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XCMS / Direct infusion peak detection - keeping low intensity peaks
Problem: When I use xcmsSet(x, method="MSW") I lose the low intensity peaks.
Question: How do I retain low intensity peaks, can I generate an xcmsSet object with direct infusion data without using method = "MSW" for m/z peak detection?
Elaboration: I acquire data using an Orbitrap Exactive by DIRECT INFUSION. Using xcmsRaw() I can create an xcmsRaw object from either profile or centroided data. Using getSpec() or getScan I can get a txt spectra/average spectra that contains the low intensity peaks of interest. However I want to work with an xcmsSet object to allow peak grouping and deisotoping with CAMERA. I don't know how to go from an xcmsRaw object to an xcmsSet object so in order to get a xcmsSet object I start over using xcmsSet. For direct infusion data this requires using method="MSW" otherwise I get a 'no peaks found' error. After xcmsSet(x, method="MSW"), reviewing the peaks by peaks() I see that the low intensity ions have been removed. I have used numerous different scale parameter settings from 1,1,5 to 1,20,40 as well as changing the nearbyPeak to T, winSize.noise, snthr, peakThr, amp.Th and still lose these peaks.
In short, using xcmsRaw i retain peaks, but I want to work with an xcmsSet object however everything I have tried has failed to retain the low intensity peaks.
Suggestions for parameters of xcmsSet that will retain low intensity ions for direct infusion would be very helpful indeed.
Kind regards,
Nick