Holman Jerry D, Ma Ze-Qiang, Tabb David L
Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
Curr Protoc Bioinformatics. 2012 Mar;Chapter 13:Unit13.17. doi: 10.1002/0471250953.bi1317s37.
The identification of peptides and proteins by LC-MS/MS requires the use of bioinformatics. Tools developed in the Tabb Laboratory contribute significant flexibility and discrimination to this process. The Bumbershoot tools (MyriMatch, DirecTag, TagRecon, and Pepitome) enable the identification of peptides represented by MS/MS scans. All of these tools can work directly from instrument capture files of multiple vendors, such as Thermo RAW format, or from standard XML-based formats, such as mzML or mzXML. Peptide identifications are written to mzIdentML or pepXML format. Protein assembly is handled by the IDPicker algorithm. Raw identifications are filtered to a confident set by use of the target-decoy strategy. IDPicker arranges large sets of input files into a hierarchy for reporting, and the software applies a parsimony algorithm to report the smallest possible number of proteins to explain the observed peptides. This protocol details the use of these tools for new users.
通过液相色谱-串联质谱（LC-MS/MS）鉴定肽和蛋白质需要使用生物信息学。塔布实验室开发的工具为这一过程提供了显著的灵活性和辨别力。Bumbershoot工具（MyriMatch、DirecTag、TagRecon和Pepitome）能够鉴定由MS/MS扫描代表的肽。所有这些工具都可以直接处理多个供应商的仪器捕获文件，如Thermo RAW格式，或基于标准XML的格式，如mzML或mzXML。肽鉴定结果被写入mzIdentML或pepXML格式。蛋白质组装由IDPicker算法处理。通过使用目标-诱饵策略，将原始鉴定结果过滤为一组可靠的结果。IDPicker将大量输入文件排列成层次结构进行报告，并且该软件应用简约算法报告尽可能少的蛋白质来解释观察到的肽。本方案详细介绍了新用户使用这些工具的方法。
