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OpenMS
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Converts between different MS file formats.
pot. predecessor tools | → FileConverter → | pot. successor tools |
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GenericWrapper (e.g. for calling external converters) | any tool operating on the output format | |
any vendor software exporting supported formats (e.g. mzML) |
The main use of this tool is to convert data from external sources to the formats used by OpenMS/TOPP. Maybe most importantly, data from MS experiments in a number of different formats can be converted to mzML, the canonical file format used by OpenMS/TOPP for experimental data. (mzML is the PSI approved format and supports traceability of analysis steps.)
Thermo raw files can be converted to mzML using the ThermoRawFileParser provided in the THIRDPARTY folder. On windows, a recent .NET framwork needs to be installed. On linux and mac, the mono runtime needs to be present and accessible via the -NET_executable parameter. The path to the ThermoRawFileParser can be set via the -ThermoRaw_executable option.
For MaxQuant-flavoured mzXML the use of the advanced option '-force_MaxQuant_compatibility' is recommended.
Many different format conversions are supported, and some may be more useful than others. Depending on the file formats involved, information can be lost during conversion, e.g. when converting featureXML to mzData. In such cases a warning is shown.
The input and output file types are determined from the file extensions or from the first few lines of the files. If file type determination is not possible, the input or output file type has to be given explicitly.
Conversion with the same output as input format is supported. In some cases, this can be helpful to remove errors from files (e.g. the index), to update file formats to new versions, or to check whether information is lost upon reading or writing.
Some information about the supported input types: mzML mzXML mzData mgf dta2d dta featureXML consensusXML ms2 fid/XMASS tsv peplist kroenik edta sqmass oms
The command line parameters of this tool are:
INI file documentation of this tool: