Direct analysis of protein complexes using mass spectrometry

Nat Biotechnol. 1999 Jul;17(7):676-82. doi: 10.1038/10890.


We describe a rapid, sensitive process for comprehensively identifying proteins in macromolecular complexes that uses multidimensional liquid chromatography (LC) and tandem mass spectrometry (MS/MS) to separate and fragment peptides. The SEQUEST algorithm, relying upon translated genomic sequences, infers amino acid sequences from the fragment ions. The method was applied to the Saccharomyces cerevisiae ribosome leading to the identification of a novel protein component of the yeast and human 40S subunit. By offering the ability to identify >100 proteins in a single run, this process enables components in even the largest macromolecular complexes to be analyzed comprehensively.

Publication types

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

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Chromatography, Liquid
  • Humans
  • Mass Spectrometry / methods*
  • Molecular Sequence Data
  • Ribosomal Proteins / analysis*
  • Ribosomal Proteins / chemistry
  • Ribosomal Proteins / genetics
  • Ribosomes / chemistry
  • Saccharomyces cerevisiae / chemistry*
  • Saccharomyces cerevisiae / genetics
  • Sensitivity and Specificity


  • Ribosomal Proteins