Shotgun proteomics: concept, key points and data mining

Abstract

First paragraph: Mass spectrometry (MS)-based approaches are used increasingly to address diverse questions in proteomics research, enabling one to comprehensively analyze complex samples of proteins on a global level. Owing to all the effort devoted to explore entire genomes, we now have access to a multitude of completed genome sequences, which has recently opened up a new era of ‘shotgun proteome sequencing’. The concept of shotgun proteomics basically consists of the multidimensional separation (MudPIT) of a complex mixture of peptides, generated from the treatment of a specific protease (e.g., trypsin), analyzed using MS/MS and then submitted to automated database searching.