The Mass Distance Fingerprint: A statistical framework for de novo detection of predominant modifications using high-accuracy mass spectrometry

Journal of Chromatography B: Analytical Technologies in the Biomedical and Life Sciences

Volumn 854, Issue 1-2, 2007, Pages 173-182

  Potthast, Frank ^a   Gerrits, Bertran ^a   Häkkinen, Jari ^b   Rutishauser, Dorothea ^c   Ahrens, Christian H ^a   Roschitzki, Bernd ^a   Baerenfaller, Katja ^d   Munton, Richard P ^a   Walther, Pascal ^d   Gehrig, Peter ^a   Seif, Philipp ^a   Seeberger, Peter H ^a   Schlapbach, Ralph ^a  

^a ETH ZURICH   (Switzerland)

^b LUND UNIVERSITY   (Sweden)

^c UNIVERSITY HOSPITAL ZURICH   (Switzerland)

^d UNIVERSITY OF ZURICH   (Switzerland)

Author keywords

Mass Distance Fingerprint; Mass Distance Histogram; Post translational modification; Protein identification

Indexed keywords

COMPUTER SOFTWARE; IDENTIFICATION (CONTROL SYSTEMS); LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PEPTIDES; QUALITY CONTROL;

MASS DISTANCE FINGERPRINT; MASS DISTANCE HISTOGRAM; POST-TRANSLATIONAL MODIFICATION; PROTEIN IDENTIFICATION;

STATISTICAL METHODS;

PEPTIDE; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; ANIMAL CELL; ANIMAL TISSUE; ARTICLE; CALCULATION; CHEMICAL MODIFICATION; COMPUTER PROGRAM; DATA BASE; DIAGNOSTIC ACCURACY; EXPERIMENT; HUMAN; HUMAN CELL; KNOWLEDGE; MASS DISTANCE FINGERPRINT; MASS SPECTROMETRY; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN MODIFICATION; QUALITY CONTROL; SAMPLE; SPECTRUM; STATISTICAL ANALYSIS;

EID: 34250702089     PISSN: 15700232     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jchromb.2007.04.020     Document Type: Article

References (29)

1. Eng J.K., McCormack A.L., and Yates J.R.r. J. Am. Soc. Mass Spectrom. 5 11 (1994) 976
2. Clauser K.R., Baker P., and Burlingame A.L. Anal. Chem. 71 14 (1999) 2871
3. Perkins D.N., Pappin D.J., Creasy D.M., and Cottrell J.S. Electrophoresis 20 18 (1999) 3551
4. Aebersold R., and Mann M. Nature 422 6928 (2003) 198
5. Yates J.R.r. J. Mass Spectrom. 33 1 (1998) 1
6. Creasy D.M., and Cottrell J.S. Proteomics 2 10 (2002) 1426
7. Gatlin C.L., Eng J.K., Cross S.T., Detter J.C., and Yates J.R.r. Anal. Chem. 72 4 (2000) 757
8. Pevzner P.A., Mulyukov Z., Dancik V., and Tang C.L. Genome Res. 11 2 (2001) 290
9. Garavelli J.S. Nucl. Acids Res. 31 1 (2003) 499
10. DeltaMass-Association of Biomolecular Resource Facilities. http://www.abrf.org/index.cfm/dm.home.
11. Wilkins M.R., Gasteiger E., Gooley A.A., Herbert B.R., Molloy M.P., Binz P.A., Ou K., Sanchez J.C., Bairoch A., Williams K.L., and Hochstrasser D.F. J. Mol. Biol. 289 3 (1999) 645
12. Creasy D.M., and Cottrell J.S. Proteomics 4 6 (2004) 1534
13. Hansen B.T., Davey S.W., Ham A.-J.L., and Liebler D.C. J. Prot. Res. 4 2 (2005) 358
14. Potthast F., Ocenasek J., Rutishauser D., Pelikan M., and Schlapbach R. J. Chromatogr. B: Anal. Technol. Biomed. Life Sci. 817 2 (2005) 225
15. Savitski M.M., Nielsen M.L., and Zubarev R.A. Mol. Cell. Prot. 5 5 (2006) 935
16. GNU General Public License. http://www.gnu.org/copyleft/gpl.html.
17. mgf format reference. http://www.matrixscience.com/help/data_file_help.html.
18. Available from http://www.peptoscope.ms.
19. Tabb D.L., Saraf A., and Yates J.R.r. Anal. Chem. 75 23 (2003) 6415
20. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. Nat. Biotechnol. 17 10 (1999) 994
21. Li J., Steen H., and Gygi S.P. Mol. Cell. Prot. 2 11 (2003) 1198
22. Carlin R.K., Grab D.J., Cohen R.S., and Siekevitz P. J. Cell Biol. 86 3 (1980) 831
23. Gschwend T.P., Krueger S.R., Kozlov S.V., Wolfer D.P., and Sonderegger P. Mol. Cell Neurosci. 9 3 (1997) 207
24. Molinari F., Rio M., Meskenaite V., Encha-Razavi F., Auge J., Bacq D., Briault S., Vekemans M., Munnich A., Attie-Bitach T., Sonderegger P., and Colleaux L. Science 298 5599 (2002) 1779
25. Mann M. Proceedings of the 43rd ASMS Conference on Mass Spectrometry and Allied Topics. Atlanta, GA (1995) 693
26. Wehofsky M., Hoffmann R., Hubert M., and Spengler B. Eur. J. Mass Spectrom. 7 (2001) 39
27. deltaMasses is available from http://www.detectorvision.com/deltaMasses.
28. Arnott D., Gawinowicz M.A., Grant R.A., Neubert T.A., Packman L.C., Speicher K.D., Stone K., and Turck C.W. J. Biomol. Tech. 14 3 (2003) 205
29. Gary J.D., and Clarke S. Prog. Nucl. Acid Res. Mol Biol. 61 (1998) 65