An efficient algorithmic approach for mass spectrometry-based disulfide connectivity determination using multi-ion analysis

BMC Bioinformatics

Volumn 12, Issue SUPPL. 1, 2011, Pages

  Murad, William ^a   Singh, Rahul ^a   Yen, Ten Yang ^a  

^a SAN FRANCISCO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMIC APPROACH; ALGORITHMIC PROBLEMS; COLLISION-INDUCED DISSOCIATION; DISSOCIATION METHODS; DISULFIDE CONNECTIVITIES; GLYCOSYLTRANSFERASES; POLYNOMIAL TIME COMPLEXITY; SPECTROMETRIC DATA; QUALITY OF RESULTS;

APPROXIMATION ALGORITHMS; COVALENT BONDS; DISSOCIATION; IONS; MASS SPECTROMETRY; POLYNOMIAL APPROXIMATION; PROTEINS; SULFUR COMPOUNDS; TOPOLOGY; BIOINFORMATICS;

REDUCTION;

EUKARYOTA;

DISULFIDE; GLYCOSYLTRANSFERASE; ION; PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; COMPARATIVE STUDY; MASS SPECTROMETRY; METHODOLOGY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DISULFIDES; GLYCOSYLTRANSFERASES; IONS; MASS SPECTROMETRY; PROTEINS;

EID: 79951542333     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S1-S12     Document Type: Article

References (23)

1. Singh R. A review of algorithmic techniques for disulfide-bond determination. Brief Funct Genomic Proteomic 2008, 7(2):157-172.
2. Nesvizhskii AI, Vitek O, Aebersold R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods 2007, 4(10):787-797.
3. Lee T, Singh R. Comparative Analysis of Disulfide Bond Determination Using Computational-Predictive Methods and Mass Spectrometry-Based Algorithmic Approach. Proc, BIRD 2008, 140-153. CCIS 13.
4. Steen H, Mann M. The abc's (and xyz's) of peptide sequencing. Nat Rev Mol Cell Biol 2004, 5:699-711.
5. Johnson RS, Martin SA, Biemann K, Stults JT, Watson JT. Novel fragmentation process of peptides by collision-induced decomposition in a tandem mass spectrometer: differentiation of leucine and isoleucine. Analytical Chemistry 1987, 59:2621-2625.
6. Schilling B, et al. MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. J Am Soc Mass Spectrom 2003, 14(8):834-850.
7. Xu H, Zhang L, Freitas MA. Identification and Characterization of Disulfide Bonds in Proteins and Peptides from Tandem MS Data by Use of the MassMatrix MS/MS Search Engine. J Proteome Res 2008, 7:138-144. 2749473, 18072732.
8. Xu H, Freitas MA. A mass accuracy sensitive probability based scoring algorithm for database searching of tandem mass spectrometry data. BMC Bionformatics 2007, 8:133.
9. Keller A, Nesvizhskii AI, Kolker E, Aebersold R. Empirical statistical model to estimate the accuracy of peptide identification made by MS/MS database search. Analytical Chemistry 2002, 74(20):5383-5392.
10. Chen T, Jaffe JD, Church GM. Algorithms for Identifying Protein Cross-links via Tandem Mass Spectrometry. Proc RECOMB 2001, 95-102.
11. Lee T, Singh R, Yen TY, Macher B. An Algorithmic approach to Automated High-Throughput Identification of Disulfide Connectivity in Proteins Using Tandem Mass Spectrometry. Proc. Computational Systems Bioinformatics, CSB 2007, 41-51.
12. Lee T, Singh R, Yen R, Macher B. A mass-based hashing algorithm for the identification of disulfide linkage patterns in protein utilizing mass spectrometry data. Proc. IEEE International Symposiumon Computer-Based Medical Systems, CBMS 2007, 397-402.
13. Murad W, Singh R, Yen TY. Polynomial-Time Disulfide Bond Determination Using Mass Spectrometry Data. Proc. IEEE Computational Structural Bioinformatics Workshop, CSBW 2009, 79-86.
14. Fariselli P, Casadio R. Prediction of disulfide connectivity in proteins. Bioinformatics 2001, 17:957-64.
15. Frank A, Tanner S, Pevzner P. Peptide Sequence Tags for Fast Database Search in Mass-Spectrometry. Proc. RECOMB 2005, 26-341. LNBI 3500.
16. Cormen TH, Leiserson CE, Rivest RL, Stein C. Introduction to Algorithms. 2005, MIT Press, Cambridge, MA, U.S.A, 2nd.
17. Gabow HN. An efficient implementation of Edmonds' Algorithm for Maximum Matching on Graphs. Journal of the ACM 2006, 23:221-234.
18. Rothberg E. MATHPROG: Solver for the maximum weight matching problem. , http://elib.zib.de/pub/Packages/mathprog/matching/weighted/
19. Thomas S, Yen TY, Macher BA. Eukaryotic glycosyltransferases: cysteines and disulfides. Glycobiology 2002, 12:4G-7G.
20. Yen TY, Macher BA. Determination of glycosylation sites and disulfide bond structures using LC/ESI-MS/MS analysis. Methods in enzymology 2006, 415:103-113.
21. Ferre F, Clote P. DiANNA: A Web Server for Disulfide Connectivity Prediction. Nucleic Acids Res 2005, 33(Web Server issue):W230-W232. 1160173, 15980459.
22. Ceroni A, et al. DISULFIND: A Disulfide Bonding State and Cysteine Connectivity Prediction Server. Nucleic Acids Res 2006, 34(Web Server issue):W177-W181. 1538823, 16844986.
23. Tsai CH, et al. Improving disulfide connectivity prediction with sequential distance between oxidized cysteines. Bioinformatics 2005, 21:4416-4419.