New algorithm for the identification of intact disulfide linkages based on fragmentation characteristics in tandem mass spectra

Journal of Proteome Research

Volumn 9, Issue 1, 2010, Pages 626-635

  Choi, Seonhwa ^a   Jeong, Jaeho ^b   Na, Seungjin ^a   Lee, Hyo Sun ^b   Kim, Hwa Young ^c   Lee, Kong Joo ^b   Paek, Eunok ^a  

^a University of Seoul   (South Korea)

^b Ewha Womans University   (South Korea)

^c Yeungnam University College of Medicine   (South Korea)

Author keywords

Dbond; Dehydroalanine; Disulfide; Disulfide fragmentation; Methionine sulfoxide reductase; NDPK; Nucleoside diphosphate kinase; Persulfide; Secretagogin; Tandem mass spectrometry

Indexed keywords

ALKYLATING AGENT; CALCIUM BINDING PROTEIN; CYSTEINE; CYSTEINE DERIVATIVE; CYSTEINE PERSULFIDE; CYSTEINE THIOALDEHYDE; DEHYDROALANINE; METHIONINE SULFOXIDE REDUCTASE; NUCLEOSIDE DIPHOSPHATE KINASE; SECRETAGOGIN; THIOL DERIVATIVE; UNCLASSIFIED DRUG;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CHEMICAL LABELING; COMPUTER PROGRAM; DISSOCIATION; DISULFIDE BOND; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN FUNCTION; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; REDUCTION; SCORING SYSTEM; STRUCTURE ANALYSIS; TANDEM MASS SPECTROMETRY; TECHNIQUE;

ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; DISULFIDES; HUMANS; MOLECULAR SEQUENCE DATA; PROTEINS; ROC CURVE; TANDEM MASS SPECTROMETRY;

EID: 73649112404     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900771r     Document Type: Article

References (29)

