Metabolomics Data formats / data sources

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Also data formats and sources of inputs and outputs of software should be included.

UMC Utrecht (WKZ)

Machine Vendor Manufacturer software Default output format Conversion software Conversion output formats
UPLC Waters Masslynx .RAW directory Wolf *.mzXML, *.cdf
QTOF Waters Masslynx .RAW directory Wolf *.mzXML, *.cdf
GC-TOF Thermo Scientific XCalibur .RAW file XConvert, ReAdW *.dat, *.ms, *.spa, *.raw, *.cdf, *.txt, *.mzXML
GC-MS Thermo Scientific XCalibur .RAW file XConvert, ReAdW *.dat, *.ms, *.spa, *.raw, *.cdf, *.txt, *.mzXML
GC-MS Agilent/HP Masshunter .d directory Trapper(?), mzStar (now mzWiff, beta) *.mzXML
LC-MS Waters Masslynx .RAW directory Wolf *.mzXML, *.cdf

Wageningen (PRI)

Machine Vendor Manufacturer software Default output format Conversion software Conversion output formats
GC-MS (TOF) Leco chromaTOF peg (pegasus) NetCDF
GC-MS (Quadrupool, SPME) Interscience XCalibur .raw NetCDF
GC-MS (Quadrupool) HP (Agilent) HPchemstation .D
LC-MS (TOF, Ultima) Waters (micromass) Masslynx V 4.0 Masslynx (.raw files) MetAlign netcdf

Wageningen (WU)

Machine Vendor Manufacturer software Default output format Conversion software Conversion output formats
NMR

Leiden

Machine Vendor Manufacturer software Default output format Conversion software Conversion output formats
LTQ-FT Thermo Scientific XCalibur .RAW file XConvert *.dat, *.cdf, *.txt
LTQ-Oribtrap Thermo Scientific XCalibur .RAW file XConvert *.dat, *.cdf, *.txt
LTQ Thermo Scientific XCalibur .RAW file XConvert *.dat, *.cdf, *.txt
TSQ Thermo Scientific XCalibur .RAW file XConvert *.dat, *.cdf, *.txt
DECA Thermo Scientific XCalibur .RAW file XConvert *.dat, *.cdf, *.txt
UPLC Thermo Scientific XCalibur
UPLC Agilent Chemstation
QTOF Applied BioSystems Analyst QS .wiff file File Translator *.cdf
GC-TOF Waters Masslynx .RAW directory
micrOTOF Bruker Hystar .d directory DataAnalysis *.cdf, *.txt
CE Agilent Chemstation .d file Chemstation *.cdf

TNO

Machine Vendor Manufacturer software Default output format Conversion software Conversion output formats
LTQ Thermo Scientific XCalibur .RAW file XConvert *.dat, *.cdf, *.txt
LTQ-FT Thermo Scientific XCalibur .RAW file XConvert *.dat, *.cdf, *.txt
LTQ-Oribtrap Thermo Scientific XCalibur .RAW file XConvert *.dat, *.cdf, *.txt
GC-MS LECO Chromatof .peg file Chromatof *.netcdf
GC-MS Agilent Chemstation .d file Chemstation *.netcdf


Data formats

Information about mzXML, mzData and mzML (new format/standard) can be found on the Mass spectrometry data formats wiki and can be found on the Proteome center wiki.

CMLSpect, an XML vocabulary for spectral data. Paper about CMLSpect can be read here.

Software


  • [http://proteowizard.sourceforge.net/download.html msconvert: general data format conversion tool. Writes mzML or mzXML. Currently reads mzML, mzXML, Thermo RAW (Windows), with more vendor formats in the near future. msdiff: comparison of two data files, for validation of conversion and preprocessing

msaccess: command line access to mass spec data files, including spectrum binary data and metadata, selected ion chromatograms, and pseudo-2D gel image creation mspicture: command line pseudo-2D gel image creation SeeMS: interactive viewer for mass spec data files (Windows only, download zip archive above)

mscat: exports data from a variety of formats into 4 column text format (Raw supported on Windows only) txt2mzml: converts data from 4 column format to mzML(Raw supported on Windows only) ]