Re: Find peaks Orbitrap
Reply #1 –
Did you try looking at your mzXML file in for example mzmine to understand what is in your scans? Do your scans only contain the MS1 data? I would guess that they might alternative between the MS1 and MS2 making the data a bit none-sense. The fact that you need msn2xcmsRaw indicate this.
As far as I remember the solution is to add --filter "msLevel 1" in msconvert. Then you shouldn't need msn2xcmsRaw and you can use xcmsSet normally instead of xcmsRaw + findPeaks.
Also I would be a bit concerned about the number of scans over each peak in your MS1 when you do this many MS2's at the same time. It might not be easy to quantify or even finds the peaks if there are very few scans over each peak.
If the data is in fact with very few scans per peak you might have better luck with matchedFilter than with centWave.