Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker.
Identifying proteomic LC-MS/MS data sets with Bumbershoot and IDPicker.
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DOI：
10.1002/0471250953.bi1317s37
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发表时间：
2012-03
影响因子：
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通讯作者：
Tabb DL
中科院分区：
文献类型：
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作者：
Holman JD;Ma ZQ;Tabb DL
通过 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着的灵活性和区分度。 Bumbershoot 工具（MyriMatch、DirecTag、TagRecon 和 Pepitome）能够识别 MS/MS 扫描所代表的肽。所有这些工具都可以直接使用多个供应商的仪器捕获文件（例如 Thermo RAW 格式）或基于标准 XML 的格式（例如 mzML 或 mzXML）。肽鉴定以 mzIdentML 或 pepXML 格式写入。蛋白质组装由 IDPicker 算法处理。通过使用目标诱饵策略将原始标识过滤为置信集。 IDPicker 将大量输入文件排列成层次结构以进行报告，并且该软件应用简约算法来报告尽可能少的蛋白质数量，以解释观察到的肽。该协议详细介绍了新用户如何使用这些工具。
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.