The collaborator for MS3D: A new cyber infra structure for the structural elucidation of biological macromolecules and their assemblies using mass spectrometry-based approaches

Journal of Proteome Research

Volumn 7, Issue 11, 2008, Pages 4848-4857

  Yu, Elzadora T ^a   Hawkins, Arie ^b   Kuntz, Irwin D ^c   Rahn, Larry A ^a   Rothfuss, Andrew ^a   Sale, Kenneth ^a   Young, Malin M ^a   Yang, Christine L ^a   Pancerella, Carmen M ^a   Fabris, Daniele ^b  

^a SANDIA NATIONAL LABORATORIES   (United States)

^b UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^c UCSF Molecular Design Institute   (United States)

Author keywords

Collaboratory; Data analysis tools; Mass spectrometry; Structural biology

Indexed keywords

ARTICLE; COMPUTER PROGRAM; COOPERATION; DATA ANALYSIS; DATA BASE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; MACROMOLECULE; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; AMINO ACID SEQUENCE; BIOLOGY; CHEMISTRY; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PERSONNEL; SYSTEM ANALYSIS;

NUCLEIC ACID; PROTEIN;

AMINO ACID SEQUENCE; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; COOPERATIVE BEHAVIOR; DATABASE MANAGEMENT SYSTEMS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; NUCLEIC ACIDS; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; RESEARCH PERSONNEL; SOFTWARE; SYSTEMS INTEGRATION;

EID: 58149382069     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800443f     Document Type: Article

References (25)

