We run different samples (Plasma, serum, and tissue extraction samples on GCxGC with chromatof and like to translate data in open format for data analysis purpose with different software to see the broader range of metabolomics data. We want to do this because NIST library has some kind of limitation to analyze the metabolamic data. Could you please help me if you have the answer. Thank you.I really appreciate.
Hello Ram,
Please use Proteowizard's MS Convert Tool for free: http://proteowizard.sourceforge.net/downloads.shtml and with the ".data format (your instrument-specific version)" tab activated. Using this you can convert the .data format to most software readable .mzXML; .mzML; .cdf formats which then can be used for all kind of down stream analyses such as mzMINE (http://mzmine.github.io/), or say Mass++ (http://www.shimadzu.co.jp/aboutus/ms_r/archive/en/index.html) where both can read any common file formats from GC-MS systems. Also, Mass++ can read directly from your .data formats and can convert to .mzXML files. Typically this would work.
Also on your platform specific file for your MS/MS instrument you MUST find a file convert option allowing you to go from .data to .cdf or .netcdf (which is fine for NIST DB to recognize) or .ASCII etc. But then, still you need to go to ProteoWizard to go from .cdf to .mzXML (most popular and recommended) or mzML to use for further analysis. You can easily consult the Tech Support of your instrument vendor to ask them to get the right file conversion tool (plugin or patch installed off-site).
Instead, also go to AMDIS Download page (free from NIST, USA!): http://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:amdis and AMDIS can recognize many vendor-specific file formats and then the data can be directly submitted to NIST or Fiehn Library or Golm DB matching!
"OpenMS/ OpenChrome" though free bit tricky and messy with having to download a lot of add-ins or plugins to make things would also work in a step wise manner.
If you are a Linux fan, then MASSyPup64 from Dr. Robert Winkler (http://www.lababi.bioprocess.org/index.php/14-sample-data-articles/78-massypup) is what you may go to!
Further, all freely available tools, software, and databases from 2014-2015 for your analyses have also been recently summarized/ reviewed by us at Updates in metabolomics tools and resources: 2014–2015 (http://onlinelibrary.wiley.com/doi/10.1002/elps.201500417/abstract), please check out the Table-1 and find your tools!!! : )
Hope it helps a little bit!
Thanks a lot,
Biswa
Thank you Biswa I'll try this and let you know.
I really appreciate your help.
Have a nice day.
Ram
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