提高单级质谱峰的肽鉴定能力。

Improving peptide identification with single-stage mass spectrum peaks.

机构信息

Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong, China.

出版信息

Bioinformatics. 2009 Nov 15;25(22):2969-74. doi: 10.1093/bioinformatics/btp501. Epub 2009 Aug 18.

DOI:10.1093/bioinformatics/btp501

PMID:19689954

Abstract

MOTIVATION

Database searching is the major peptide identification method in shotgun proteomics. It searches tandem mass spectrometry (MS/MS) spectra against a protein database to identify target peptides. The success of such a database searching method relies on a scoring algorithm that can evaluate the quality of peptide-spectrum matches (PSMs) accurately. However, current scoring algorithms frequently generate inaccurate assignments due to variations and noises in the MS/MS spectra. To address this issue, we like to improve peptide identification by using additional information from other data sources.

RESULTS

Single-stage MS data is complementary to MS/MS data in the sense that it provides broader mass coverage but less sequence information. In this article, we show that single-stage MS data can be used to re-rank PSMs. The proposed method explores a linear combination of scores between MS and MS/MS data to perform re-ranking. Experimental results on real data show that such a re-ranking strategy improves the identification performance significantly.

AVAILABILITY

http://bioinformatics.ust.hk/ReRankPSMwMS1.rar

摘要

动机

数据库搜索是 shotgun 蛋白质组学中的主要肽段鉴定方法。它根据蛋白质数据库搜索串联质谱（MS/MS）谱，以鉴定目标肽段。这种数据库搜索方法的成功依赖于一种评分算法，该算法可以准确地评估肽段谱匹配（PSM）的质量。然而，由于 MS/MS 谱中的变化和噪声，当前的评分算法经常会产生不准确的分配。为了解决这个问题，我们希望通过使用来自其他数据源的附加信息来改进肽段鉴定。