MRMaid-DB: A repository of published SRM transitions

Journal of Proteome Research

Volumn 9, Issue 1, 2010, Pages 620-625

  Cham, Jennifer A ^a,b   Bianco, Luca ^a   Barton, Chris ^c   Bessant, Conrad ^a  

^a CRANFIELD UNIVERSITY   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c Quotient Bioresearch Ltd   (United Kingdom)

Author keywords

Biomart; Database; Multiple reaction monitoring (MRM); Selected reaction monitoring (SRM); Web based

Indexed keywords

ARTICLE; COMPUTER PROGRAM; DATA BASE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; INFORMATION SERVICE; MULTIPLE REACTION MONITORING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DETERMINATION; PUBLICATION; QUANTITATIVE ANALYSIS; SCIENTIFIC LITERATURE; SELECTED REACTION MONITORING; TANDEM MASS SPECTROMETRY; TECHNIQUE; VALIDITY;

DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; TANDEM MASS SPECTROMETRY; USER-COMPUTER INTERFACE;

EID: 73649085180     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr900713u     Document Type: Article

References (21)

1. Walsh, G. M.; Lin, S.; Evans, D. M.; Khosrovi-Eghbal, A.; Beavis, R. C.; Kast, J. Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring. J. Proteomics 2009, 72 (5), 838-52.
2. Martin, D. B.; Holzman, T.; May, D.; Peterson, A.; Eastham, A.; Eng, J.; McIntosh, M. MRMer: An interactive open-source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol. Cell. Proteomics 2008, 7 (11), 2270-78.
3. Lange, V.; Malmstrom, J.; Didion, J.; King, N. L.; Johansson, B. P.; Schaefer, J.; Rameseder, J.; Wong, C.-H.; Deutsch, E. W.; Brusniak, M.-Y.; Buehlmann, P.; Bjoerck, L.; Domon, B.; Aebersold, R. Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol. Cell. Proteomics 2008, 7 (8), 1489-1500.
4. Prakash, A.; Tomazela, D. M.; Frewen, B.; MacLean, B.; Merrihew, G.; Peterman, S.; MacCoss, M. J. Expediting the development of targeted SRM assays: using data from shotgun proteomics to automate method development. J. Proteome Res. 2009, 8 (6), 2733-2739.
5. Mead, J. A.; Bianco, L.; Ottone, V.; Barton, C.; Kay, R. G.; Lilley, K. S.; Bond, N. J.; Bessant, C. MRMaid: the web-based tool for designing multiple reaction monitoring (MRM) transitions. Mol. Cell. Proteomics 2009, 8 (4), 696-705.
6. Sherwood, C.; Eastham, A.; Peterson, A.; Eng, J. K.; Shteynberg, D.; Mendoza, L.; Deutsch, E.; Risler, J.; Lee, L. W.; Tasman, N.; Aebersold, R.; Lam, H.; Martin, D. B. MaRiMba: a software application for spectral library-based MRM transition list assembly. J. Proteome Res. 2009, 8 (10), 4396-4405.
7. Picotti, P.; Lam, H.; Campbell, D.; Deutsch, E. W.; Mirzaei, H.; Ranish, J.; Domon, B.; Aebersold, R. A database of mass spectrometric assays for the yeast proteome. Nat. Methods 2008, 5, 913-914.
8. Marzolf, B.; Deutsch, E.; Moss, P.; Campbell, D.; Johnson, M.; Galitski, T. SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinf. 2006, 7 (1), 286.
9. Gerber, S. A.; Rush, J.; Stemman, O.; Kirschner, M. W.; Gygi, S. P. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (12), 6940-6945.
10. Kuhn, E.; Wu, J.; Karl, J.; Liao, H.; Zolg, W.; Guild, B. Quantification of C-reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C-labeled peptide standards. Proteomics 2004, 4, 1175-1186.
11. Zhang, F.; Bartels, M. J.; Stott, W. T. Quantitation of human glutathione S-transferases in complex matrices by liquid chromatography/tandem mass spectrometry with signature peptides. Rapid Commun. Mass Spectrom. 2004, 18, 491-498.
12. Cox, D. M.; Zhong, F.; Du, M.; Duchoslav, E.; Sakuma, T.; McDermott, J. C. Multiple reaction monitoring as a method for identifying protein posttranslational modifications. J. Biomol. Tech. 2005, 16 (2), 83-90.
13. Anderson, L.; Hunter, C. L. Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteomics 2006, 5 (4), 573-588.
14. Stahl-Zeng, J.; Lange, V.; Ossola, R.; Eckhardt, K.; Krek, W.; Aebersold, R.; Domon, B. High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell. Proteomics 2007, 6 (10), 1809-1817.
15. Kay, R. G.; Gregory, B.; Grace, P. B.; Pleasance, S. The application of ultra-performance liquid chromatography/tandem mass spectrometry to the detection and quantitation of apolipoproteins in human serum. Rapid Commun. Mass Spectrom. 2007, 21 (16), 2585-2593.
16. McKay, M. J.; Sherman, J.; Laver, M. T.; Baker, M. S.; Clarke, S. J.; Molloy, M. P. The development of multiple reaction monitoring assays for liver-derived plasma proteins. Proteomics: Clin. Appl. 2007, 1 (12), 1570-1581.
17. Keshishian, H.; Addona, T.; Burgess, M.; Kuhn, E.; Carr, S. A. Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution. Mol. Cell. Proteomics 2007, 6 (12), 2212-2229.
18. Barton, C.; Beck, P.; Kay, R.; Teale, P.; Roberts, J. Multiplexed LC-MS/MS analysis of horse plasma proteins to study doping in sport. Proteomics 2009, 9 (11), 3058-3065.
19. Durinck, S.; Moreau, Y.; Kasprzyk, A.; Davis, S.; De Moor, B.; Brazma, A.; Huber, W. BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 2005, 21 (16), 3439-3440.
20. Côté, R. G.; Jones, P.; Martens, L.; Kerrien, S.; Reisinger, F.; Lin, Q.; Leinonen, R.; Apweiler, R.; Hermjakob, H. The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinf. 2007, 18 (8), 401.
21. Deutsch, E. W.; Brusniak, M.-Y.; Chambers, M. TraML: Transitions Markup Language; 2009.