Detection and identification of protein isoforms using cluster analysis of MALDI-MS mass spectra

Journal of Proteome Research

Volumn 5, Issue 4, 2006, Pages 785-792

  Alm, Rikard ^a   Johansson, Peter ^a   Hjernø, Karin ^b   Emanuelsson, Cecilia ^a   Ringnér, Markus ^a   Häkkinen, Jari ^a  

^a LUND UNIVERSITY   (Sweden)

^b UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

Author keywords

Hierarchical clustering; Isoforms; Mass spectra; Protein identification; Proteomics

Indexed keywords

ISOPROTEIN;

ARTICLE; CLUSTER ANALYSIS; HIERARCHICAL CLUSTERING; INFORMATION PROCESSING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NUCLEOTIDE SEQUENCE; PEPTIDE MASS FINGERPRINTING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; TECHNIQUE; TWO DIMENSIONAL ELECTROPHORESIS;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CLUSTER ANALYSIS; PLANT PROTEINS; PROTEIN ISOFORMS; REPRODUCIBILITY OF RESULTS; SOFTWARE; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 33645779007     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr050354v     Document Type: Article

References (27)

1. Pandey, A.; Mann, M. Proteomics to study genes and genomes. Nature 2000, 405 (6788), 837-846.
2. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics. Nature 2003, 422 (6928), 198-207.
3. Larsen, M. R.; Roepstorff, P. Mass spectrometric identification of proteins and characterization of their post-translational modifications in proteome analysis. Fresenius J. Anal. Chem. 2000, 366 (6-7), 677-690.
4. Mann, M.; Jensen, O. N. Proteomic analysis of post-translational modifications. Nat. Biotechnol. 2003, 21 (3), 255-261.
5. Jensen, O. N. Modification-specific proteomics: characterization of posttranslational modifications by mass spectrometry. Curr. Opin. Chem. Biol. 2004, 8 (1), 33-41.
6. Rappsilber, J.; Mann, M. What does it mean to identify a protein in proteomics? Trends Biochem. Sci. 2002, 27 (2), 74-78.
7. Appel, R. D.; Bairoch, A. Posttranslational modifications: a challenge for proteomics and bioinformatics. Proteomics 2004, 4 (6), 1525-1526.
8. Hansen, M. E.; Smedsgaard, J. A new matching algorithm for high-resolution mass spectra. J. Am. Soc. Mass Spectrom. 2004, 15 (8), 1173-1180.
9. Pevzner, P. A.; Dancik, V.; Tang, C. L. Mutation-tolerant protein identification by mass spectrometry. J. Comput. Biol. 2000, 7 (6), 777-787.
10. Pevzner, P. A.; Mulyukov, Z.; Dancik, V.; Tang, C. L. Efficiency of database search for identification of mutated and modified proteins via mass spectrometry. Genome Res. 2001, 11 (2), 290-299.
11. Potthast, F.; Ocenasek, J.; Rutishauser, D.; Pelikan, M.; Schlapbach, R. Database independent detection of isotopically labeled MS/MS spectrum peptide pairs. J. Chromatogr. B Analyt Technol. Biomed Life Sci. 2005, 817 (2), 225-230.
12. Schmidt, F.; Schmid, M.; Jungblut, P. R.; Mattow, J.; Facius, A.; Pleissner, K. P. Iterative data analysis is the key for exhaustive analysis of peptide mass fingerprints from proteins separated by two-dimensional electrophoresis. J. Am. Soc. Mass Spectrom. 2003, 14 (9), 943-956.
13. Binz, P. A.; Muller, M.; Walther, D.; Bienvenut, W. V.; Gras, R.; Hoogland, C.; Bouchet, G.; Gasteiger, E.; Fabbretti, R.; Gay, S.; Palagi, P.; Wilkins, M. R.; Rouge, V.; Tonella, L.; Paesano, S.; Rossellat, G.; Karmime, A.; Bairoch, A.; Sanchez, J. C.; Appel, R. D.; Hochstrasser, D. F. A molecular scanner to automate proteomic research and to display proteome images. Anal. Chem. 1999, 71 (21), 4981-4988.
14. Muller, M.; Gras, R.; Appel, R. D.; Bienvenut, W. V.; Hochstrasser, D. F. Visualization and analysis of molecular scanner peptide mass spectra. J. Am. Soc. Mass Spectrom. 2002, 13 (3), 221-231.
15. Tibshirani, R.; Hastie, T.; Narasimhan, B.; Soltys, S.; Shi, G.; Koong, A.; Le, Q. T. Sample classification from protein mass spectrometry, by 'peak probability contrasts'. Bioinformatics 2004, 20 (17), 3034-3044.
16. Beer, I.; Barnea, E.; Ziv, T.; Admon, A. Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics 2004, 4 (4), 950-960.
17. Monigatti, F.; Berndt, P. Algorithm for accurate similarity measurements of peptide mass fingerprints and its application. J. Am. Soc. Mass Spectrom. 2005, 76 (1), 13-21.
18. Schubert, M.; Petersson, U. A.; Haas, B. J.; Funk, C.; Schroder, W. P.; Kieselbach, T. Proteome map of the chloroplast lumen of Arabidopsis thaliana. J. Biol. Chem. 2002, 277 (10), 8354-8365.
19. Hjerno, K.; Aim, R.; Canback, B.; Matthiesen, R.; Trajkovski, K.; Bjork, L.; Roepstorff, P.; Emanuelsson, C. S. Down-regulation of the strawberry Bet v 1-homologous allergen in concert with the flavonoid biosynthesis pathway in colourless strawberry mutant. Proteomics 2005, 6 (5), 1574-1587.
20. Karlsson, A. L.; Aim, R.; Ekstrand, B.; Fjelkner-Modig, S.; Schiott, A.; Bengtsson, U.; Bjork, L.; Hjerno, K.; Roepstorff, P.; Emanuelsson, C. S. Bet v 1 homologues in strawberry identified as IgE-binding proteins and presumptive allergens. Allergy 2004, 59 (12), 1277-1284.
21. Perkins, D. N.; Pappin, D. J.; Creasy, D. M.; Cottrell, J. S. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20 (18), 3551-3567.
22. Samuelsson, J.; Dalevi, D.; Levander, F.; Rognvaldsson, T. Modular, scriptable and automated analysis tools for high-throughput peptide mass fingerprinting. Bioinformatics 2004, 20 (18), 3628-3635.
23. Levander, F.; Rognvaldsson, T.; Samuelsson, J.; James, P. Automated methods for improved protein identification by peptide mass fingerprinting. Proteomics 2004, 4 (9), 2594-2601.
24. Ward, J. H. Hierarchical Grouping to optimize an objective function. J. Am. Stat. Assoc. 1963, 58 (301), 236-244.
25. de Hoon, M. J.; Imoto, S.; Nolan, J.; Miyano, S. Open source clustering software. Bioinformatics 2004, 20 (9), 1453-1454.
26. Quackenbush, J. Computational analysis of microarray data. Nat. Rev. Genet. 2001, 2 (6), 418-427.
27. Needleman, S. B.; Wunsch, C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970, 48 (3), 443-453.