Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra

doi:10.1021/pr070479v

	Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra
	Sun, Shiwei 1; Yu, Chungong 1; Qiao, Yantao 1; Lin, Yu 1; Dong, Gongjin 1; Liu, Changning 1; Zhang, Lingfen 2; Zhang, Zhuo 3; Cai, Jinjin 2; Zhang, Hong 4; Bu, Dongbo 1
	2008
发表期刊	JOURNAL OF PROTEOME RESEARCH
ISSN	1535-3893
卷号	7 期号:1 页码:202-208
摘要	In protein identification through tandem mass spectrometry, it is critical to accurately predict the theoretical spectrum for a peptide sequence. The widely used prediction models, such as SEQUEST and MASCOT, ignore the intensity of the ions with important neutral losses, including water loss and ammonia loss. However, ignoring these neutral losses results in a significant deviation between the predicted theoretical spectrum and its experimental counterpart. Here, based on the "one peak, multiple explanations" observation, we proposed an expectation-maximization (EM) method to automatically learn the probabilities of water loss and ammonia loss for each amino acid. Then we employed these probabilities to design an improved statistical model for theoretical spectrum prediction. We implemented these methods and tested them on practical data. On a training set containing 1803 spectra, the experimental results show a good agreement with some known knowledge about neutral losses, such as the tendency of water loss from Asp, Glu, Ser, and Thr. Furthermore, on a testing set containing 941 spectra, the improved similarity between the experimental and predicted spectra demonstrates that this method can generate more reasonable predictions relative to the model that ignores neutral losses. As an application of the derived probabilities, we implemented a database searching method adopting the improved theoretical spectrum model with neutral loss ions estimated. Experimental results on Keller's data set demonstrate that this method can identify peptides more accurately than SEQUEST. In another application to validate SEQUEST's results, the reported peptide-spectrum pairs are reranked with respect to the similarity between experimental and predicted spectra. Experimental results on both LTQ and Q (S) over bar TAR data sets suggest that this reranking strategy can effectively distinguish the false negative predictions reported by SEQUEST.
关键词	protein identification tandem mass spectrum expectation-maximization neutral loss probability
DOI	10.1021/pr070479v
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemical Research Methods
WOS记录号	WOS:000252154200024
出版者	AMER CHEMICAL SOC
引用统计	被引频次：21[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/11158
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Bu, Dongbo
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Ctr Adv Comp Res, Bioinformat Grp, Beijing 100080, Peoples R China 2.Chinese Acad Sci, Joint Res Dev Lab Adv Comp & Commun Technol, Inst Comp Technol, Beijing 100080, Peoples R China 3.Chinese Acad Sci, Inst Biophys, Beijing 100035, Peoples R China 4.Zhejiang Gongshang Univ, Coll Food Sci & Biol Engn, Zhejiang, Peoples R China
推荐引用方式 GB/T 7714	Sun, Shiwei,Yu, Chungong,Qiao, Yantao,et al. Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra[J]. JOURNAL OF PROTEOME RESEARCH,2008,7(1):202-208.
APA	Sun, Shiwei.,Yu, Chungong.,Qiao, Yantao.,Lin, Yu.,Dong, Gongjin.,...&Bu, Dongbo.(2008).Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra.JOURNAL OF PROTEOME RESEARCH,7(1),202-208.
MLA	Sun, Shiwei,et al."Deriving the probabilities of water loss and ammonia loss for amino acids from tandem mass spectra".JOURNAL OF PROTEOME RESEARCH 7.1(2008):202-208.