GAPP: A fully automated software for the confident identification of human peptides from tandem mass spectra
GAPP: A fully automated software for the confident identification of human peptides from tandem mass spectra
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DOI：
10.1021/pr060205s
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发表时间：
2006-10-06
影响因子：
4.4
通讯作者：
Bessant, Conrad
中科院分区：
文献类型：
--
作者：
Shadforth, Ian;Xu, Weibing;Bessant, Conrad
本文介绍了基因组注释蛋白质组管道（GAPP），这是一种完全自动化的公开软件管道，用于从人类蛋白质组串联质谱数据中识别肽和蛋白质。该管道将给定实验样品中的一系列 MS/MS 峰列表作为输入，并生成与样品中观察到的肽相对应的一系列数据库条目以及相关的置信度分数。该管道能够找到任何预期的肽，包括跨越内含子-外显子边界的肽，以及由于单核苷酸多态性 (SNP)、可变剪接和翻译后修饰 (PTM) 引起的肽。因此，GAPP 可用于重新注释基因组，这是通过包含分布式注释系统 (DAS) 服务器来支持的，该服务器允许管道识别的肽在 Ensembl 基因组浏览器中的基因组上下文中显示。 GAPP 可通过网站 www.gapp.info 免费获取。
This paper introduces the genome annotating proteomic pipeline (GAPP), a totally automated publicly available software pipeline for the identification of peptides and proteins from human proteomic tandem mass spectrometry data. The pipeline takes as its input a series of MS/MS peak lists from a given experimental sample and produces a series of database entries corresponding to the peptides observed within the sample, along with related confidence scores. The pipeline is capable of finding any peptides expected, including those that cross intron-exon boundaries, and those due to single nucleotide polymorphisms (SNPs), alternate splicing, and post-translational modifications (PTMs). GAPP can therefore be used to re-annotate genomes, and this is supported through the inclusion of a Distributed Annotation System (DAS) server, which allows the peptides identified by the pipeline to be displayed in their genomic context within the Ensembl genome browser. GAPP is freely available via the web, at www.gapp.info.