NDLI: Database Search Algorithm for Identification of Intact Cross-Links in Proteins and Peptides Using Tandem Mass Spectrometry

Content Provider	PubMed Central
Author	Xu, Hua Hsu, Pang-hung Zhang, Liwen Tsai, Ming-daw Freitas, Michael A.
Copyright Year	2010
Abstract	A new database search algorithm has been developed for identification of intact cross-links in proteins and peptides from tandem mass spectrometric data. Using this algorithm, intact cross-links can be identified and characterized in proteins and peptides with high confidence. The algorithm was tested using BS3 (bis[sulfosuccinimidyl] suberate) cross-linked Cytochrome C. Five cross-links were identified and verified for spatial plausibility by comparison with its three-dimensional structure at optimized experimental conditions. The distributions of statistical scores for true and false positives and receiver operating characteristic analysis indicate that the algorithm is capable of discriminating true positive cross-linked peptide-spectrum matches from false ones. It has also been demonstrated that the MassMatrix database search engine is capable of searching for intact cross-links in complex Escherichia coli proteome samples cross-linked by BS3. The new algorithm in MassMatrix offers an additional approach for the discovery of cross-links in proteins and peptides from tandem mass spectrometric data.
Related Links	http://dx.doi.org/10.1021/pr100369y
Ending Page	3393
Page Count	10
Starting Page	3384
File Format	PDF
ISSN	15353893
e-ISSN	15353907
Journal	Journal of proteome research
Issue Number	7
Volume Number	9
Language	English
Publisher Date	2010-07-02
Access Restriction	Open
Subject Keyword	Biochemistry Chemistry(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Chemistry Biochemistry

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