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MS (and NMR) data standards in Metabolomics why, how and some caveats

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Presentation help at the Metabolomics Scoiety meeting 2014 in Tsuruoka on netCDF, mzData, mzML and nmrML for Metabolomics

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MS (and NMR) data standards in Metabolomics why, how and some caveats

  1. 1. MS (and NMR) data standards in Metabolomics why, how and some caveats Steffen Neumann Leibniz Institute of Plant Biochemistry ScienceCampus Halle (WCH) June 23, 2014 S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  2. 2. Metabolomics – The Pipeline S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  3. 3. IPB machine Park Data processing from LC-QqTOF-MS: QStar Pulsar i, microTOF Q Bruker Apex (FTICR) HCT Ultra (IT-MS, CID+ETD) Reflex III (Maldi-TOF) Thermo Finnigan Quantum Ultra AM, LCQ Deca XP S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  4. 4. netCDF: Grandfather is still alive netCDF as file format, ANDI-MS as content specification fine for GC/MS and simple LC/MS widely supported in software and programming languages no mix of MS and MS/MS very poor metadata Defined in Standard: “ASTM E1947 – 98(2009) Standard Specification for Analytical Data Inter- change Protocol for Chromatographic Data” available for only $42 S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  5. 5. netCDF in action: I § ¤ 1 dataset_completeness = "C1+C2" ; 2 ms_template_revision = "1.0.1" ; 3 dataset_origin = "PE−SCIEX" ; 4 experiment_date_time_stamp = "20050928190327+0100" ; 5 operator_name = "SYSTEM" ; 6 source_file_reference = "d:tt4_4_1.wiff " ; 7 source_file_format = "PE−SCIEX Wiff version 1" ; 8 experiment_type = "Continuum Mass Spectrum" ; 9 test_separation_type = "Normal Phase Liquid Chromatography" ; 0 test_ms_inlet = "Electrospray Inlet " ; 1 test_ms_inlet_temperature = 20.f ; 2 test_ionization_mode = "Electrospray Ionization" ; 3 test_ionization_polarity = "Positive Polarity " ; 4 test_detector_type = "Electron Multiplier " ; 5 test_resolution_type = "Constant Resolution" ; 6 test_scan_function = "Mass Scan" ; 7 test_scan_direction = "Up" ; 8 test_scan_law = "Linear" ; 9 actual_run_time_length = 3480.54 ; ¦ ¥ S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  6. 6. netCDF in action: II § ¤ 1 2 scan_acquisition_time = 2.00100016593933, 4.00200033187866, 3 6.00100040435791, 8.00100040435791, 10.0040006637573, 12.0020008087158, 4 14.0020008087158, 16.0020008087158, 18.0040016174316, 20.0020008087158, 5 6 total_intensity = 10541, 10640, 10697, 10455, 10707, 10554, 10612, 10434, 7 10738, 10504, 10567, 10646, 10675, 10660, 10676, 10638, 10498, 10581, 8 10655, 10843, 10650, 10703, 10792, 10667, 10564, 10732, 10613, 10766, 9 0 mass_values = 106.0288, 106.038, 106.0564, 106.061, 106.0656, 106.0702, 1 106.0748, 106.0794, 106.0931, 106.9725, 106.9771, 106.9817, 106.9863, 2 106.9909, 106.9955, 107.0001, 107.0047, 107.0094, 107.014, 107.0324, ¦ ¥ S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  7. 7. More metadata in XML: mzData Proteome Standards Initiative Raw / Measurement Data: Mass Spec Equipment Software (Raw) Peaks Isolation windows, collision energies, . . . Vendor Support: Bruker, Applied Biosystems, Kratos Analytical, Matrix Science, . . . “Competitor”: mzXML S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  8. 8. mzData + mzXML = mzML mzData 1.05 mzXML 3.0 mzML 0.90 SFO 2006-05 dataXML 0.6 DC 2006-09 Lyon 2007-04 EBI 2007-06 mzML 0.91 PSI Doc Proc 2007-11 mzML 0.99 RC Toledo 2008-04 mzML 1.0.0 Release! 2008-06 Early Development Final Development mzML 1.1.0RC5 Turku 2009-04 mzML 1.1.0 Release! 