1. Adams, M. W.; Dailey, H. A.; DeLucas, L. J.; Luo, M.; Prestegard, J. H.; Rose, J. P.; Wang, B. C. The Southeast Collaboratory for Structural Genomics: a high-throughput gene to structure factory. Acc. Chem. Res. 2003, 36 (3), 191-8.
2. Bhandarkar, M., Budescu, G.; Humphrey, W. F.; Izaguirre, J. A.; Izrailev, S.; Kale, L. V.; Kosztin, D.; Molnar, F.; Phillips, J. C.; Schulten, K. In BioCoRE: A Collaboratory for Structural Biology, Bruzzone, A. G., Uchrmacher, A.; Page, E. H., Eds.; SCS International Conference on Web-Based Modeling and Simulation, San Francisco, CA, 1999; pp 242-51.
3. Burkhardt, K.; Schneider, B.; Ory, J. A biocurator perspective: annotation at the Research Collaboratory for Structural Bioinformatics Protein Data Bank. PLoS Comput. Biol. 2006, 2 (10), e99.
4. Gantenbein, R. E. Designing an Internet-based collaboratory for biomedical research. Biomed. Sci. Instrum. 2002, 38, 399-404.
5. Myers, D.; Allison, T. C.; Bittner, S.; Didier, B.; Frenklach, M.; Green, W. H. J.; Ho, Y.-L.; Hewson, J.; Koegler, W.; Lansing, C.; Leahy, D.; Lee, M.; McCoy, R.; Minkoff, M.; Nijsure, S.; von Laszewski, G.; Montoya, D.; Pancerella, G; Pinzon, R.; Pitz, W.; Rahn, L. A.; Ruscic, B.; Schuchardt, K.; Stephan, E.; Wagner, A.; Windus, T.; Yang, C. A collaborative informatics infrastructure for multi-scale science. Cluster Comput. 2005, 8, 243-53.
6. 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), 1459-66.
7. Schwenk, T. L.; Green, L. A. The Michigan Clinical Research Collaboratory: following the NIH Roadmap to the community. Ann. Fam. Med. 2006, 4 (Suppl. 1), S49-54, discussion S58-60.
8. Grethe, J. S.; Baru, C.; Gupta, A.; James, M.; Ludaescher, B.; Martone, M. E.; Papadopoulos, P. M.; Peltier, S. T.; Rajasekar, A.; Santini, S.; Zaslavsky, I. N.; Ellisman, M. H. Biomedical informatics research network: building a national collaboratory to hasten the derivation of new understanding and treatment of disease. Stud. Health Technol. Inform. 2005, 112, 100-9.
9. Pancerella, C.; Myers, J. D.; Allison, T. C.; Amin, K.; Bittner, S.; Didier, B.; Frenklach, M.; Green, W. H. J.; Ho, Y.-L.; Hewson, J.; Koegler, W.; Lansing, C.; Leahy, D.; Lee, M.; McCoy, R.; Minkoff, M.; Nijsure, S.; von Laszewski, G.; Montoya, D.; Pinzon, R.; Pitz, W.; Rahn, L.; Ruscic, B.; Schuchardt, K.; Stephan, E.; Wagner, A.; Wang, B.; Windus, T.; Xu, L.; Yang, C. Metadata in the Collaboratory for Multi-Scale Chemical Science. Proceedings of the 2003 Dublin Core Conference: Supporting Communities of Discourse and Practice Metadata Research and Applications (DC 2003), Seattle, WA, 2003.
10. Myers, J. D.; Allison, T. C.; Bittner, S.; Didier, D.; Frenklach, M.; Green, W. H. J.; Ho, Y.-L.; Hewson, J.; Koegler, W.; Lansing, C.; Leahy, D.; Lee, M.; McCoy, R.; Minkoff, M.; Nijsure, S.; von Laszewski, G.; Montoya, D.; Pancerella, C.; Pinzon, R.; Pitz, W.; Rahn, L.; Ruscic, B.; Schuchardt, K.; Stephan, E.; Wagner, A.; Windus, T.; Yang, C. A Collaborative Informatics Infrastructure for Multi-Scale Science. Cluster Comput. 2005, 8 (4), 243-53.
11. Myers, J. D.; Pancerella, C.; Lansing, C.; Schuchardt, K. L.; Didier, B. Multi-scale Science: Supporting Emerging Practice with Semantically-Derived Provenance. Proceedings of the Workshop on Semantic Web Technologies for Searching and Retrieving Scientific Data held at the 2nd International Semantic Web Conference, Sanibel Island, FL, 2003.
12. KnECS open source software, http://sourceforge.net/projects/ knees/.
13. Pancerella, C., Leahy, D.; Yang, C.; Young, M. M.; Sale, K.; Rahn, L.; Kuntz, I. D.; Fabris, D. Data portal enabling new protein structure collaboration. In 19th Protein Society Meeting, Boston, MA, 2005.
14. CHEF Collaborative Portal Framework website, http://www.chefproject.org.
15. Myers, J. D.; Chappell, A.; M., E.; A., G.; Schwidder, J. Re-Integrating the Research Record. IEEE Comput. Sci. Eng. 2003, 5 (3), 44-50.
16. Orchard, S.; Hermjakob, H.; Apweiler, R. The proteomics standards initiative. Proteomics 2003, 3 (7), 1374-6.
17. Orchard, S.; Hermjakob, H.; Julian, R. K., Jr.; Runte, K.; Sherman, D.; Wojcik, J.; Zhu, W.; Apweiler, R. Common interchange standards for proteomics data: Public availability of tools and schema. Proteomics 2004, 4 (2), 490-1.
18. Proteomics Standards Initiative. mzML Development, http://www.psidev. info/index.php?q=node/257.
19. Jaitly, N., Monroe, M. E.; Tolić, N., Littlefield, K., Daly, D. S., Adkins, J. N., Anderson, G. A.; Smith, R. D. Open Source Tools for the Accurate Mass and Time (AMT) Tag Proteomics Pipeline. 54th ASMS Conference on Mass Spectrometry, Seattle, WA, 2006.
20. Young, M. M.; Tang, N.; Hempel, J. C.; Oshiro, C. M.; Taylor, E. W.; Kuntz, I. D.; Gibson, B. W.; Dollinger, G. High throughput protein fold identification by using experimental constraints derived from intramolecular cross-links and mass spectrometry. Proc. Natl. Acad. Sci. U.SA. 2000, 97 (11), 5802-6.
21. Kellersberger, K. A.; Yu, E.; Kruppa, G. H.; Young, M. M.; Fabris, D. Top-down characterization of nucleic acids modified by structural probes using high-resolution tandem mass spectrometry and automated data interpretation. Anal. Chem. 2004, 76 (9), 2438-45.
22. Schilling, B.; Row, R. H.; Gibson, B. W.; Guo, X.; Young, M. M. MS2Assign, automated assignment and nomenclature of tandem mass spectra of chemically crosslinked peptides. J. Am. Soc. Mass Spectrom. 2003, 14 (8), 834-50.
23. de Koning, L. J.; Kasper, P. T.; Back, J. W.; Nessen, M. A.; Vanrobaeys, F.; Van Beeumen, J.; Gherardi, E.; de Koster, C. G.; de Jong, L. Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes. FEBS J. 2006, 273 (2), 281-91.
24. Green, N. S.; Reisler, E.; Houk, K. N. Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulers. Protein Sci. 2001, 10 (7), 1293-304.
25. Zhang, Q.; Crosland, E.; Fabris, D. Nested Arg-specific bifunctional crosslinkers for MS-based structural analysis of proteins and protein assemblies. Anal Chim. Acta 2008, 627 (1), 117-28.