XCMS in R

August 21, 2019, 10:51:48 PM

Hello,

I'm new using LCMS to identify venom profiles. I'm trying to visualize and analyze data in R using XCMS. I have tried with this code to read rawdata
cdffiles <-list.files("~/LCMS/cdf/Dave", recursive=T, full=T)
xrms<-readMSData(cdffiles, mode = "onDisk", centroid= TRUE)

but I have got this error
No MS 1 data present.

Then when I tried this code to create xcmsSet object, I received a similar error
Error in readRawData(fileName(object), includeMSn = includeMSn) :
No MS1 data found in file C:/Users/jc554411/Documents/LCMS/cdf/Dave/A13.mzXML!

I export the data from the LCMS 2020 SHIDMAZU.

Can someone help me?

Thanks,

Linda

Re: XCMS in R

Reply #1 – August 22, 2019, 03:04:30 AM

Quadrupole instruments sometimes save data as chromatograms and not spectra.
You can try converting your original files with msconvert from Proteowizard and add: --simAsSpectra --srmAsSpectra