qcML: An exchange format for quality control metrics from mass spectrometry experiments

Molecular and Cellular Proteomics

Volumn 13, Issue 8, 2014, Pages 1905-1913

  Walzer, Mathias ^a   Pernas, Lucia Espona ^b   Nasso, Sara ^b,c   Bittremieux, Wout ^d   Nahnsen, Sven ^a   Kelchtermans, Pieter ^e,f,g   Pichler, Peter ^h,i   Van Den Toorn, Henk W P ^j,k   Staes, An ^e,f   Vandenbussche, Jonathan ^e,f   Mazanek, Michael ^h,i   Taus, Thomas ^h,i   Scheltema, Richard A ^l   Kelstrup, Christian D ^m   Gatto, Laurent ⁿ   Van Breukelen, Bas ^j,k   Aiche, Stephan ^o   Valkenborg, Dirk ^d,g,p   Laukens, Kris ^d   Lilley, Kathryn S ⁿ   Olsen, Jesper V ^m   Heck, Albert J R ^j,k   Mechtler, Karl ^h,i   Aebersold, Ruedi ^b,c   Gevaert, Kris ^e,f   Vizcaíno, Juan Antonio ^q   Hermjakob, Henning ^q   Kohlbacher, Oliver ^a   Martens, Lennart ^e,f   more..

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b ETH ZURICH   (Switzerland)

^c UNIVERSITY OF ZURICH   (Switzerland)

^d UNIVERSITY OF ANTWERP   (Belgium)

^e DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^f GHENT UNIVERSITY   (Belgium)

^g FLEMISH INSTITUTE FOR TECHNOLOGICAL RESEARCH VITO   (Belgium)

^h RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

ⁱ INSTITUTE OF MOLECULAR BIOTECHNOLOGY   (Austria)

^j UTRECHT UNIVERSITY   (Netherlands)

^k NETHERLANDS PROTEOMICS CENTRE   (Netherlands)

^l MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^m University of Copenhagen   (Denmark)

ⁿ UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^o FREIE UNIVERSITÄT BERLIN   (Germany)

^p HASSELT UNIVERSITY   (Belgium)

^q EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; LINGUISTICS; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEOMICS; QUALITY CONTROL; COMPUTER LANGUAGE; PROTEIN DATABASE; STANDARDS;

DATABASES, PROTEIN; MASS SPECTROMETRY; PROGRAMMING LANGUAGES; PROTEOMICS; QUALITY CONTROL; SOFTWARE;

EID: 84903728943     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M113.035907     Document Type: Article

References (34)

