PeakML/mzMatch: A file format, Java library, R library, and tool-chain for mass spectrometry data analysis

Analytical Chemistry

Volumn 83, Issue 7, 2011, Pages 2786-2793

  Scheltema, Richard A ^a   Jankevics, Andris ^a,b   Jansen, Ritsert C ^a   Swertz, Morris A ^a,c   Breitling, Rainer ^a,b  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c UNIVERSITY MEDICAL CENTER GRONINGEN   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

CUSTOMIZABLE; DATA ANALYSIS METHODS; DIRECT ACCESS; FILE FORMATS; FLEXIBLE INTEGRATION; HIGH RESOLUTION; JAVA LIBRARY; MASS SPECTRA; MASS SPECTROMETRY DATA ANALYSIS; OPEN SOURCES; PROCESSING TOOLS; RESEARCH QUESTIONS; SOFTWARE DEVELOPMENT; TRACE INFORMATION; VISUALIZATION ENVIRONMENT;

DATA REDUCTION; MASS SPECTROMETERS; MASS SPECTROMETRY; PIPELINE PROCESSING SYSTEMS; SOFTWARE DESIGN; TRACE ANALYSIS; VISUALIZATION;

DATA VISUALIZATION;

ARTICLE; COMPUTER GRAPHICS; COMPUTER PROGRAM; INFORMATION RETRIEVAL; MASS SPECTROMETRY; METHODOLOGY; STATISTICS;

COMPUTER GRAPHICS; INFORMATION STORAGE AND RETRIEVAL; MASS SPECTROMETRY; SOFTWARE; STATISTICS AS TOPIC;

EID: 79953267955     PISSN: 00032700     EISSN: None     Source Type: Journal    
DOI: 10.1021/ac2000994     Document Type: Article

References (26)

