蛋白组学是从整体角度分析细胞内动态变化的蛋白质组成、表达水平与修饰状态，了解蛋白质之间的相互作用与联系，揭示蛋白质功能与细胞生命活动规律的新的研究领域。 蛋白质是生命活动的体现者和执行者。要对生命活动有全面深入的认识，必然要在整体、动态、网络的水平对蛋白进行研究。传统的研究方法已经不能满足后基因组时代的需求，高通量，高精度质谱技术的普及使蛋白组学分析成为可能。

蛋白组分析平台可以进行标准分析和个性化分析，其中标准分析包括：蛋白表达分析和蛋白注释分析。设定参数后点击提交进行分析，分析完成后在流程定制页面下生成标准化结题报告，实现一键式生成。

蛋白组分析以定量结果表格作为输入，使用T检验进行差异分析，获取两个分组间的差异表达蛋白。

应用Gene Ontology（简称GO）数据库和KEGG数据库对蛋白进行功能注释，并使用超几何检验，找出与所有蛋白质背景相比，在差异蛋白质中显著富集的GO term和KEGG pathway.

参考文献：

[1] Zhou T, Li C, Zhao W, Wang X, Wang F, Sha J. MaxReport: An Enhanced Proteomic Result Reporting Tool for MaxQuant. PLoS One. 2016; 11(3): e0152067. Park GW, Hwang H, Kim KH, Lee JY, Lee HK, Park JY, Ji ES, Park SR, Yates JR 3rd, Kwon KH, Park YM, Lee HJ, Paik YK, Kim JY, Yoo JS. Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate. J Proteome Res. 2016 Aug 30. Sandberg A et.al.Tumor proteomics by multivariate analysis on individual pathway data for characterization of vulvar cancer phenotypes. Mol Cell Proteomics. 2012 Jul;11(7):M112.016998.

[2] Cox J and Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotech. 26, 1367-72.

[3] Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M. Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment. J. Proteome Res., 2011, 10 (4), 1794–1805

[4] Cox J, Hein MY, Luber CA, Paron I, Nagaraj N, Mann M. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol Cell Proteomics. 2014 Sep; 13(9): 2513–2526.

[5] Matrix Science. Introduction to Database Searching using MASCOT. Mascot 2.5.

[6] Jimmy K. Eng, Ashley L. McCormack, and John R. Yates, III (1994). An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database. J Am Soc Mass Spectrom. 5 (11): 976–989.

[7] Sadygov RG. Using SEQUEST with theoretically complete sequence databases. J Am Soc Mass Spectrom. 2015 Nov;26(11):1858-64.

[8] Ingvar E, Kristian F, Lennart M, Svein-Ole M. Computational Methods for Mass Spectrometry Proteomics. ISBN: 978-0-470-51297-5. 296 .

[9] Thermo Scientific. Xcalibur Proteome Discoverer Version 1.3 User Guide. May 2011. User Guide.May 2011.