2009-06 HUPO-PSI More stable than mzXML Better defined than mzData Reference implementations Early vendor involvement mzML run spectrum spectrumDescription binaryDataArray binaryDataArray • • • precursorList scan spectrumList • • • spectrum spectrum cvList referenceableParamGroupList sampleList acquisitionSettingsList dataProcessingList softwareList instrumentConfigurationList chromatogramList • • • chromatogram chromatogram chromatogram binaryDataArray binaryDataArray S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014 Martens, Chambers, Sturm, Kessner, Levander, Shofstahl, Tang, Römpp, Neumann, Pizarro, Montecchi- Palazzi, Tasman, Coleman, Reisinger, Souda, Hermjakob, Binz, Deutsch. mzML–a community standard for mass spectrometry data. Mol Cell Proteomics. (2011)
  9. 9. mzML in action: I § ¤ 1 <mzML > 2 <cv id="MS" fullName="PSI MS Vocabularies" /> 3 <cv id="UO" fullName="unit" /> 4 5 <fileContent> 6 <cvParam cv="MS" name="MS1 spectrum"/> 7 <cvParam cv="MS" name="MSn spectrum"/> 8 <cvParam cv="MS" name="centroid spectrum"/> 9 </fileContent> 0 1 <sourceFile id="sourceFile" location="C:/MSMSpos15_MM48_1_2−18485.d/analysis.baf"> 2 <cvParam cv="MS" name="Bruker BAF file"/> 3 <cvParam cv="MS" name="SHA−1" value="4ef...7c0"/> 4 </sourceFile> ¦ ¥ S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  10. 10. mzML in action: II § ¤ 1 <software id="exportSoftware" version="3.0.5"> 2 <cvParam cv="MS" name="CompassXport"/> 3 </software> 4 <software id="recalibrationSoftware" version="4.0.234.0"> 5 </software> 6 7 <instrumentConfiguration id="instrument"> 8 <cvParam cv="MS" name="micrOTOF−Q"/> 9 </instrumentConfiguration> 0 1 <dataProcessing id="export"> 2 <processingMethod order="1" softwareRef="instrumentSoftware"> 3 <cvParam cv="MS" accession="MS:1000035" name="peak picking"/> 4 </processingMethod> 5 <processingMethod order="2" softwareRef="recalibrationSoftware"> 6 <cvParam cv="MS" name="m/z calibration"/> 7 </processingMethod> 8 <processingMethod order="3" softwareRef="exportSoftware"> 9 <cvParam cv="MS" name="Conversion to mzML"/> 0 </processingMethod> 1 </dataProcessing> ¦ ¥ S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  11. 11. mzML in action: your data § ¤ 1 <spectrum id="scan=16" > 2 <cvParam cv="MS" name="positive scan"/> 3 <cvParam cv="MS" name="MS2 spectrum"/> 4 <cvParam cv="MS" name="centroid spectrum"/> 5 <precursor> 6 <cvParam cv="MS" name="selected ion m/z" value="542.1" unitName="m/z"/> 7 <activation> 8 <cvParam cv="MS" name="collision energy" value="15.0" unitName="electronvolt"/> 9 <cvParam cv="MS" name="low−energy collision−induced dissociation"/> 0 </ activation > 1 </precursor> 2 <binaryData> 3 <cvParam cv="MS" name="zip compression"/> 4 <cvParam cv="MS" name="m/z array" unitName="m/z"/> 5 <binary>eNrj/luT+KC02sEswyJj5...doaB42HsdAItdCw4=</binary> 6 </binaryDat> 7 <binaryData> 8 <cvParam cv="MS" name="zip compression"/> 9 <cvParam cv="MS" name="intensity array" unitName="counts"/> 0 <binary>eNpjYACCBkcHBjCwhdKWD...gAXvgH4</binary> 1 </binaryDataArray> 2 </spectrum> ¦ ¥ S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  12. 12. www.openms.de Originally for MS-based Proteomics Reads mzData, mzXML, mzML NetCDF (Not on 64bit!) FileInfo, FileConverter, FileFilter, ... plus Calibration, Merge, NoiseFilter, . . . TOPPView Viewer and GUI ⇒ Very useful for preprocessing S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014 M. Sturm, A. Bertsch, C. Gröpl, A. Hildebrandt, R. Hussong, E. Lange, N. Pfeifer, O. Schulz-Trieglaff, A. Zerck, K. Reinert, O. Kohlbacher, 2008. OpenMS – an Open-Source Software Framework for Mass Spectrometry BMC Bioinformatics doi:10.1186/1471-2105-9-163.
