The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics

Molecular and Cellular Proteomics

Volumn 12, Issue 8, 2013, Pages 2332-2340

  Walzer, Mathias ^a   Qi, Da ^b   Mayer, Gerhard ^c   Uszkoreit, Julian ^c   Eisenacher, Martin ^c   Sachsenberg, Timo ^a   Gonzalez Galarza, Faviel F ^b   Fan, Jun ^d   Bessant, Conrad ^d   Deutsch, Eric W ^e   Reisinger, Florian ^f   Vizcaíno, Juan Antonio ^f   Medina Aunon, J Alberto ^g   Albar, Juan Pablo ^g   Kohlbacher, Oliver ^a   Jones, Andrew R ^a,b  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b UNIVERSITY OF LIVERPOOL   (United Kingdom)

^c RUHR UNIVERSITY BOCHUM   (Germany)

^d CRANFIELD UNIVERSITY   (United Kingdom)

^e INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^f WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^g CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEIN;

ARTICLE; COMPUTER PROGRAM; MASS SPECTROMETRY; METABOLOMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS; STANDARD; PROCEDURES; PROTEIN DATABASE; STANDARDS; THEORETICAL MODEL;

DATABASES, PROTEIN; MASS SPECTROMETRY; MODELS, THEORETICAL; PROTEOMICS; SOFTWARE;

EID: 84881104272     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O113.028506     Document Type: Article

References (23)

