How to get MS spectrum from features extracted with findChromPeaks ?
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@julienkermorvant-23634
Last seen 9 months ago

Hello,

I'm trying to create a GC-MS database of standard by using XCMS. I'm using findChromPeaks (with centWave method) to search for my standard peak followed by refineChromPeaks and groupChromPeaks.

I can get the value of each feature with featureValues, but I would like to get the mz (or mz range) corresponding to each of these features in order to build my standard spectrum.

Best regards, Julien

xcms • 120 views
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Johannes Rainer ★ 1.9k
@johannes-rainer-6987
Last seen 5 days ago
Italy

Have a look at what featureDefinitions returns you - you will get a DataFrame. In columns "mzmed", "mzmin" and "mzmax" you'll have the median m/z value and the range (calculated from all chromatographic peaks assigned to that feature).

Alternatively, you could get the m/z of each individual feature in each individual file by using featureValues function with parameter value = "mz"". This parameter lets you choose which column from the chromPeaks matrix should be returned.

Hope this helps.

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Thank you Joahnnes.

That's exactly what I needed.

Best regards, Julien