  13. 13. http://proteowizard.sourceforge.net/ Originally for MS-based Proteomics cross-platform (MSVC on Windows, gcc on Linux, XCode on OSX) open source (Apache v2) Formats supported on all platforms: mzML, mzXML, MGF Formats supported on Windows with vendor libraries installed: Thermo RAW, Waters RAW, Bruker FID/YEP/BAF msconvert: conversion tool. msdiff: validation of conversion/preprocessing msaccess: command line access:binary data and metadata, EICs & pseudo-2D gel image creation SeeMS: interactive viewer for mass spec data files (Windows only) S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014 Chambers, Maclean, Burke, Amodei, Ruderman, Neumann, Gatto, Fischer, Pratt, Egertson, Hoff, Kessner, Tasman, Shulman, Frewen, Baker, Brusniak, Paulse, Creasy, Flashner, Kani, Moulding, Seymour, Nuwaysir, Lefebvre, Kuhlmann, Roark, Rainer, Gerd, Hemenway, Huhmer, Langridge, Eckels, Connolly, Stearns, Deutsch, Katz, Agus, MacCoss, Tabb, Mallick. A cross-platform toolkit for mass spectrometry and proteomics.
  14. 14. Converters: Notes https://xcmsonline.scripps.edu/docs/fileformats.html Bruker: Calibration requires setting a specific Registry Key: HKEY_CURRENT_USERSoftwareBruker DaltonikCompassXport UseRecalibratedSpectra=1 Waters: No support for calibration in Waters DLL used by msconvert DataBridge writes netCDF only, and writes calibrated data Ancient massWolf requires full MassLynx installed, will use calibrated data, but intermingle LockMass Scans S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  15. 15. Plumbing: libraries for mzML pymzML (Python) http://pymzml.github.io/ jmzML (Java) https://code.google.com/p/jmzml/ OpenMS (C++) https://www.openms.de/ Proteowizard (C++) http://proteowizard.sourceforge.net/ mzR (R/Bioconductor) http://www.bioconductor.org/packages/ release/bioc/html/mzR.html . . . and many more! S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  16. 16. MS and Metabolomics in BioC Collection of biology-related R packages Started back in 2002 Current release: >500 packages! Package Maintainer Title mzR Gatto,me,Fischer parser for netCDF, mzXML, mzData and mzML xcms Ralf Tautenhahn LC/MS and GC/MS Data Analysis MassSpecWavelet Pan Du Mass spectrum processing by wavelet-based algorithms CAMERA Carsten Kuhl Collection of Annotation related MEthods for mass spectRometry dAta Rdisop Steffen Neumann Decomposition of Isotopic Patterns MSnbase Laurent Gatto Base Functions and Classes for MS-based Proteomics iontree Mingshu Cao Data management and analysis of ion trees from ion-trap MS rpubchem Rajarshi Guha Interface to the PubChem Collection KEGGSOAP R. Gentleman client interface to the KEGG SOAP server apComplex D. Scholtens Estimate protein complex membership using AP-MS protein data PROcess X. Li Ciphergen SELDI-TOF Processing simulatorAPMS Tony Chiang Computationally simulates the AP-MS technology. TargetSearch Cuadros-Inostroza et al. analysis of GC-MS metabolite profiling data. flagme Mark Robinson Analysis of Metabolomics GC/MS Data S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014
  17. 17. LC-MS Data preprocessing with XCMS www.bioconductor.org Import: netCDF, mzXML, mzData, mzML Peak detection Peak alignment Peak integration “Differential” metabolites Compatible with all MS instruments at the IPB S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014 Lange, Tautenhahn, Neumann, Gröpl. Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC Bioinformatics (2008)
