Metabolomics Data formats / data sources
Also data formats and sources of inputs and outputs of software should be included.
Contents
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.
- Sashimi, a set of tools for MS
- MS spectre
- Open MS
- massWolf converter
- ReAdW converter
- mzStar converter
- 'Supported' MS devices in mzXML
Software
- MS software list
- MS software list, partly useful?
- Java NetCDF software list
- Java NetCDF library
- XCMS (R-package) pre-processing paper
- MetAlign
- [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) ]
