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Next to the use of 1D and 2D-gel purification systems, proteome studies can also be made starting from total digests. The resulting peptide mixture is generally too complex in order to purify and to analyze each individual peptide, leading to a shotgun approach. In order to solve this problem, we have recently developed a chromatographic sorting system able to select a subset of peptides characterized by rare amino acids or functional groups. These sorted peptides represent their corresponding parent proteins present in the original mixture. The sorting procedure is based on the concept of diagonal chromatography, consisting of two identical chromatographic separations with a specific chemical or enzymatic alteration, introduced in between the runs on a subset of peptides. Altered peptides will shift in the second chromatographic run compared to their position in the primary run and therefore separate from the bulk of non-altered peptides. This concept was adapted in order to handle highly complex mixtures such as tryptic digests of total cell lysates and was named COmbined FRActional DIagonal Chromatographic (COFRADIC[sup TM] ). The procedure is illustrated by the sorting and MS-MS-based identification of methionine-containing peptides from an E. coli and human platelet proteome. Results of a full cysteine-peptide proteome of human platelets are also shown. COFRADIC[sup TM] also allows specific selection of the N-terminal peptides of proteins present in a platelet lysate. This strategy reduces the complexity to a one peptide – one protein ratio, leading to a much better protein coverage. In addition, it allows to study protein processing in a global context or to select for proteins with an in vivo α -N-acetyl group. The technology can be extended to any amino acid side chain or post-translational modification, which can be fully automated and leads to the discovery of a broad range of proteins. [ABSTRACT FROM AUTHOR]