NDLI: Separation of ion types in tandem mass spectrometry data interpretation

Content Provider	IEEE Xplore Digital Library
Author	Bo Yan Chongle Pan Olman, V.N. Hettich, R.L. Ying Xu
Copyright Year	2004
Description	Author affiliation: Georgia Univ., Athens, GA, USA (Bo Yan)
Abstract	Mass spectrometry is one of the most popular analytical techniques for identification of individual proteins in a protein mixture, one of the basic problems in proteomics. It identifies a protein through identifying its unique mass spectral pattern. While the problem is theoretically solvable, it remains a challenging problem computationally. One of the key challenges comes from the difficulty in distinguishing the N- and C-terminus ions, mostly b- and y-ions respectively. In this paper, we present a graph algorithm for solving the problem of separating b- from y-ions in a set of mass spectra. We represent each spectral peak as a node and consider two types of edges: a type-1 edge connects two peaks possibly of the same ion types and a type-2 edge connects two peaks possibly of different ion types, predicted based on local information. The ion-separation problem is then formulated and solved as a graph partition problem, which is to partition the graph into three subgraphs, namely b-, y-ions and others respectively, so to maximize the total weight of type-1 edges while minimizing the total weight of type-2 edges within each subgraph. We have developed a dynamic programming algorithm for rigorously solving this graph partition problem and implemented it as a computer program PRIME. We have tested PRIME on 18 data sets of high accurate FT-ICR tandem mass spectra and found that it achieved /spl sim/90% accuracy for separation of b- and y-ions.
Starting Page	236
Ending Page	244
File Size	365279
Page Count	9
File Format	PDF
ISBN	0769521940
DOI	10.1109/CSB.2004.1332437
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2004-08-19
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Sequences Databases Peptides Genomics Proteomics Mass spectroscopy Protein sequence Bioinformatics Chemical technology Computational biology
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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