combineSpectra of a feature

[Rico Derks]

Hi,

I'am analysing 3 data files with MSMS data. I used centwave for the peak picking and obiwarp for the alignment. I use the function featureSpectra (method closest_rt) to extract the MSMS of a feature. This means for each feature I have 3 MSMS spectra. Below the code I used and an example of 3 MSMS spectra of a feature.

spectra_closest <- xcms::featureSpectra(x = xdata, 
                                        msLevel = 2L, 
                                        return.type = "Spectra",
                                        expandMz = 0.01,
                                        ppm = 100,
                                        method = "closest_rt")

Spectra::plotSpectra(spectra_closest[which(spectra_closest$feature_id == "FT469")])

If I then use the function combineSpectra (from Spectra). I still get the same 3 MSMS spectra.

spectra_closest_combine <- Spectra::combineSpectra(x = spectra_closest,
                                                   FUN = Spectra::combinePeaks, 
                                                   tolerance = 0.025,
                                                   ppm = 100,
                                                   peaks = "union", 
                                                   intensityFun = base::mean, 
                                                   mzFun = base::mean,
                                                   f = spectra_closest$feature_id)

Spectra::plotSpectra(spectra_closest_combine[which(spectra_closest_combine$feature_id == "FT469")])

I'am doing something wrong here?

If I use combineSpectra a second time I get one MSMS spectrum per feature, but it doesn't really that nice.

spectra_closest_combine2 <- Spectra::combineSpectra(x = spectra_closest_combine,
                                                   FUN = Spectra::combinePeaks,
                                                   tolerance = 0.025,
                                                   ppm = 100,
                                                   peaks = "union",
                                                   intensityFun = base::mean,
                                                   mzFun = base::mean,
                                                   f = spectra_closest_combine$feature_id)

Spectra::plotSpectra(spectra_closest_combine2[which(spectra_closest_combine2$feature_id == "FT469")])

Can you help me with this? Why do I need to use the combineSpectra function twice? The intensities are quite off in the last MSMS spectrum compared to the MSMS spectra above?

Cheers, Rico

[Rico Derks]

I just noticed an extra parameter p in combineSpectra. This will give me one spectrum per feature.

spectra_closest_combine <- Spectra::combineSpectra(x = spectra_closest,
                                                   FUN = Spectra::combinePeaks, 
                                                   tolerance = 0.025,
                                                   ppm = 100,
                                                   peaks = "union", 
                                                   intensityFun = base::mean, 
                                                   mzFun = base::mean,
                                                   f = spectra_closest$feature_id,
                                                   p = spectra_closest$feature_id)

Spectra::plotSpectra(spectra_closest_combine[which(spectra_closest_combine$feature_id == "FT469")])

Remains only the problem with the intensities.

Cheers, Rico

[Rico Derks]

Ok, it depends a lot on the settings of ppm and tolerance. I'll close this issue.

[Johannes Rainer]

Thanks for posting also your solution and closing the issue!