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I am analyzing data from 908 devices - zipchip data - from Thermo. I converted the .raw files to centroid mode using msconvert. I am able to use xcms to to untargeted analysis on the files but sometimes the peaks are not getting integrated, but when I plot the EICs, I see the peaks. This is my code:
datapath <- "path/to/mzml files"
datafiles_list <- list.files(datapath, recursive = FALSE, full.names = TRUE, pattern = ".mzML")
raw_data <- readMsExperiment(datafiles_list)
# I set a range for filtering things because I am looking for certain compounds within a window
RT1 <- ((min(std_mz_list$RT))*60) - 120
RT2 <- ((max(std_mz_list$RT))*60) + 120
if (RT1 <= 0) {
RT1 <- min(raw_data@spectra@backend@spectraData$rtime)
}
raw_data_filt <- filterRt(raw_data, rt = c(RT1, RT2))
cwp_zipchip_lowppm <- CentWaveParam(peakwidth = c(1, 20), ppm = 20, mzdiff = 0.002,
snthresh = 10, noise = 1000, prefilter = c(2,400),
verboseBetaColumns = TRUE)
raw_data_processed <- findChromPeaks(raw_data_filt, param = cwp_zipchip, BPPARAM = param)
mpp <- MergeNeighboringPeaksParam(expandRt = 2, minProp = 0.8)
raw_data_processed_mp <- refineChromPeaks(raw_data_processed, mpp)
### plotting chromatograms for certain files
# I filtered for the 8 files I am interested in:
raw_data_processed2_mp_filt <- filterFile(raw_data_processed2_mp, file = c(grep("R1", datafiles_list),
grep("R4", datafiles_list)))
# I then extracted the chromatograms
chr_glycine <- chromatogram(raw_data_processed2_mp_filt,
mz = c( 76.0355, 76.0431), # 50 ppm
rt = c(200, 300),
BPPARAM = param)
plot(chr_glycine[[5]]) # this shows a peak thats integrated
plot(chr_glycine[[6]]) # this shows a peak thats not integrated
Please let me know if there is something I am doing thats wrong.
Hi,
I am analyzing data from 908 devices - zipchip data - from Thermo. I converted the .raw files to centroid mode using msconvert. I am able to use xcms to to untargeted analysis on the files but sometimes the peaks are not getting integrated, but when I plot the EICs, I see the peaks. This is my code:
Please let me know if there is something I am doing thats wrong.
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