Computational proteomics analysis system (CPAS): An extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments

Journal of Proteome Research

Volumn 5, Issue 1, 2006, Pages 112-121

  Rauch, Adam ^a,b   Bellew, Matthew ^a,b   Eng, Jimmy ^a   Fitzgibbon, Matthew ^a   Holzman, Ted ^a   Hussey, Peter ^a,b   Igra, Mark ^a,b   Maclean, Brendan ^a,b   Lin, Chen Wei ^a   Detter, Andrea ^a   Fang, Ruihua ^a   Faca, Vitor ^a   Gafken, Phil ^a   Zhang, Heidi ^a   Whitaker, Jeffrey ^a   States, David ^c   Hanash, Sam ^a   Paulovich, Amanda ^a   McIntosh, Martin W ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

^b LabKey Software   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Adenocarcinoma; FuGE; mzXML; pepXML; Proteomics; X! Tandem

Indexed keywords

ADENOCARCINOMA; AMINO ACID SEQUENCE; ANALYTIC METHOD; ARTICLE; COMPUTATIONAL PROTEOMICS ANALYSIS SYSTEM; COMPUTER PROGRAM; DATA BASE; HIGH THROUGHPUT SCREENING; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEOMICS; PUBLICATION;

COMPUTATIONAL BIOLOGY; DATABASE MANAGEMENT SYSTEMS; PROTEOMICS;

EID: 30744438115     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr0503533     Document Type: Article

References (22)

1. Craig, R.; Beavis, R. C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20 (9), 1466-1467.
2. Keller, A.; Eng, J. K.; Zhang, N.; Li, X. J.; Aebersold, R., A uniform proteomics MS/MS analysis platform utilizing open XML file formats. Mol. Syst. Biol. 2005, EPub, (August).
3. 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.
4. Keller, A.; Nesvizhskii, A. I.; Kolker, E.; Aebersold, R., Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal. Chem. 2002, 74 (20), 5383-5392.
5. Martens, L.; Hermjakob, H.; Jones, P.; Adamski, M.; Taylor, C.; States, D.; Gevaert, K.; Vandekerckhove, J.; Apweiler, R., PRIDE: the proteomics identifications database. Proteomics 2005, 5 (13), 3537-3545.
6. Desiere, F.; Deutsch, E. W.; Nesvizhskii, A. I.; Mallick, P.; King, N. L.; Eng, J. K.; Aderem, A.; Boyle, R.; Brunner, E.; Donohoe, S.; Fausto, N.; Hafen, E.; Hood, L.; Katze, M. G.; Kennedy, K. A.; Kregenow, F.; Lee, H.; Lin, B.; Martin, D.; Ranish, J. A.; Rawlings, D. J.; Samelson, L. E.; Shiio, Y.; Watts, J. D.; Wollscheid, B.; Wright, M. E.; Yan, W.; Yang, L.; Yi, E. C.; Zhang, H.; Aebersold, R., Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 2005, 6 (1), R9.
7. Craig, R.; Cortens, J. P.; Beavis, R. C., Open source system for analyzing, validating, and storing protein identification data. J. Proteome Res. 2004, 3 (6), 1234-1242.
8. Systems Biology Experiment Analysis System (SBEAMS). http://www.sbeams. org.
9. Proteome Research Information Management Environment (PRIME). http://prime.proteome.med.umich.edu.
10. Jones, A.; Hunt, E.; Wastling, J. M.; Pizarro, A.; Stoeckert, C. J., Jr., An object model and database for functional genomics. Bioinformatics 2004, 20 (10), 1583-1590.
11. Pedrioli, P. G.; 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., A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 2004, 22 (11), 1459-1466.
12. Bairoch, A.; Apweiler, R.; Wu, C. H.; Barker, W. C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M. J.; Natale, D. A.; O'Donovan, C.; Redaschi, N.; Yeh, L. S., The Universal Protein Resource (UniProt). Nucleic Acids Res. 2005, 33, (Database issue), D154-159.
13. Apweiler, R.; Bairoch, A.; Wu, C. H.; Barker, W. C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M. J.; Natale, D. A.; O'Donovan, C.; Redaschi, N.; Yeh, L. S., UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 2004, 32, (Database issue), D115-119.
14. Clark, T.; Martin, S.; Liefeld, T., Globally distributed object identification for biological knowledgebases. Brief Bioinform. 2004, 5 (1), 59-70.
15. Faca, V.; Deng, B.; Phanstiel, D.; Newcomb, L.; Hanash, S. In Identification of glycoproteins in lung adenocarcinoma cell surface HUPO 4th Annual World Congress, Munich, Germany, Aug 29-Sep 1, 2005; Molecular & Cellular Proteomics: Munich, Germany, 2005; S190.
16. Shin, B. K.; Wang, H.; Yim, A. M.; Le Naour, F.; Brichory, F.; Jang, J. H.; Zhao, R.; Puravs, E.; Tra, J.; Michael, C. W.; Misek, D. E.; Hanash, S. M., Global profiling of the cell surface proteome of cancer cells uncovers an abundance of proteins with chaperone function. J. Biol. Chem. 2003, 278 (9), 7607-7616.
17. Jang, J. H.; Hanash, S., Profiling of the cell surface proteome. Proteomics 2003, 3 (10), 1947-1954.
18. Ashburner, M.; Ball, C. A.; Blake, J. A.; Botstein, D.; Butler, H.; Cherry, J. M.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.; Hill, D. P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock, G., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25 (1), 25-29.
19. GenoLogics http://www.genologics.com/cpas.
20. Gygi, S. P.; Rist, B.; Gerber, S. A.; Turecek, F.; Gelb, M. H.; Aebersold, R., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17 (10), 994-999.
21. Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1 (5), 376-386.
22. Proteomics Standards Initiative http://psidev.sourceforge.net.