PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum

doi:10.1186/1471-2105-12-234

	PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum
	Qiao,Yantao 1; Zhang,Hong 2; Bu,Dongbo 1; Sun,Shiwei 1
	2011-06-15
发表期刊	BMC Bioinformatics
ISSN	1471-2105
卷号	12 期号:1
摘要	AbstractBackgroundTandem mass spectrometry (MS/MS) has emerged as the leading method for high- throughput protein identification in proteomics. Recent technological breakthroughs have dramatically increased the efficiency of MS/MS data generation. Meanwhile, sophisticated algorithms have been developed for identifying proteins from peptide MS/MS data by searching available protein sequence databases for the peptide that is most likely to have produced the observed spectrum. The popular SEQUEST algorithm relies on the cross-correlation between the experimental mass spectrum and the theoretical spectrum of a peptide. It utilizes a simplified fragmentation model that assigns a fixed and identical intensity for all major ions and fixed and lower intensity for their neutral losses. In this way, the common issues involved in predicting theoretical spectra are circumvented. In practice, however, an experimental spectrum is usually not similar to its SEQUEST -predicted theoretical one, and as a result, incorrect identifications are often generated.ResultsBetter understanding of peptide fragmentation is required to produce more accurate and sensitive peptide sequencing algorithms. Here, we designed the software PI of novel and exquisite algorithms that make a good use of intensity property of a spectrum.ConclusionsWe designed the software PI with the novel and effective algorithms which made a good use of intensity property of the spectrum. Experiments have shown that PI was able to validate and improve the results of SEQUEST to a more satisfactory degree.
DOI	10.1186/1471-2105-12-234
语种	英语
WOS记录号	BMC:10.1186/1471-2105-12-234
出版者	BioMed Central
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/3978
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Sun,Shiwei
作者单位	1.Chinese Academy of Sciences; Institute of Computing Technology 2.Zhejiang Gongshang University
推荐引用方式 GB/T 7714	Qiao,Yantao,Zhang,Hong,Bu,Dongbo,et al. PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum[J]. BMC Bioinformatics,2011,12(1).
APA	Qiao,Yantao,Zhang,Hong,Bu,Dongbo,&Sun,Shiwei.(2011).PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum.BMC Bioinformatics,12(1).
MLA	Qiao,Yantao,et al."PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum".BMC Bioinformatics 12.1(2011).