Department of Biological Chemistry, The Hebrew University of Jerusalem, Israel.
Proteomics. 2010 Dec;10(23):4306-10. doi: 10.1002/pmic.201000270.
Recent developments in MS-based proteomics have increased the emphasis on peptides as a primary observable. While peptides are identified by tandem mass spectra, the link between peptide and protein remains implicit given the bottom-up nature of the experiment in which proteins are enzymatically digested prior to sequencing. It is therefore useful to provide a fast lookup from peptide to protein in order to systematically establish the broadest possible protein basis for the observed peptides. Here, we describe Pep2Pro, a fast web-service providing protein lookup by peptides covering the entire protein space comprising ∼10 million UniRef100 sequences. We demonstrate the usefulness of the service by reanalyzing peptides from two recent meta-proteomic data sets and identifying taxon-specific peptides, thereby implicating individual species as being present in these complex samples. The Pep2Pro web service can be accessed at http://www.pep2pro.org.
基于 MS 的蛋白质组学的最新进展增加了对肽作为主要可观察物的重视。虽然肽是通过串联质谱鉴定的，但由于实验采用的是自下而上的方法，即在测序之前用酶将蛋白质进行消化，因此肽与蛋白质之间的联系仍然是隐含的。因此，提供从肽到蛋白质的快速查找功能非常有用，以便为观察到的肽系统地建立尽可能广泛的蛋白质基础。在这里，我们描述了 Pep2Pro，这是一个快速的网络服务，通过肽提供对覆盖包含约 1000 万个 UniRef100 序列的整个蛋白质空间的蛋白质的查找。我们通过重新分析两个最近的元蛋白质组学数据集的肽来证明该服务的有用性，并鉴定出具有分类特异性的肽，从而表明这些复杂样本中存在特定的物种。Pep2Pro 网络服务可在 http://www.pep2pro.org 访问。
