Charting the proteomes of organisms with unsequenced genomes by MALDI-quadrupole time-of-flight mass spectrometry and BLAST homology searching

Anal Chem. 2001 May 1;73(9):1917-26. doi: 10.1021/ac0013709.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Animals
  • Cell Line
  • Databases, Factual*
  • Dogs
  • Genome, Fungal*
  • Kidney / cytology
  • Membrane Proteins / chemistry
  • Molecular Sequence Data
  • Peptide Mapping / instrumentation
  • Peptide Mapping / methods
  • Pichia / genetics*
  • Proteome / chemistry*
  • Sequence Analysis, Protein / methods*
  • Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization*
  • Trypsin / metabolism


  • Membrane Proteins
  • Proteome
  • Trypsin