I have metabolite data aquired on newly launch q-exactive orbitrap from Thermo. Can I use this data for analysis on XC MS online?
Yes, of course.
You can use the Orbitrap parameter set.
Thank you very much for your reply. I have metabolite data of differnet developmental stages of tissue, aquired on biological duplicate and analytical triplicate. Is this sufficient for statistical analysis? could you let me know how many (minimum) anlytical and biological replicates is acceptable for publication? Sorry to bother you with questions.
You might be interested in reading:
Standard reporting requirements for biological samples in metabolomics experiments: mammalian/in vivo experiments: http://www.springerlink.com/content/x8l4h4903t1m8058/ (http://www.springerlink.com/content/x8l4h4903t1m8058/)
Proposed minimum reporting standards for data analysis in metabolomics: http://www.springerlink.com/content/jj702j370k701128/ (http://www.springerlink.com/content/jj702j370k701128/)
and more here: http://scholar.google.dk/scholar?q=meta ... as_sdtp=on (http://scholar.google.dk/scholar?q=metabolomics+minimum+requirements&hl=en&btnG=Search&as_sdt=1%2C5&as_sdtp=on)
I just created a UPLC/Q-Exactive parameter set. [s:2z1xhi8d]It seems that it is beneficial to use 30-40 ppm for centWave feature detection with Q-Exactive data.[/s:2z1xhi8d]
EDIT: There was a problem with the converter that is fixed now. See here. (http://https://xcmsonline.scripps.edu/docs/fileformats.html)
Dear Dr. Ralf,
Can I use XC MS online for data acquired on Q Exactive orbitrap in + and -ve mode simultaneously (on Q exactive we can acquire data in positive and negative mode at a time). Please let me know how do analysis of untargeted metabolomics data in positive and negative mode at a time.
Best regards,
Yashwant
Yes it would be possible, although it is not implemented at the moment.
XCMS can split up the file in its negative and positive mode spectra and then analyse the resulting files separately.
Maybe you can give me access to one of those files so I can use it for testing.
All,
I have the same problem. I have acquired my metabolomic datas on a UPLC-Q-excative in positive and negative mode simultenaously. I have converted datas to .cdf.
I use the xcms package. There is no nothing in the polarity column.
Otherwise, I don't know if my datas are in centroid or profile.
Someone have solutions?
Thanks!