Shotgun proteomics refers to the use of bottom-up proteomics techniques in identifying proteins in complex mixtures using a combination of high performance liquid chromatography combined with mass spectrometry.[1][2][3][4][5][6] The name is derived from shotgun sequencing of DNA which is itself named after the rapidly expanding, quasi-random firing pattern of a shotgun. The most common method of shotgun proteomics starts with the proteins in the mixture being digested and the resulting peptides are separated by liquid chromatography. Tandem mass spectrometry is then used to identify the peptides.
Targeted proteomics using SRM and data-independent acquisition methods are often considered alternatives to shotgun proteomics in the field of bottom-up proteomics. While shotgun proteomics uses data-dependent selection of precursor ions to generate fragment ion scans, the aforementioned methods use a deterministic method for acquisition of fragment ion scans.
^Alves P, Arnold RJ, Novotny MV, Radivojac P, Reilly JP, Tang H (2007). "Advancement in protein inference from shotgun proteomics using peptide detectability". Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing: 409–20. PMID 17990506.
^Washburn MP, Wolters D, Yates JR (March 2001). "Large-scale analysis of the yeast proteome by multidimensional protein identification technology". Nature Biotechnology. 19 (3): 242–7. doi:10.1038/85686. PMID 11231557. S2CID 16796135.
^Wolters DA, Washburn MP, Yates JR (December 2001). "An automated multidimensional protein identification technology for shotgun proteomics". Analytical Chemistry. 73 (23): 5683–90. doi:10.1021/ac010617e. PMID 11774908.
^Hu L, Ye M, Jiang X, Feng S, Zou H (August 2007). "Advances in hyphenated analytical techniques for shotgun proteome and peptidome analysis--a review". Analytica Chimica Acta. 598 (2): 193–204. doi:10.1016/j.aca.2007.07.046. PMID 17719892.
^Nesvizhskii AI (2007). "Protein identification by tandem mass spectrometry and sequence database searching". Mass Spectrometry Data Analysis in Proteomics. Methods Mol. Biol. Vol. 367. pp. 87–119. doi:10.1385/1-59745-275-0:87. ISBN 978-1-59745-275-5. PMID 17185772.
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