1. Martens, L., Vizcaíno, J. A., and Banks, R. (2011) Quality control in proteomics. Proteomics 11, 1015-1016
2. Martens, L. (2013) Bringing proteomics into the clinic: the need for the field to finally take itself seriously. Proteomics 7, 388-391
3. 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: April 12-14th, 2012, San Diego, U.S.A. Proteomics 12, 2767-2772
4. Bell, A. W., Deutsch, E. W., Au, C. E., Kearney, R. E., Beavis, R., Sechi, S., Nilsson, T., Bergeron, J. J. M., and HUPO Test Sample Working Group. (2009) A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat. Methods 6, 423-430
5. Foster, J. M., Degroeve, S., Gatto, L., Visser, M., Wang, R., Griss, J., Apweiler, R., and Martens, L. (2011) A posteriori quality control for the curation and reuse of public proteomics data. Proteomics 11, 2182-2194
6. Ivanov, A. R., Colangelo, C. M., Dufresne, C. P., Friedman, D. B., Lilley, K. S., Mechtler, K., Phinney, B. S., Rose, K. L., Rudnick, P. A., Searle, B. C., Shaffer, S. A., and Weintraub, S. T. (2013) Interlaboratory studies and initiatives developing standards for proteomics. Proteomics 13, 904-909
7. Flikka, K., Martens, L., Vandekerckhove, J., Gevaert, K., and Eidhammer, I. (2006) Improving the reliability and throughput of mass spectrometrybased proteomics by spectrum quality filtering. Proteomics 6, 2086-2094
8. Rudnick, P. A., Clauser, K. R., Kilpatrick, L. E., Tchekhovskoi, D. V., Neta, P., Blonder, N., Billheimer, D. D., Blackman, R. K., Bunk, D. M., Cardasis, H. L., Ham, A.-J. L., Jaffe, J. D., Kinsinger, C. R., Mesri, M., Neubert, T. A., Schilling, B., Tabb, D. L., Tegeler, T. J., Vega-Montoto, L., Variyath, A. M., Wang, M., Wang, P., Whiteaker, J. R., Zimmerman, L. J., Carr, S. A., Fisher, S. J., Gibson, B. W., Paulovich, A. G., Regnier, F. E., Rodriguez, H., Spiegelman, C., Tempst, P., Liebler, D. C., and Stein, S. E. (2010) Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol. Cell. Proteomics 9, 225-241
9. Ma, Z.-Q., Polzin, K. O., Dasari, S., Chambers, M. C., Schilling, B., Gibson, B. W., Tran, B. Q., Vega-Montoto, L., Liebler, D. C., and Tabb, D. L. (2012) QuaMeter: multivendor performance metrics for LC-MS/MS pro-teomics instrumentation. Anal. Chem. 84, 5845-5850
10. Taylor, R. M., Dance, J., Taylor, R. J., and Prince, J. T. (2013) Metriculator: quality assessment for mass spectrometry-based proteomics. Bioinformatics, 29, 2948-2949
11. Teleman, J., Waldemarson, S., Malmström, J., and Levander, F. (2013) Automated quality control system for LC-SRM setups. J. Proteomics, 10.1016/j.jprot. 2013.03.029
12. Sandin, M., Teleman, J., Malmström, J., and Levander, F. (2013) Data processing methods and quality control strategies for label-free LC-MS protein quantification. Biochim. Biophys. Acta, 10.1016/j.bbapap. 2013.03.026
13. Pichler, P., Mazanek, M., Dusberger, F., Weilnböck, L., Huber, C. G., Stingl, C., Luider, T. M., Straube, W. L., Köcher, T., and Mechtler, K. (2012) SIMPATIQCO: a server-based software suite which facilitates monitoring the time course of LC-MS performance metrics on orbitrap instruments. J. Proteome Res. 11, 5540-5547
14. Tabb, D. L. (2013) Quality assessment for clinical proteomics. Clin. Biochem. 46, 411-420
15. Sutton, J., Richmond, T., Shi, X., Athanas, M., Ptak, C., Gerszten, R., and Bonilla, L. (2008) Performance characteristics of an FT MS-based workflow for label-free differential MS analysis of human plasma: standards, reproducibility, targeted feature investigation, and application to a model of controlled myocardial infarction. Proteomics - Clin. Appl. 2, 862-881 (Pubitemid 351943767)
16. 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, R110.000133
17. Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O., Siepen, J., Hubbard, S. J., Selley, J. N., Searle, B. C., Shofstahl, J., Seymour, S. L., 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, 10.1074/mcp.M111.014381