  18. 18. FTICR Peak Picking Bioconductor Package “MassSpecWavelet” Integration into XCMS: Same Annotation and Identification Same statistics (Same database schema) 380 381 382 383 384 0e+002e+064e+06 a) MS raw spectrum m/z value Intensity b) CWT coefficients m/z value CWTcoefficientscale 380 381 382 383 384 158111723 380 381 382 383 384 0e+002e+064e+06 c) Identified peaks with SNR > 3 m/z value Intensity S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014 Projektarbeit Sebastian Wolf & Michael Gerlich: Du, Kibbe, Lin: Peak Detection of Mass Spectrometry Spec- trum by Continuous Wavelet Transform based Pattern Matching, Bioinformatics (2008)
  19. 19. Plumbing: mzR for MS raw data New in BioC 2.10 (Oct 2011) Joint work Fischer/Gatto/Neumann Conglomerate of former XCMS code, ISB Ramp, Proteowizard via Rcpp Read netCDF, mzXML, mzData, mzML (mz5 soon ?) Read mzIdentML mzQuantML one day ? To become the affyIO of MS data ?! GSoC project 2014 to improve mzR mzR mzRramp mzRpwiz mzRnetCDF S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014 Chambers, Maclean, Burke, Amodei, Ruderman, Neumann, Gatto, Fischer, Pratt, Egertson, Hoff, Kessner, Tasman, Shulman, Frewen, Baker, Brusniak, Paulse, Creasy, Flashner, Kani, Moulding, Seymour, Nuwaysir, Lefebvre, Kuhlmann, Roark, Rainer, Gerd, Hemenway, Huhmer, Langridge, Eckels, Connolly, Stearns, Deutsch, Katz, Agus, MacCoss, Tabb, Mallick. A cross-platform toolkit for mass spectrometry and proteomics.
  20. 20. imzML: imaging mass spectrometry in mzML Huge data files, complex access patterns imzML: same ’ol mzML, but base64 in 2nd data file Some new CV terms faster access 7/8 space reduction lossless mzML imzML http://www.imzml.org ⇒ Open MS imaging software! S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014 Schramm T, Hester A, Klinkert I, Both J-P, Heeren RMA, Brunelle A, Laprévote O, Desbenoit N, Robbe M- F, Stoeckli M, Spengler B, Römpp A (2012) imzML — A common data format for the flexible exchange and processing of mass spectrometry imaging data. J. of Proteomics 10.1016/j.jprot.2012.07.026
  21. 21. mz5: netCDF meets mzML Convert from XML to HDF5 HDF5: big cousin of netCDF Pros: size reduction 54% read/write speed 3–4-fold Fully implemented in pwiz HDF5 API for most languages Cons: Not human-readable Kills emacs and wordpad S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014 mz5: Space- and Time-efficient Storage of Mass Spectrometry Data Sets M. Wilhelm, M. Kirchner, J. Steen, H Steen, MCP 10.1074/mcp.O111.011379
  22. 22. Focus of standards in NMR D2.6Metadata ISAtab D2.4Raw data nmrML Metabolite Identification mzTab Metabolite Quantification mzTab
  23. 23. Capture NMR raw data (equivalent to mzML) Ingredients for nmrML standard: ● XML Schema and controlled vocabulary (CV) ● Examples, converters and validation suite ● COSMOS partners involved: IPB, EMBL-EBI, UB2, UBHAM, UOXF, IMPERIAL, MRC, Mike Wilson (Canada), Matthias Klein (D), Ian Lewis (US) New format: nmrML D2.4Raw data nmrML
  24. 24. github.org as development platform ● Web site with content management http://nmrml.org/ ● Version control system, Issue tracker, activity statistics ● Free for open source projects nmrML infrastructure D2.4Raw data nmrML
  25. 25. ● Controlled vocabulary developed as OWL ontology ● Based on earlier work by MSI, D. Rubtsov and J.Cruz ● ISAtab can leverage ontologies ● With semantic web / RDF / SparQL in mind for later deliverables nmrML Ontology D2.4Raw data nmrML
