鸟枪蛋白质组学
管道(软件)
数据库搜索引擎
蛋白质组学
工作流程
计算机科学
软件
原始数据
样品(材料)
数据挖掘
错误发现率
定量蛋白质组学
计算生物学
数据库
搜索引擎
色谱法
化学
情报检索
生物
操作系统
生物化学
基因
程序设计语言
作者
Andrew Keller,David Shteynberg
标识
DOI:10.1007/978-1-60761-977-2_12
摘要
The LC-MS/MS shotgun proteomics workflow is widely used to identify and quantify sample peptides and proteins. The technique, however, presents a number of challenges for large-scale use, including the diverse raw data file formats output by mass spectrometers, the large false positive rate among peptide assignments to MS/MS spectra, and the loss of connectivity between identified peptides and the sample proteins that gave rise to them. Here we describe the Trans-Proteomic Pipeline, a freely available open source software suite that provides uniform analysis of LC-MS/MS data from raw data to quantified sample proteins. In a straightforward manner, users can extract MS/MS information from raw data of many instrument formats, submit them to search engines for peptide identification, validate the results to remove false hits, combine together results of multiple search engines, infer sample proteins that gave rise to the identified peptides, and perform quantitation at the peptide and protein levels.
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