Hello,
I had a problem of contaminant ions on my Q-Exactive, so I used a new full-MS instrumental with 2 scan ranges (50-123 and 123.2-750).
However, when I process my files with XCMS, there are no ions with m/z < 123 in the final peak table.
I tryied to directly process the RAW files or to convert the files in mzxml but the result is the same.
Would you have any advice ?
Thanks in advance.
stangd
What happens if you split the file into two mass ranges using MSconvert? Using the subset filter.
Also I seem to remember that the Qex sometimes does something strange with the data file: it will label one scan as "full scan" and the other as "SIM". You can check that when going through the scans in Xcalibur. If that's the problem, there is a way to get your data into mz(X)ML correctly, I would have to look it up though.
Thank you for your answer, spliting the file into two ranges was a good option.
Best regards.