Charting the Proteomes of Organisms with Unsequenced Genomes by MALDI-Quadrupole Time-of-Flight Mass Spectrometry and BLAST Homology Searching

peer-reviewed · Analytical Chemistry · 2001

peer-reviewed · Analytical Chemistry · 2001. Andrej Shevchenko et al. MALDI-quadrupole time-of-flight mass spectrometry was applied to identify proteins from organisms whose…
Date 2001-05-01
Type peer-reviewed
Venue Analytical Chemistry
Publisher American Chemical Society (ACS)
Contribution adjacent
DOI 10.1021/ac0013709
Citations (OpenAlex) 582
Venue 2-year citedness 7.10

Abstract

MALDI-quadrupole time-of-flight mass spectrometry was applied to identify proteins from organisms whose genomes are still unknown. The identification was carried out by successively searching a sequence database-first with a peptide mass fingerprint, then with a packet of noninterpreted MS/MS spectra, and finally with peptide sequences obtained by automated interpretation of the MS/MS spectra. A “MS BLAST” homology searching protocol was developed to overcome specific limitations imposed by mass spectrometric data, such as the limited accuracy of de novo sequence predictions. This approach was tested in a small-scale proteomic project involving the identification of 15 bands of gel-separated proteins from the methylotrophic yeast Pichia pastoris, whose genome has not yet been sequenced and which is only distantly related to other fungi.

Authors

  1. Andrej Shevchenko · European Molecular Biology Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics, Max Planck Society, University of California San Diego
  2. Shamil Sunyaev · Brigham & Women’s Hospital and Harvard Medical School, Brigham and Women’s Hospital, European Molecular Biology Laboratory, Harvard University
  3. Alexander Loboda · MDS Sciex, University of Manitoba
  4. Anna Shevchenko · European Molecular Biology Laboratory, Max Planck Institute of Molecular Cell Biology and Genetics
  5. Peer Bork · European Molecular Biology Laboratory
  6. Werner Ens · University of Manitoba
  7. Kenneth G. Standing · University of Manitoba

Methods and tools

  • MS BLAST: Homology search of error-tolerant de novo sequences against a protein database, introduced for charting the proteomes of organisms with unsequenced genomes and later used to validate borderline identifications.

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