1. Thornton, J. M. Disulphide bridges in globular proteins. J. Mol. Biol. 1981, 151, 261-287.
2. Wetzel, R. Harnessing disulfide-bonds using protein engineering. Trends Biochem. Sci. 1987, 12, 478-482.
3. Lay, A. J.; Jiang, X. -M.; Kisker, O.; Flynn, E.; Underwood, A.; Condron, R.; Hogg, P. J. Phosphoglycerate kinase acts in tumour angiogenesis as a disulphide reductase. Nature 2000, 408, 869-873.
4. 2, A necessary evil for cell signaling. Science 2006, 312, 1882-1883.
5. Matthias, L. J.; Yam, P. T.W.; Jiang, X. -M.; Vandegraaff, N.; Li, P.; Poumbourios, P.; Donoghue, N.; Hogg, P. J. Disulfide exchange in domain 2 of CD4 is required for entry of the human immunodeficiency virus type 1. Nat. Immun. 2002, 3, 727-732.
6. Zheng, M.; Aslund, F.; Storz, G. Activation of the OxyR transcription factor by reversible disulfide bond formation. Science 1998, 279, 1718-1721.
7. Dickinson, D. A.; Forman, H. Y. Cellular glutathione and thiols metabolism. Biochem. Pharmacol. 2002, 64, 1019-1026.
8. Walter, H. W.; Jan, P.; William, R. M.; Olga, S.; Matthew, S. R.; Garth, P.; Dean, P. J. Redox potential of human thioredoxin 1 and identification of a second dithiol/disulfide motif. J. Biol. Chem. 2003, 278, 33408-33415.
9. Annan, R. S.; Carr, S. A. The essential role of mass spectrometry in characterizing protein structure: mapping posttranslational modifications. J. Protein Chem. 1997, 16, 391-402.
10. Gorman, J. J.; Wallis, T. P.; Pitt, J. J. Protein disulfide bond determination by mass spectrometry. Mass Spectrom. Rev. 2002, 21, 183-216.
11. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence database using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
12. Eng, J. K.; McCormack, A. I.; Yates, J. R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
13. Xu, H.; Zhang, L.; Freitas, M. A. 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 (1), 138-144.
14. Lioe, H.; O'Hair, R. A. A novel salt bridge mechanism highlights the need for nonmobile proton conditions to promote disulfide bond cleavage in protonated peptides under low-energy collisional activation. J. Am. Soc. Mass Spectrom. 2007, 18, 1109-1123.
15. Suman, S.; Thakur Padmanabhan, B. Fragmentation of peptide disulfides under conditions of negative ion mass spectrometry: studies of oxidized glutathione and contryphan. J. Am. Soc. Mass Spectrom. 2008, 19, 358-366.
16. Rubino, F. M.; Verduci, C.; Giampiccolo, R.; Pulvirenti, S.; Brambilla, G.; Colombi, A. Characterization of the disulfides of biothiols by electrospray ionization and triple-quadrupole tandem mass spectrometry. J. Mass Spectrom. 2004, 39, 1408-1416.
17. Min, K.; Song, H. K.; Chang, C.; Kim, S. Y.; Lee, K.-J.; Suh, S. W. Crystal structure of human nucleoside diphosphate kinase A, a metastasis suppressor. Proteins 2002, 46, 340-342.
18. Song, E. J.; Kim, Y. S.; Chung, J. Y.; Kim, E.; Chae, S. K.; Lee, K.-J. Oxidative modification of nucleoside diphosphate kinase and its identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Biochemistry 2000, 39, 10090-10097.
19. Kim, S. Y.; Chang, K. H.; Doh, H. J.; Jung, J. A.; Kim, E. Rapid purification and characterization of nucleoside diphosphate kinase isoforms using ATP-sepharose affinity column chromatography. Mol. Cells 1997, 7, 630-634.
20. Kim, H. Y.; Kim, J. R. Thioredoxin as a reducing agent for mammalian methionine sulfoxide reductases B lacking resolving cysteine. Biochem. Biophys. Res. Commun. 2008, 371, 490-494.
21. Seo, J.; Jeong, J.; Kim, Y. M.; Hwang, N.; Paek, E.; Lee, K.-J. A strategy for comprehensive identification of post-translational modifications in cellular proteins, including low abundant modifications: application to glyceraldehyde-3-phosphate dehydrogenase. J. Proteome Res. 2008, 7, 587-602.
22. Harrison, A. G.; Young, A. B.; Bleiholder, C.; Suhai, S.; Paizs, B. Scrambling of Sequence Information in Collision-Induced Dissociation of Peptides. J. Am. Chem. Soc. 2006, 128, 10364-10365.
23. Mouls, L.; Aubagnac, J. L.; Martinez, J.; Enjalbal, C. Low Energy Peptide Fragmentations in an ESI-Q-Tof Type Mass Spectrometer. J. Proteome Res. 2007, 6, 1378-1391.
24. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
25. Steen, H.; Mann, M. The ABC's (and XYZ's) of peptide sequencing. Nat. Rev. Mol. Cell Biol. 2004, 5, 699-711.
26. Nesvizhskii, A. I.; Vitek, O.; Aeversold, R. Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat. Methods 2007, 4, 7787-797.
27. Na, S.; Jeong, J.; Park, H.; Lee, K.-J.; Paek, E. Unrestrictive identification of multiple post-translational modifications from tandem mass spectrometry using an error-tolerant algorithm based on an extended sequence tag approach. Mol. Cell. Proteomics 2008, 7, 2452-2463.
28. Bitto, E.; Bingman, C. A.; Bittova, L.; Frederick, R. O.; Fox, B. G.; Phillips, G. N., Jr. X-ray structure of Danio rerio secretagogin A hexa-EF-hand calcium sensor. Proteins 2009, 76, 477-483.
29. Kim, H. Y.; Gladyshev, V. N. Different catalytic mechanisms in mammalian selenocysteine- and cysteine-containing methionine-R-sulfoxide reductases. PLoS Biol. 2005, 3, e375.