Keller Andrew, Shteynberg David
Rosetta Biosoftware, Seattle, WA, USA.
Methods Mol Biol. 2011;694:169-89. doi: 10.1007/978-1-60761-977-2_12.
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.
液相色谱-串联质谱鸟枪法蛋白质组学工作流程被广泛用于鉴定和定量样品中的肽段和蛋白质。然而，该技术在大规模应用中面临诸多挑战，包括质谱仪输出的各种原始数据文件格式、肽段与串联质谱谱图匹配中的高假阳性率，以及已鉴定肽段与产生这些肽段的样品蛋白质之间的联系缺失。在此，我们介绍跨蛋白质组学管道（Trans-Proteomic Pipeline），这是一套免费的开源软件套件，可对液相色谱-串联质谱数据从原始数据到定量的样品蛋白质进行统一分析。用户能够以直接的方式从多种仪器格式的原始数据中提取串联质谱信息，将其提交给搜索引擎进行肽段鉴定，验证结果以去除错误匹配，合并多个搜索引擎的结果，推断产生已鉴定肽段的样品蛋白质，并在肽段和蛋白质水平上进行定量。
