The HUPO proteomics standards initiativemass spectrometry controlled vocabulary

Database

Volumn 2013, Issue , 2013, Pages

  Mayer, Gerhard ^a   Montecchi Palazzi, Luisa ^b   Ovelleiro, David ^b   Jones, Andrew R ^c   Binz, Pierre Alain ^d   Deutsch, Eric W ^e   Chambers, Matthew ^f   Kallhardt, Marius ^g   Levander, Fredrik ^h   Shofstahl, James ⁱ   Orchard, Sandra ^b   Vizcaíno, Juan Antonio ^b   Hermjakob, Henning ^b   Stephan, Christian ^a,j   Meyer, Helmut E ^a   Eisenacher, Martin ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF LIVERPOOL   (United Kingdom)

^d SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^e INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^f VANDERBILT UNIVERSITY MEDICAL CENTER   (United States)

^g BRUKER DALTONIK GMBH   (Germany)

^h LUND UNIVERSITY   (Sweden)

ⁱ Thermo Fisher Scientific   (United States)

^j KAIROS GMBH   (Germany)

more..

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

ARTICLE; HUMAN; LINGUISTICS; MASS SPECTROMETRY; METABOLISM; PROTEOMICS; STANDARD; STATISTICS; WORKFLOW;

HUMANS; MASS SPECTROMETRY; PROTEOME; PROTEOMICS; REFERENCE STANDARDS; STATISTICS AS TOPIC; VOCABULARY, CONTROLLED; WORKFLOW;

MLCS; MLOWN;

EID: 84879329259     PISSN: 17580463     EISSN: None     Source Type: Journal    
DOI: 10.1093/database/bat009     Document Type: Article

References (39)

