Enabling proteomics-based identification of human cancer variations
© Zhang et al; licensee BioMed Central Ltd. 2010
Published: 23 July 2010
Shotgun proteomics is a powerful technology for protein identification in complex samples with remarkable applications in elucidating cellular and subcellular proteomes [1, 2], and discovering disease biomarkers [3, 4]. Shotgun proteomics data analysis usually relies on database search. Commonly used protein sequence databases in shotgun proteomics data analysis do not contain mutation information. This becomes a problem in cancer studies in which the detection of disease-related mutated peptides/proteins is crucial for understanding cancer biology . Including protein mutation information into sequence databases can help alleviate this problem.
Owing to its protein-centric nature, the approach we proposed can serve as a bridge between genomic variation data and proteomics studies in human cancer.
This work was supported by the National Institutes of Health (NIH)/ National Cancer Institute (NCI) through grant R01 CA126218 and the NIH/National Institute of General Medical Sciences through grant R01 GM88822.
- Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, Mann M: A mammalian organelle map by protein correlation profiling. Cell 2006, 125: 187–199. 10.1016/j.cell.2006.03.022View ArticlePubMedGoogle Scholar
- Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallet MT, Rossant J, Hughes TR, Frey B, Emili A: Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. Cell 2006, 125: 173–186. 10.1016/j.cell.2006.01.044View ArticlePubMedGoogle Scholar
- Decramer S, Wittke S, Mischak H, Zürbig P, Walden M, Bouissou F, Bascands JL, Schanstra P: Predicting the clinical outcome of congenital unilateral ureteropelvic junction obstruction in newborn by urinary proteome analysis. Nat Med 2006, 12: 398–400. 10.1038/nm1384View ArticlePubMedGoogle Scholar
- Whiteaker JR, Zhang H, Zhao L, Wang P, Kelly-Spratt KS, Ivey RG, Piening BD, Feng LC, Kasarda E, Gurley KE, Eng JK, Chodosh LA, Kemp CJ, McIntosh MW, Paulovich AG: Integrated pipeline for mass spectrometry-based discovery and confirmation of biomarkers demonstrated in a mouse model of breast cancer. J Proteome Res 2007, 6: 3962–3975. 10.1021/pr070202vView ArticlePubMedGoogle Scholar
- Wang Z, Moult J: SNPs, protein structure, and disease. Hum mutat. 2001, 17: 263–270. 10.1002/humu.22View ArticlePubMedGoogle Scholar
- Li J, Duncan DT, Zhang B: CanProVar: a human cancer proteome variation database. Hum Mutat 2010, 31(3):219–28. 10.1002/humu.21176PubMed CentralView ArticlePubMedGoogle Scholar
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