of acquired tandem mass spectra, all of which are recorded in the Orbitrap mass analyzer. To identify proteins, the PIITA algorithm compares deconvoluted, deisotoped, observed tandem mass spectra to all possible theoretical tandem mass spectra for each protein in a genomic sequence database without regard for measured parent ion mass. Only after a protein is identified, is any difference in measured and theoretical precursor mass used to identify and locate post-translation modifications. We demonstrate the application of PIITA to data generated via our wet-lab approach on a Salmonella typhimurium outer membrane extract and compare these results to bottom-up analysis. From these data, we identify 154 proteins by top-down analysis, 73 of which were not identified in a parallel bottom-up analysis. We also identify 201 unique isoforms of these 154 proteins at a false discovery rate (FDR) of <1%. More... »

PAGES

2154-2166

References to SciGraph publications

  • 2003-03. Mass spectrometry-based proteomics in NATURE
  • 2007-09-27. Decoding protein modifications using top-down mass spectrometry in NATURE METHODS
  • 2003-09-01. Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 2006-07-01. Determination of peptide and protein ion charge states by fourier transformation of isotope-resolved mass spectra in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 2008-06. On the benefits of acquiring peptide fragment ions at high measured mass accuracy in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 2000-04-01. Automated reduction and interpretation of in JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
  • 2003-04-14. A method for the comprehensive proteomic analysis of membrane proteins in NATURE BIOTECHNOLOGY
  • 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
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1016/j.jasms.2009.07.024

    DOI

    http://dx.doi.org/10.1016/j.jasms.2009.07.024

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1009789336

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/19773183


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