18. 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, 10.1074/mcp.R111.015040
19. Walzer, M., Qi, D., Mayer, G., Uszkoreit, J., Eisenacher, M., Sachsenberg, T., Gonzalez-Galarza, F. F., Fan, J., Bessant, C., Deutsch, E. W., Reisinger, F., Vizcaino, J. A., Medina-Aunon, J. A., Albar, J. P., Kohlbacher, O., and Jones, A. R. (2013) The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics. Mol. Cell. Proteomics, mcp.O113.028506
20. Côté, R., Reisinger, F., Martens, L., Barsnes, H., Vizcaino, J. A., and Hermjakob, H. (2010) The ontology lookup service: bigger and better. Nucleic Acids Res. 38, W155-W160
21. Sturm, M., Bertsch, A., Gröpl, 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
22. Montecchi-Palazzi, L., Kerrien, S., Reisinger, F., Aranda, B., Jones, A. R., Martens, L., and Hermjakob, H. (2009) The PSI semantic validator: a framework to check MIAPE compliance of proteomics data. Proteomics 9, 5112-5119
23. Stephan, C., Kohl, M., Turewicz, M., Podwojski, K., Meyer, H. E., and Eisenacher, M. (2010) Using laboratory information management systems as central part of a proteomics data workflow. Proteomics 10, 1230-1249
24. Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L. J., Eilbeck, K., Ireland, A., Mungall, C. J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S.-A., Scheuermann, R. H., Shah, N., Whetzel, P. L., and Lewis, S. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25, 1251-1255 (Pubitemid 350076511)
25. Mayer, G., Jones, A. R., Binz, P.-A., Deutsch, E. W., Orchard, S., Montec-chi- Palazzi, L., Vizcaíno, J. A., Hermjakob, H., Oveillero, D., Julian, R., Stephan, C., Meyer, H. E., and Eisenacher, M. Controlled vocabularies and ontologies in proteomics: overview, principles and practice. Biochim. Biophys. Acta 1844, 98-107
26. Mayer, G., Montecchi-Palazzi, L., Ovelleiro, D., Jones, A. R., Binz, P.-A., Deutsch, E. W., Chambers, M., Kallhardt, M., Levander, F., Shofstahl, J., Orchard, S., Antonio Vizcaino, J., Hermjakob, H., Stephan, C., Meyer, H. E., and Eisenacher, M. (2013) The HUPO proteomics standards initiative-mass spectrometry controlled vocabulary. Database J. Biol. Databases Curation 2013, 10.1093/database/bat009
27. Gkoutos, G. V., Schofield, P. N., and Hoehndorf, R. (2012) The units ontology: a tool for integrating units of measurement in science. Database 2012, bas033-bas033
28. Kohlbacher, O., Reinert, K., Gröpl, C., Lange, E., Pfeifer, N., Schulz-Trieglaff, O., and Sturm, M. (2007) TOPP-the OpenMS proteomics pipeline. Bioinformatics 23, e191-e197
29. Berthold, M. R., Cebron, N., Dill, F., Gabriel, T. R., Kötter, T., Meinl, T., Ohl, P., Sieb, C., Thiel, K., and Wiswedel, B. (2007) KNIME: the konstanz information miner. In Studies in classification, data analysis, and knowledge organization. (GfKL 2007). Springer, 2007
30. De la Garza, L., Krüger, J., Schärfe, C., Röttig, M., Aiche, S., Reinert, K., and Kohlbacher, O. (2013) From the desktop to the grid: conversion of KNIME Workflows to gUSE. Proc. 5th Int. Work. Sci. Gateways 993, 9
31. Helsens, K., Colaert, N., Barsnes, H., Muth, T., Flikka, K., Staes, A., Timmerman, E., Wortelkamp, S., Sickmann, A., Vandekerckhove, J., Gevaert, K., and Martens, L. (2010) ms-lims, a simple yet powerful open source laboratory information management system for MS-driven proteomics. Proteomics 10, 1261-1264
32. Staes, A., Van Damme, P., Helsens, K., Demol, H., Vandekerckhove, J., and Gevaert, K. (2008) Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC). Proteomics, 8, 1362-1370 (Pubitemid 351518548)
33. Craig, R., and Beavis, R. C. (2004) TANDEM: matching proteins with tandem mass spectra. Bioinformatics, 20, 1466-1467 (Pubitemid 38931421)
34. Boutet, E., Lieberherr, D., Tognolli, M., Schneider, M., and Bairoch, A. (2007) Uniprotkb/swiss-prot. In Plant bioinformatics (pp. 89-112). Humana Press.