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Topic: Parameters for HPLC-Q Exactive (Read 281 times) previous topic - next topic

  • MSlady
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Parameters for HPLC-Q Exactive
I am new to XCMS online and have been struggling with finding the best parameters to extract the features from the raw files. The data files I am testing have been acquired by running an HILIC gradient on a HPLC hyphenated to a  Q Exactive (operated in polarity switching mode).

I have tried all the pre-defined parameters available on XCMS online that could apply to my case (UPLC/Q Exactive, and the various HPLC/Orbitrap), besides creating a few or my own. Nevertheless, I invariably receive the following message "There were no features detected in at least one of your samples. Please check feature detection settings and make sure the selected method is applicable for your data."

I would be very grateful for any advice you might have.

Thanks in advance!

  • Jan Stanstrup
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  • Administrator
Re: Parameters for HPLC-Q Exactive
Reply #1
Your problem is probably the polarity switching.
I suggest you try splitting to two files when you do the conversion of your raw data. You should be able to do that with the polarity filter in msconvert.

  • University of Copenhagen, Denmark
Blog: stanstrup.github.io

  • MSlady
  • [*]
Re: Parameters for HPLC-Q Exactive
Reply #2
Thank you for the swift reply, Jan.
For spectra acquired in either just positive or only negative ion mode, would I be able to submit the .raw files directly on XCMS - thus skipping the conversion from .raw to mzXML files?

Many thanks!

  • Jan Stanstrup
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  • Administrator
Re: Parameters for HPLC-Q Exactive
Reply #3
XCMS online faq would suggest yes https://xcmsonline.scripps.edu/docs/fileformats.html.
In XCMS in R you cannot use vendor formats.

I would however be careful with waters files. Whether or not the lockmass correction is applied seems to depends on the version of masslynx and the msconvert version... So since it is unknown how XCMS online converts I would make sure my files are OK converted to mzML and upload that.
  • University of Copenhagen, Denmark
Blog: stanstrup.github.io