1. Yang,Y., Adelstein,S.J. and Kassis,A.I. (2012) Target discovery from data mining approaches. Drug Discov. Today, 17 (Suppl.), S16-S23.
2. Vizcaíno,J.A., Coté,R., Reisinger,F. et al. (2010) The proteomics identifications database: 2010 update. Nucleic Acids Res., 38, D736-D742.
3. Martens,L., Chambers,M., Sturm,M. et al. (2011) mzML - a community standard for mass spectrometry data. Mol. Cell Proteomics, 10, R110000133.
4. Deutsch,E.W., Chambers,M., Neumann,S. et al. (2012) TraML - a standard format for exchange of selected reaction monitoring transition lists. Mol. Cell Proteomics, 11, R111.015040.
5. Holman,S.W., Sims,P.F. and Eyers,C.E. (2012) The use of selected reaction monitoring in quantitative proteomics. Bioanalysis, 4, 1763-1786.
6. Jones,A.R., Eisenacher,M., Mayer,G. et al. (2012) The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell Proteomics, 11, M111.014381.
7. Deutsch,E.W. (2010) The PeptideAtlas project. Methods Mol. Biol., 604, 285-296.
8. Schramm,T., Hester,A., Klinkert,I. et al. (2012) imzML - a common data format for the flexible exchange and processing of mass spectrometry imaging data. J. Proteomics, 75, 5106-5110.
9. Jones,A.R. and Paton,N.W. (2005) An analysis of extensible modelling for functional genomics data. BMC Bioinformatics, 6, 235.
10. Taylor,C.F., Paton,N.W., Lilley,K.S. et al. (2007) The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol., 25, 887-893.
11. Rodriguez,H., Snyder,M., Uhlen,M. et al. (2009) Recommendations from the 2008 International Summit on Proteomics Data Release and Sharing Policy: the Amsterdam principles. J. Proteome Res., 8, 3689-3692.
12. Montecchi-Palazzi,L., Kerrien,S., Reisinger,F. et al. (2009) The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics, 9, 5112-5119.
13. Pearson,W.R. (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol., 132, 185-219.
14. Wilhelm,M., Kirchner,M., Steen,J.A. and Steen,H. (2012) mz5: spaceand time-efficient storage of mass spectrometry data sets. Mol. Cell Proteomics, 11, O111.011379.
15. Orchard,S., Jones,P., Taylor,C. et al. (2007) Proteomic data exchange and storage: the need for common standards and public repositories. Methods Mol. Biol., 367, 261-270.
16. Pedrioli,P.G., Eng,J.K., Hubley,R. et al. (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol., 22, 1459-1466.
17. Day-Richter,J., Harris,M.A., Haendel,M. and Lewis,S. (2007) OBO-Edit - an ontology editor for biologists. Bioinformatics, 23, 2198-2200.
18. Gkoutos,G.V., Schofield,P.N. and Hoehndorf,R. (2012) The Units Ontology: a tool for integrating units of measurement in science. Database (Oxford), 2012, bas033.
19. Gallien,S., Duriez,E. and Domon,B. (2011) Selected reaction monitoring applied to proteomics. J. Mass Spectrom., 46, 298-312.
20. Kiyonami,R. and Domon,B. (2010) Selected reaction monitoring applied to quantitative proteomics. Methods Mol. Biol., 658, 155-166.
21. Geiger,T., Wisniewski,J.R., Cox,J. et al. (2011) Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nat. Protocols, 6, 147-157.
22. Dudoit,S., Shaffer,J.P. and Boldrick,J.C. (2003) Multiple hypothesis testing in microarray experiments. Stat. Sci., 18, 71-103.
23. Scheer,M., Grote,A., Chang,A. et al. (2011) BRENDA, the enzyme information system in 2011. Nucleic Acids Res., 39, D670-D676.
24. Smith,B., Ceusters,W., Klagges,B. et al. (2005) Relations in biomedical ontologies. Genome Biol., 6, R46.
25. Noy,N.F., Shah,N.H., Whetzel,P.L. et al . (2009) BioPortal: ontologies and integrated data resources at the click of a mouse. Nucleic Acids Res., 37, W170-W173.
26. Degtyarenko,K., de Matos,P., Ennis,M. et al . (2008) ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res., 36, D344-D350.
27. Wang,Y., Xiao,J., Suzek,T.O. et al. (2009) PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res., 37, W623-W33.
28. Rocca-Serra,P., Brandizi,M., Maguire,E. et al. (2010) ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level. Bioinformatics, 26, 2354-2356.
29. Jonquet,C., Shah,N.H. and Musen,M.A. (2009) The open biomedical annotator. Summit on Translat. Bioinforma., 2009, 56-60.
30. Jonquet,C., Lependu,P., Falconer,S. et al. (2011) NCBO resource index: ontology-based search and mining of biomedical resources. Web Semant., 9, 316-324.
31. Adamusiak,T., Burdett,T., Kurbatova,N. et al . (2011) OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript. BMC Bioinformatics, 12.
32. Ferry-Dumazet,H., Gil,L., Deborde,C. et al. (2011) MeRy-B: a web knowledgebase for the storage, visualization, analysis and annotation of plant NMR metabolomic profiles. BMC Plant Biol., 11, 104.
33. Plumb,R.S., Johnson,K.A., Rainville,P. et al. (2006) UPLC/MSE; a new approach for generating molecular fragment information for biomarker structure elucidation (vol 20, pg 1989, 2006). Rapid Commun. Mass Spectrom., 20, 2234-2234.
34. Holcapek,M., Jirasko,R. and Lisa,M. (2012) Recent developments in liquid chromatography-mass spectrometry and related techniques. J. Chromatogr. A, 1259, 3-15.
35. Yang,S.J., Nie,A.Y., Zhang,L. et al. (2012) A novel quantitative proteomics workflow by isobaric terminal labeling. J. Proteomics, 75, 5797-5806.
36. Roepstorff,P. (2012) Mass spectrometry based proteomics, background, status and future needs. Protein Cell, 3, 641-647.
37. Koek,M.M., Jellema,R.H., van der Greef,J. et al. (2011) Quantitative metabolomics based on gas chromatography mass spectrometry: status and perspectives. Metabolomics, 7, 307-328.
38. Sansone,S.A., Fan,T., Goodacre,R. et al. (2007) The metabolomics standards initiative. Nat. Biotechnol., 25, 846-848.
39. Zhang,A., Sun,H., Wang,P. et al. (2012) Modern analytical techniques in metabolomics analysis. Analyst, 137, 293-300.