For this Wikipedia page, I will be adding more advantages and disadvantages to the whole concept of Bottom-up proteomics, as well as possibly changing the "definition" portion of the page to something more straightforward and easier to understand. Overall, I think it will be a good idea to find more information about the whole concept in general, as the page is very sparse. I'm also thinking about adding some examples or possible laboratory procedures/experiments in which this method is used. I will also include other concepts that relate to bottom-up proteomics -- such as shotgun proteomics and what makes bottom-up proteomics distinct from other forms/methods.
Bottom-up proteomics From Wikipedia, the free encyclopedia
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Bottom-up versus top-down proteomics Bottom-up proteomics is a common method to identify proteins and characterize their amino acid sequences and post-translational modifications by proteolytic digestion of proteins prior to analysis by mass spectrometry.[1][2] The major alternative workflow used in high-throughput proteomics is called top-down proteomics and does not use proteolytic digestion. In bottom-up proteomics, the proteins may first be purified by a method such as gel electrophoresis resulting in one or a few proteins in each proteolytic digest. Alternatively, the crude protein extract is digested directly, followed by one or more dimensions of separation of the peptides by liquid chromatography coupled to mass spectrometry, a technique known as shotgun proteomics.[3][4] By comparing the masses of the proteolytic peptides or their tandem mass spectra with those predicted from a sequence database or annotated peptide spectral in a peptide spectral library, peptides can be identified and multiple peptide identifications assembled into a protein identification.
Contents [hide] 1 Advantages 2 Disadvantages 3 See also 4 References
Advantages[edit source] There is better front-end separation of peptides compared with proteins and higher sensitivity than the top-down method.[5] Disadvantages[edit source] There is limited protein sequence coverage by identified peptides, loss of labile PTMs, and ambiguity of the origin for redundant peptide sequences.[5] Recently the combination of bottom-up and top-down proteomics, so called middle-down proteomics, is receiving a lot of attention as this approach not only can be applied to the analysis of large protein fragments but also avoids redundant peptide sequences.[6] See also[edit source] Protein mass spectrometry Top-down proteomics Shotgun proteomics References[edit source] Jump up ^ Aebersold R, Mann M (March 2003). "Mass spectrometry-based proteomics". Nature. 422 (6928): 198–207. doi:10.1038/nature01511. PMID 12634793. Jump up ^ Chait BT (2006). "Chemistry. Mass spectrometry: bottom-up or top-down?". Science. 314 (5796): 65–6. doi:10.1126/science.1133987. PMID 17023639. Jump up ^ Washburn MP, Wolters D, Yates JR (2001). "Large-scale analysis of the yeast proteome by multidimensional protein identification technology". Nat. Biotechnol. 19 (3): 242–247. doi:10.1038/85686. PMID 11231557. Jump up ^ Wolters DA, Washburn MP, Yates JR (2001). "An automated multidimensional protein identification technology for shotgun proteomics". Anal. Chem. 73 (23): 5683–5690. doi:10.1021/ac010617e. PMID 11774908. ^ Jump up to: a b Yates JR, Ruse CI, Nakorchevsky A (2009). "Proteomics by Mass Spectrometry: Approaches, Advances, and Applications" (PDF). Annu. Rev. Biomed. Eng. 11: 49–79. doi:10.1146/annurev-bioeng-061008-124934. PMID 19400705. Jump up ^ Zhang, Yaoyang; Fonslow, Bryan R.; Shan, Bing; Baek, Moon-Chang; Yates, John R. (2014-04-10). "Protein analysis by shotgun/bottom-up proteomics". Chem Rev. 113 (4): 2343. doi:10.1021/cr3003533. Retrieved 10 February 2017.