Figure 1.

A prototypical proteomics pipe-line coupled to bioinformatics useful for clinical research. Depending on the application, different samples processed and fed into the proteomics pipeline yield different results. The pipeline's several steps are listed in the different panels: (1) proteolytic digest, (2) the separation and ionization of peptides, (3) their analysis by mass spectrometry, (4) fragmentation of selected peptides and analysis of the resulting MS/MS spectra and, (5) (6) data-computer bioinformatic-analysis, which mainly includes: Conversion-data format, Spectrum identification with a search engine, Validation of identifications, Protein inference, Organization in local data managements systems, Interpretation and classification of the protein lists, Transfer to public data repositories, Identification and Classification of proteins, Quantification, Structural Analysis of proteins, PTM analysis and Cellular composition.