Taking the shortcut for high-throughput shotgun proteomic analysis of bacteria

Erica Marie Hartmann, François Allain, Jean Charles Gaillard, Olivier Pible, Jean Armengaud

Research output: Contribution to journalArticlepeer-review

74 Scopus citations


Currently, proteomic tools are able to establish a complete list of the most abundant proteins present in a sample, providing the opportunity to study at high resolution the physiology of any bacteria for which the genome sequence is available. For a comprehensive list, proteins should be first resolved into fractions that are then proteolyzed by trypsin. The resulting peptide mixtures are analyzed by a high-throughput tandem mass spectrometer that records thousands of MS/MS spectra for each fraction. These spectra are then assigned to peptides, which are used as evidence of the existence of proteins. In addition to generating a list of protein identifications, this shortcut to proteomics uses the number of spectra recorded for each protein to quantify the observations. Here, we describe one of the most simple sample preparation methods for high-throughput proteomics of bacteria, as well as the subsequent data processing to extract quantitative information based on the spectral count approach.

Original languageEnglish (US)
Pages (from-to)275-285
Number of pages11
JournalMethods in Molecular Biology
StatePublished - Jan 1 2014


  • Bacterial proteome
  • High-throughput proteomics
  • Quantitative proteomics
  • Spectral count
  • Tandem mass spectrometry

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics


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