Protein identification by mass spectrometry

The platform hosts 4 mass spectrometers allowing protein identification:

  • LC-MS/MS (Orbitrap)
  • LC-MS/MS (Q-Exactive)
  • LC-MS/MS (Orbitrap Fusion Lumos Tribrid)


Samples may either be liquid protein samples not subjected to preliminary separation or fractions resulting from gel electrophoresis (1-D or 2-D) or from fractional liquid chromatography. After protein digestion, peptides are separated by reverse phase liquid chromatography and fragmented in the mass spectrometer.

Protein identification is based on one of the two following approaches:

  • "Mass matching", which is possible only if protein sequence database or EST information are available (sequenced genome, sequenced related species, large amount of ESTs, ...);
  • "De novo sequencing", which is used when there is few or no sequences available. In this case, protein identification is performed in two steps. First, fragmentation spectra are translated in primary sequences of amino acids (automatic determination). Then, these sequences are used to identify proteins by sequence alignment.

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