PhenoMeNal is a powerful package. I'd like to apply it to my research data. Unluckily, I was stuck in the beginning. The data I collected was from SCIEX triple tof. It's in .wiff data format. However, the Ramid package can only deal with netcdf data format. Is it still possible to read mass spectra correctly from LC-MS raw data after concerting the data format?
Many thanks for answering my question!
Luojiao Huang Thank you for choosing Ramid. We still have implemented in PnenoMeNal one of the earliest versions of Ramid, now we have much more advanced version, but it still deals with netcdf format and was checked for GC-MS data. However we continue developing it and our next step is adapting it to mzML format and LC-MS. I think it will be available soon. Probably if you change the format of your data to netcdf it will work with your data now, but we did not check it. The new version is available at https://github.com/seliv55/ramidcor/tree/develop, in the file 'R/ramidwin.R', but we still need to update documentation for it. If you can send me some examples of your data I can check how Ramid works with them. If you send netcdf files I can check now, for mzML I need to extend the functionality, which will take some time.
Thank you, Vitaly! We decide to change our data format into netcdf first. And then check how Ramid works in this new version. We will keep you updated. Vitaly Selivanov
There is a free tool MSConvert that runs on Windows that will convert most MS file types into open formats. You might try that.
You can convert the wiff file to netcdf and then should be able to process the data. We do that for matlab processing of LC MS data obtained from Sciex MS.
Luke V Schneider Thanks for the answer. We have tried to use MSconvert, it doesn't have the output of netcdf format. We are still searching for some possible tools.
Hi Navid Jubaer , thanks for the answer. Do you have any good tools to convert wiff file to netcdf?
Hi, This is a very interesting and relevant question for the entire research community working in metabolomics. Please feel free to register (for free to create a login with your Email ID!) and join the International Metabolomics Society’s Forum: http://www.metabolomics-forum.com/index.php?action=forum;?action=forum#c12 to ask more specific questions any software, database, approach and platform (mass spectrometry, NMR) issues where you can get very specific responses from expert users and researchers! Thanks again, Biswa
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