Problem with peakpicking when multiple scan ranges are used during acquisition November 18, 2016, 04:13:25 AM 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 Quote Selected
Re: Problem with peakpicking when multiple scan ranges are used during acquisition Reply #1 – March 02, 2017, 09:58:05 AM 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. Quote Selected
Re: Problem with peakpicking when multiple scan ranges are used during acquisition Reply #2 – May 04, 2017, 01:35:26 AM Thank you for your answer, spliting the file into two ranges was a good option.Best regards. Quote Selected