1. Taylor, C. F., Paton, N. W., Lilley, K. S., Binz, P.-A., Julian, R. K., 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., and Hermjakob, H. (2007) The minimum information about a proteomics experiment (MIAPE). Nat. Biotechnol. 25, 887-893
2. Orchard, S., Salwinski, L., Kerrien, S., Montecchi-Palazzi, L., Oesterheld, M., Stumpflen, V., Ceol, A., Chatr-Aryamontri, A., Armstrong, J., Woollard, P., Salama, J. J., Moore, S., Wojcik, J., Bader, G. D., Vidal, M., Cusick, M. E., Gerstein, M., Gavin, A.-C., Superti-Furga, G., Greenblatt, J., Bader, J., Uetz, P., Tyers, M., Legrain, P., Fields, S., Mulder, N., Gilson, M., Niepmann, M., Burgoon, L., Rivas, J. D. L., Prieto, C., Perreau, V. M., Hogue, C., Mewes, H.-W., Apweiler, R., Xenarios, I., Eisenberg, D., Cesareni, G., and Hermjakob, H. (2007) The minimum information required for reporting a molecular interaction experiment (MIMIx). Nat. Biotechnol. 25, 894-898
3. Martens, L., Chambers, M., Sturm, M., Kessner, D., Levander, F., Shofstahl, J., Tang, W. H., Römpp, A., Neumann, S., Pizarro, A. D., Montecchi-Palazzi, L., Tasman, N., Coleman, M., Reisinger, F., Souda, P., Hermjakob, H., Binz, P.-A., and Deutsch, E. W. (2011) mzML-A community standard for mass spectrometry data. Mol. Cell. Proteomics 10, R1000133
4. Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O., Siepen, J., Hubbard, S., Selley, J., Searle, B., Shofstahl, J., Seymour, S., Julian, R., Binz, P.-A., Deutsch, E. W., Hermjakob, H., Reisinger, F., Griss, J., Vizcaino, J. A., Chambers, M., Pizarro, A., and Creasy, D. (2012) The mzIdentML data standard for mass spectrometry-based proteomics results. Mol. Cell. Proteomics 11, M1014381
5. Deutsch, E. W., Chambers, M., Neumann, S., Levander, F., Binz, P.-A., Shofstahl, J., Campbell, D. S., Mendoza, L., Ovelleiro, D., Helsens, K., Martens, L., Aebersold, R., Moritz, R. L., and Brusniak, M.-Y. (2012) TraML-A standard format for exchange of selected reaction monitoring transition lists. Mol. Cell. Proteomics 11, R1015040
6. Hermjakob, H., Montecchi-Palazzi, L., Bader, G., Wojcik, J., Salwinski, L., Ceol, A., Moore, S., Orchard, S., Sarkans, U., von Mering, C., Roechert, B., Poux, S., Jung, E., Mersch, H., Kersey, P., Lappe, M., Li, Y., Zeng, R., Rana, D., Nikolski, M., Husi, H., Brun, C., Shanker, K., Grant, S. G. N., Sander, C., Bork, P., Zhu, W., Pandey, A., Brazma, A., Jacq, B., Vidal, M., Sherman, D., Legrain, P., Cesareni, G., Xenarios, I., Eisenberg, D., Steipe, B., Hogue, C., and Apweiler, R. (2004) The HUPO PSI's molecular interaction format-A community standard for the representation of protein interaction data. Nat. Biotechnol. 22, 177-183
7. Gonzalez-Galarza, F. F., Lawless, C., Hubbard, S. J., Hermjakob, H., and Jones, A. R. (2012) A critical appraisal of techniques, software packages and standards for quantitative proteomic analysis. OMICS 16, 431-442
8. Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., Purkayastha, S., Juhasz, P., Martin, S., Bartlet-Jones, M., He, F., Jacobson, A., and Pappin, D. J. (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154-1169
9. Pratt, J. M., Simpson, D. M., Doherty, M. K., Rivers, J., Gaskell, S. J., and Beynon, R. J. (2006) Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat. Protoc. 1, 1029-1043
10. Eisenacher, M., Schnabel, A., and Stephan, C. (2011) Quality meets quantity- quality control, data standards and repositories. Proteomics 11, 1031-1036
11. Vizcaíno, J. A., Martens, L., Hermjakob, H., Julian, R. K., and Paton, N. W. (2007) The PSI formal document process and its implementation on the PSI website. Proteomics 7, 2355-2357
12. Orchard, S., Jones, A., Albar, J.-P., Cho, S. Y., Kwon, K.-H., Lee, C., and Hermjakob, H. (2010) Tackling quantitation: a report on the Annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea. Proteomics 10, 3062-3066
13. Orchard, S., Albar, J. P., Deutsch, E. W., Eisenacher, M., Vizcaíno, J. A., and Hermjakob, H. (2011) Enabling BioSharing-A report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany. Proteomics 11, 4284-4290
14. Orchard, S., Binz, P.-A., Borchers, C., Gilson, M. K., Jones, A. R., Nicola, G., Vizcaino, J. A., Deutsch, E. W., and Hermjakob, H. (2012) Ten years of standardizing proteomic data: a report on the HUPO-PSI Spring Workshop. Proteomics 12, 2767-2772
15. Mayer, G., Montecchi-Palazzi, L., Ovelleiro, D., Jones, A. R., Binz, P.-A., Deutsch, E., Orchard, S., Vizcaíno, J. A., Hermjakob, H., Stephan, C., Meyer, H. E., and Eisenacher, M. (2013) The HUPO Proteomics Standards Initiative-mass spectrometry controlled vocabulary. Database (Oxford) Vol. 2013, doi: 1093/database/bat009
16. Qi, D., Brownridge, P., Beynon, R. J., Xia, D., Mackay, K., Gonzalez, F., Kenyani, J., and Jones, A. R. (2012) A software toolkit and interface for performing stable isotope labelling and top3 quantification using Progenesis LC-MS. OMICS 16, 489-495
17. Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 26, 1367-1372
18. Sturm, M., Bertsch, A., Gropl, C., Hildebrandt, A., Hussong, R., Lange, E., Pfeifer, N., Schulz-Trieglaff, O., Zerck, A., Reinert, K., and Kohlbacher, O. (2008) OpenMS-An open-source software framework for mass spectrometry. BMC Bioinformatics 9, 163
19. Kohlbacher, O., Reinert, K., Gropl, C., Lange, E., Pfeifer, N., Schulz- Trieglaff, O., and Sturm, M. (2007) TOPP-the OpenMS proteomics pipeline. Bioinformatics 23, e191-e197
20. Vizcaíno, J. A., Foster, J. M., and Martens, L. (2010) Proteomics data repositories: providing a safe haven for your data and acting as a springboard for further research. J. Proteomics 73, 2136-2146
21. Vizcaíno, J. A., Côté, R., Reisinger, F., Barsnes, H., Foster, J. M., Rameseder, J., Hermjakob, H., and Martens, L. (2010) The Proteomics Identifications database: 2010 update. Nucleic Acids Res. 38, D736-D742
22. Desiere, F., Deutsch, E. W., King, N. L., NesvizhskIII, A. I., Mallick, P., Eng, J., Chen, S., Eddes, J., Loevenich, S. N., and Aebersold, R. (2006) The PeptideAtlas project. Nucleic Acids Res. 34, D655-D658
23. Bradshaw, R. A., Burlingame, A. L., Carr, S., and Aebersold, R. (2006) Reporting protein identification data: the next generation of guidelines. Mol. Cell. Proteomics 5, 787-788