Manual Peak Processing Parameter

MetaboAnalyst
1

Hi everyone,

Currently I am processing .mzML LC-MS/MS data to detect mammalian serum metabolomics.

Since auto-optimized parameter sets with OptiLCMS failed to capture the peak of internal standard, I would like to manually fine-tune peak processing parameter sets in XCMS for R package, following the vignette here.

Does my plan make sense? If it does, I would appreciate your advise on which parameter(s) to adjust. Currently there is very poor peaks detected around the theoretical m/z, even if the metabolite is known to be very abundant in mammalian serum.

My current parameter is:

cwp <- CentWaveParam(snthresh = 50,
                      noise = 2000,
                      ppm = 2,
                      prefilter = c(3, 300),
                      peakwidth = c(10, 50))

PeakDensityParam(sampleGroups = sampleData(pos_chr)$sample_type,
                        minFraction = 0.4, bw = 10, ppm = 3)

Here is my current analytical environment:
R version 4.4.2 (2024-10-31)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.2.1

xcms_4.4.0
MsExperiment_1.8.0
Spectra_1.16.1

Thank you for your attention!