1. Dunn, W. B. Phys. Biol. 2008, 5, 11001
2. Han, J.; Danell, R. M.; Patel, J. R.; Gumerov, D. R.; Scarlett, C. O.; Speir, J. P.; Parker, C. E.; Rusyn, I.; Zeisel, S.; Borchers, C. H. Metabolomics 2008, 4, 128-140
3. Pedrioli, P. G. A.; Eng, J. K.; Hubley, R.; Vogelzang, M.; Deutsch, E. W.; Raught, B.; Pratt, B.; Nilsson, E.; Angeletti, R. H.; Apweiler, R.; Cheung, K.; Costello, C. E.; Hermjakob, H.; Huang, S.; Julian, R. K.; Kapp, E.; McComb, M. E.; Oliver, S. G.; Omenn, G.; Paton, N. W.; Simpson, R.; Smith, R.; Taylor, C. F.; Zhu, W.; Aebersold, R. Nat. Biotechnol. 2004, 22, 1459-1466
4. Deutsch, E. W. In Proteome Bioinformatics; Humana Press: Totowa, NJ, 2010; pp 319 - 331.
5. Smith, C. A.; Want, E. J.; O Maille, G.; Abagyan, R.; Siuzdak, G. Anal. Chem. 2006, 78, 779-787
6. Pluskal, T.; Castillo, S.; Villar-Briones, A.; Oresic, M. BMC Bioinf. 2010, 11, 395
7. Sturm, M.; Kohlbacher, O. J. Proteome Res. 2009, 8, 3760-3763
8. Kuhn, S.; Helmus, T.; Lancashire, R. J.; Murray-Rust, P.; Rzepa, H. S.; Steinbeck, C.; Willighagen, E. L. J. Chem. Inf. Model. 2007, 47, 2015-2034
9. Scheltema, R. A.; Kamleh, A.; Wildridge, D.; Ebikeme, C.; Watson, D. G.; Barrett, M. P.; Jansen, R. C.; Breitling, R. Proteomics 2008, 8, 4647-4656
10. Scheltema, R.; Decuypere, S.; Dujardin, J.; Watson, D.; Jansen, R.; Breitling, R. Bioanalysis 2009, 1, 1551-1557
11. Arbona, V.; Iglesias, D. J.; Talón, M.; Gómez-Cadenas, A. J. Agric. Food Chem. 2009, 57, 7338-7347
12. Dai, Y.; Li, Z.; Xue, L.; Dou, C.; Zhou, Y.; Zhang, L.; Qin, X. J. Ethnopharmacology 2010, 128, 482-489
13. Lin, H.-M.; Edmunds, S. J.; Helsby, N. A.; Ferguson, L. R.; Rowan, D. D. J. Proteome Res. 2009, 8, 2045-2057
14. Bodenreider, O. Nucleic Acids Res. 2004, 32, D267-270
15. Stoeckert, C. J.; Parkinson, H. Comp. Funct. Genom. 2003, 4, 127-132
16. Whetzel, P. L.; Brinkman, R. R.; Causton, H. C.; Fan, L.; Field, D.; Fostel, J.; Fragoso, G.; Gray, T.; Heiskanen, M.; Hernandez-Boussard, T.; Morrison, N.; Parkinson, H.; Rocca-Serra, P.; Sansone, S.-A.; Schober, D.; Smith, B.; Stevens, R.; Stoeckert, C. J.; Taylor, C.; White, J.; Wood, A. Omics 2006, 10, 199-204
17. Shah, V. P.; Midha, K. K.; Findlay, J. W.; Hill, H. M.; Hulse, J. D.; McGilveray, I. J.; McKay, G.; Miller, K. J.; Patnaik, R. N.; Powell, M. L.; Tonelli, A.; Viswanathan, C. T.; Yacobi, A. Pharm. Res. 2000, 17, 1551-1557
18. Eisenacher, M. In Data Mining in Proteomics; Humana Press: Totowa, NJ, 2011; pp 161 - 177.
19. Jones, A. R.; Lister, A. L. Methods Mol. Biol. 2010, 604, 333-343
20. Taylor, C. F.; Paton, N. W.; Lilley, K. S.; Binz, P.-A.; Julian, R. K., Jr.; Jones, A. R.; Zhu, W.; Apweiler, R.; Aebersold, R.; Deutsch, E. W.; Dunn, M. J.; Heck, A. J. R.; Leitner, A.; Macht, M.; Mann, M.; Martens, L.; Neubert, T. A.; Patterson, S. D.; Ping, P.; Seymour, S. L.; Souda, P.; Tsugita, A.; Vandekerckhove, J.; Vondriska, T. M.; Whitelegge, J. P.; Wilkins, M. R.; Xenarios, I.; Yates, J. R., III; Hermjakob, H. Nat. Biotechnol. 2007, 25, 887-893
21. Swertz, M. A.; Velde, K. J.; van der; Tesson, B. M.; Scheltema, R. A.; Arends, D.; Vera, G.; Alberts, R.; Dijkstra, M.; Schofield, P.; Schughart, K.; Hancock, J. M.; Smedley, D.; Wolstencroft, K.; Goble, C.; de Brock, E. O.; Jones, A. R.; Parkinson, H. E.; Jansen, R. C. Genome Biol. 2010, 11, R27
22. Windig, W. Chemom. Int. Lab. Syst. 2004, 77, 206-214
23. Kuhn, T.; Willighagen, E. L.; Zielesny, A.; Steinbeck, C. BMC Bioinf. 2010, 11, 159
24. Kol, S.; Merlo, M. E.; Scheltema, R. A.; de Vries, M.; Vonk, R. J.; Kikkert, N. A.; Dijkhuizen, L.; Breitling, R.; Takano, E. Appl. Environ. Microbiol. 2010, 76, 2574-2581
25. t'Kindt, R.; Scheltema, R. A.; Jankevics, A.; Brunker, K.; Rijal, S.; Dujardin, J.-C.; Breitling, R.; Watson, D. G.; Coombs, G. H.; Decuypere, S. PLoS Negl. Trop. Dis. 2010, 4, e904
26. t'Kindt, R.; Jankevics, A.; Scheltema, R. A.; Zheng, L.; Watson, D. G.; Dujardin, J.-C.; Breitling, R.; Coombs, G. H.; Decuypere, S. Anal. Bioanal. Chem. 2010, 398, 2059-2069