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?
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.
