As the term genomics makes reference to the systematic study of genes, proteomics refers to the systematic study of proteins. But, when the term genome can be used to denote the exhaustive set of genes of a living organism, the definition of proteome is far less straightforward. As a matter of facts, a same polypeptide may lead to several proteins which differ one from the others by post-translation modifications. In this context, the term proteomics is better understood as the set of proteins which is expressed in a cell at a given time under given circonstances.

Mass spectrometry provides very efficient techniques for identifying proteins. Mass spectrometers produce large volumes of data which obviously require dedicated algorithms and software for their management and analysis.

More specifically, nanoLC MS/MS QTOF experiments generate up to 1500 peptides per day that can no longer be analyzed manually. There is therefore a growing need for software pipelines which allow fully automated protein identification from raw MS/MS data.