  26. 26. The need for an open nmr standard nmrML: an XML-based open standard for NMR data storage and exchange NMR data is currently accumulating in local data silos, hindering distribution and secondary data usage. Cross platform NMR data access, integration and comparison is hindered by incompatible vendor formats and the lack of a robust vendor-agnostic NMR data standard. Data in proprietary data formats ages fast, posing the danger of irreproducible data from older studies. An open vendor-neutral storage standard is needed as long-term archival format, if emerging metabolomics repositories are to capture data from all vendor formats in a persistent way, yet supporting the dynamics in this field. To ease format conversions we deliver parsers for Bruker and Varian data formats, which can be incorporated into open NMR processing and analysis software. Parsers Although coverage is good at raw data capture, the XSD and CV will be expanded for better processed data and quantification data. Our standard is accepted by major open source nmr data processing tools and will serve the MetaboLights repository with a stable storage format. Daniel Schober 1, Michael Wilson2, Daniel Jacob3, Annick Moing3, Catherine Deborde3, Luis de Figueiredo4, Kenneth Haug4, Philippe Rocca-Serra5, John Easton6, Christian Ludwig7, Antonio Rosato8, David Wishart2, Christoph Steinbeck4, Reza Salek4, Steffen Neumann1 1Leibniz Institute of Plant Biochemistry, Dept. of Stress and Developmental Biology, Weinberg 3, 06120 Halle, Germany 2Department of Computing/Biological Sciences, University of Alberta, Edmonton, Canada 3INRA, Univ. Bordeaux, Metabolome Facility of Bordeaux Functional Genomics Center, 71 av Edouard Bourlaux, F-33140 Villenave d’Ornon, France 4European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK 5University of Oxford, e-Research Centre, 7 Keble Road, Oxford, OX1 3QG, UK 6School of Electronic, Electrical and Computer Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK 7School of Cancer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK 8Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino (FI), Italy nmrML XML schema excerpt nmrML data example nmrML use cases The COordination of Standards in MetabOlomicS, COSMOS EU consortium has teamed up with the metabolomics standards initiative to create an open exchange and storage format for NMR data. We largely follow design principles already established in the Proteomics Standards Initiative (PSI) for the mzML data standard for mass spectrometry. The standard is composed of an XML schema (nmrML.xsd) and an accompanying controlled vocabulary (nmrCV.owl), which ensures update flexibility and schema robustness by allowing to outsource more variant and dynamic descriptors into the vocabulary which is referenced from within an nmrML file. •Website: http://www.nmrML.org •Github: https://github.com/nmrML/nmrML •nmrML validator: http://msbi.ipb-halle.de/nmrML/index.php •Cosmos: http://www.cosmos-fp7.eu/ •Email: info@nmrml.org •Google Group: https://groups.google.com/forum/?hl=en#!forum/nmrml/join Data from a paper: Farag, M., Porzel, A., Schmidt, J. & Wessjohann, L. Metabolite profiling and fingerprinting of commercial cultivars of Humulus lupulus L. (hop) - a comparision of MS and NMR methods in metabolomics, Metabolomics 8, 492-507, (2012) <nmrML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://nmrml.org/schema ../../../xml-schemata/nmrML.xsd" xmlns="http://nmrml.org/schema" version="1.0.0"> <cvList count="2"> <cv fullName="nmrML Controlled Vocabulary" version="0.0.1" id="NMRCV" URI="http://www.nmrml.org/nmrml-cv.0.0.1.owl"/> <cv fullName="Unit Ontology" version="3.2.0" id="UO" URI="http://unit- ontology.googlecode.com/svn/trunk/uo.owl/"/> </cvList> <contactList> <contact