Shotgun Proteomics

Shotgun Proteomics General Details:

• "'Shotgun proteomics' refers to the direct analysis of complex protein mixtures to rapidly generate a global profile of the protein complement within the mixture." (Wu et al, 2002)
• The approach is enhanced by the use of multidimensional protein identification technology (MudPIT).
• MudPIT uses multidimensional high-pressure liquid chromatography (LC/LC), tandem mass spectrometry (MS/MS) & database-searching algorithms.
• Various algorithms can be used to increase the rate of confident peptide identifications, i.e. Percolator algorithm. (Käll L et al, 2007)
• Shotgun proteomics can also aid discovery of novel protein-coding genes, alternative splicing, & “resurrected” pseudogenes. (Florens & Washburn, 2006)

References:

• Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS, Hubbard T (2011). Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome. Genome Res. 2011. 21: 756-767 [Full Text]
• Ding Y, Choi H, Nesvizhskii A. 2008. Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics. J Proteome Res 7: 4878–4889.
• Florens L, Washburn MP. 2006. Proteomic analysis by multidimensional protein identification technology. Methods Mol Biol. 2006;328:159-75.
• Käll L, Canterbury J, Weston J, Noble W, MacCoss M. 2007. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat Methods 4: 923–925.
• Wu CC, MacCoss MJ. 2002. Shotgun proteomics: tools for the analysis of complex biological systems. Curr Opin Mol Ther. 2002 Jun;4(3):242-50.

Tags: Algorithm - Database Searching - HPLC - MudPIT - Proteomics - Shotgun Proteomics - Tandem Mass Spectrometry

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