Identification of microorganisms based on identification of peptides using a liquid separation device coupled with a mass spectrometer and processing means

A method for the identification of at least one microorganism present in a sample based on the detection of peptides issued from the cleavage of ribosomal proteins of said microorganism, comprising the following steps:

• a) lysis of microorganism(s) and cleavage of the proteins present in said sample to obtain a mixture of peptides,
• b) decomplexing said peptides mixture using a liquid separation device coupled with a mass spectrometer,
• c) nebulizing a liquid eluted from the separation device using an ion source in order to produce an ion current,
• d) receiving said ion current from the ion source using said mass spectrometer and, for each cycle of a plurality of cycles, executing on the ion current a series of filtering steps for detecting a transition, said transition comprising a precursor ion and at least one fragment ion of said precursor ion, said transition being read from a predefined list of transitions using the mass spectrometer, wherein for each transition of the series, the mass spectrometer selects and fragments a precursor ion of the each transition,
• e) receiving data concerning a plurality of transitions to be used to monitor the mixture of peptides using the processor,
• f) assigning said plurality of transitions into two or more contiguous groups of transitions, into said predefined list of transitions using the processor,
• g) monitoring at least one sentinel transition associated with one sentinel compound in each group of the two or more contiguous groups, wherein said at least one sentinel transition is selected as having the latest expected retention time in the group, using the processor,
• h) when the signal of at least one sentinel transition of a group is detected with the mass spectrometer, starting the monitoring of at least one sentinel transition in a next contiguous group while stopping the monitoring of the transitions of the preceding group, using the processor,
• i) optionally, generating a chromatogram or electropherogram, from the detection of transitions read from a predefined list with said mass spectrometer, using the processor,
• wherein each transition read from the predefined listed is associated to a peptide,
• wherein the predefined list of transitions comprises at least one transition that is associated to a peptide presenting a sequence selected from SEQ ID NO:1 to SEQ ID NO:423, and
• wherein the microorganism is identified according to the detection of said peptide(s).