IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.
IDPicker 2.0: Improved protein assembly with high discrimination peptide identification filtering.
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DOI：
10.1021/pr900360j
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发表时间：
2009-08
影响因子：
4.4
通讯作者：
Tabb, David L.
中科院分区：
文献类型：
--
作者：
Ma, Ze-Qiang;Dasari, Surendra;Chambers, Matthew C.;Litton, Michael D.;Sobecki, Scott M.;Zimmerman, Lisa J.;Halvey, Patrick J.;Schilling, Birgit;Drake, Penelope M.;Gibson, Bradford W.;Tabb, David L.
基于串联质谱的散弹枪蛋白质组学已经成为分析复杂蛋白质混合物的广泛技术。已经开发了许多数据库搜索算法来将肽序列分配到串联质谱中。然而，由于许多肽在多个蛋白质中是共享的，因此将肽识别组装到蛋白质上是一个具有挑战性的问题。IDPicker是一个开源的蛋白质组装工具，从肽鉴定筛选到指定的错误发现率派生最小的蛋白质列表。在这里，我们更新了IDPicker，通过结合数据库搜索工具产生的多个分数来增加自信的肽识别。IDPicker通过前体电荷状态和色氨酸末端的数量分离肽识别阈值，检索更多的肽用于蛋白质组装。新版本对假阳性蛋白的抗性更强，特别是在使用多物种数据库的搜索中，通过在简约过程中需要额外的新肽。通过添加图形用户界面和从pepXML格式读取标识的能力，IDPicker被设计成可以整合到许多标识工作流中。这些进展为IDPicker在大规模蛋白质组学研究中提供了高肽鉴别和可靠的蛋白质组装。最新版本IDPicker的源代码和二进制文件可从http://fenchurch.mc.vanderbilt.edu/获得。
Tandem mass spectrometry-based shotgun proteomics has become a widespread technology for analyzing complex protein mixtures. A number of database searching algorithms have been developed to assign peptide sequences to tandem mass spectra. Assembling the peptide identifications to proteins, however, is a challenging issue because many peptides are shared among multiple proteins. IDPicker is an open-source protein assembly tool that derives a minimum protein list from peptide identifications filtered to a specified False Discovery Rate. Here, we update IDPicker to increase confident peptide identifications by combining multiple scores produced by database search tools. By segregating peptide identifications for thresholding using both the precursor charge state and the number of tryptic termini, IDPicker retrieves more peptides for protein assembly. The new version is more robust against false positive proteins, especially in searches using multispecies databases, by requiring additional novel peptides in the parsimony process. IDPicker has been designed for incorporation in many identification workflows by the addition of a graphical user interface and the ability to read identifications from the pepXML format. These advances position IDPicker for high peptide discrimination and reliable protein assembly in large-scale proteomics studies. The source code and binaries for the latest version of IDPicker are available from http://fenchurch.mc.vanderbilt.edu/.
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