id="ID004" fullname="Lutger A. Wessjohann" email="Ludger.Wessjohann [a] ipb- halle.de"/> <contact id="ID044" fullname="Mohamed A. Farag" email="mfarag73 [a] yahoo.com"/> </contactList> <sourceFileList count="2"> <sourceFile sha1="fd99c095046e2356c7d31154d45353fa79cbc844" location=file:///Users/mike/Projects/nmrML/nmrML/examples/IPB_HopExample/FIDs/FAM013_ AHTM.PROTON_04.fid/procpar id="SOURCE_FILE_0" name="procpar"> <cvTerm cvRef="NMRCV" accession="NMR:1400297" name="Varian VNMR Format"/> <cvTerm cvRef="NMRCV" accession="NMR:1002006" name="acquisition parameter file"/> </sourceFile> <sourceFile sha1="e4ffeb41da28b1e9017e72819252ec6d78f8179f“ location= file:///Users/mike/Projects/nmrML/nmrML/examples/IPB_HopExample/FIDs/FAM013_AHTM.PROTON_04.fid/fi d id="SOURCE_FILE_1" name="fid"> <cvTerm cvRef="NMRCV" accession="NMR:1400297" name="Varian VNMR Format"/> <cvTerm cvRef="NMRCV" accession="NMR:1400119" name="FID file"/> </sourceFile> </sourceFileList> <softwareList count="1"> <software cvRef="NMRCV" accession="NMR:1000277" name="VnmrJ software" version="2.2C" id="SOFTWARE_1"/> </so<instrumentConfigurationList count="4"> <instrumentConfiguration id="INST_CONFIG_1"> <cvTerm cvRef="NMRCV" accession="NMR:1400234" name="Varian NMR instrument"/> <cvTerm cvRef="NMRCV" accession="NMR:1000235" name="Varian probe"/> <cvTerm cvRef="NMRCV" accession="NMR:1400234" name="Varian NMR instrument"/> <cvTerm cvRef="NMRCV" accession="NMR:1000236" name="5mm HCN probe"/> </instrumentConfiguration> </instrumentConfigurationList> <acquisition> <acquisition1D> <acquisitionParameterSet numberOfScans="160" numberOfSteadyStateScans="0"> <sampleAcquisitionTemperature unitName="kelvin" unitCvRef="UO" value="299.15" unitAccession="UO:0000012"/> <spinningRate unitName="hertz" unitCvRef="UO" value="0" unitAccession="UO:0000106"/> <relaxationDelay unitName="second" unitCvRef="UO" value="22.2737024" unitAccession="UO:0000010"/> <pulseSequence/> <DirectDimensionParameterSet numberOfDataPoints="65536" decoupled="false"> <acquisitionNucleus cvRef="NMRCV" accession="NMR:1400151" name="1H"/> <gammaB1PulseFieldStrength unitName="hertz" unitCvRef="UO" value="34482.7586207" unitAccession="UO:0000106"/> <irradiationFrequency unitName="hertz" unitCvRef="UO" value="599.8311617" unitAccession="UO:0000106"/> </DirectDimensionParameterSet> </acquisitionParameterSet> <fidData byteFormat="Complex128" encodedLength="324160" compressed="true">eJwMl4dfzl8Ux7U3lYZKy0qiomQ […]</fidData> </acquisition1D> </acquisition> </nmrML> ftwareList> MetaboLights The nmrML setup We also deliver a content validator which checks a data file is syntactically well formatted, sufficiently complete and that aspects of minimal information requirements like the Core Information for Metabolomics Reporting (CIMR) are met. Validators Outlook Project resources nmrML setup •MetaboLights: http://www.ebi.ac.uk/metabolights/ •MSI: http://msi-workgroups.sourceforge.net/ •CIMR-MI: http://mibbi.sourceforge.net/projects/CIMR.shtml Validation Layer Onion Validation webservice & resultValidation rules (html)
  27. 27. My pleas for the future . . . to the vendors: Please start (or continue!) to support Open Data formats . . . to the computational mass spec community: Please use (and improve!) joint data I/O libraries . . . to YOU (the users): Please start (or continue!) to REQUEST open formats when inviting to bid for a new instrument S. Neumann (IPB-Halle.DE) (Raw) data standards in metabolomics June 23, 2014

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