Metabolomics Society Forum

Hi all,

I am trying to run MSConvert with R, but I got 127 error. What could be the problem?

msconvert <- "C:/Program Files (x86)/ProteoWizard/ProteoWizard 3.0.21175.5b6d9afee/msconvert.exe"
file <- "C:/Users/Desktop/Data/QC1.raw"
outfile <- "C:/Users/Desktop/Data"
convert <- paste0(msconvert," --mzXML, -o outfile -v", file)
system(convert)

Thanks for your help.

Does it work in the GUI?
You at least need a space after "-v" for that to work.

Take a look at the example here: https://gitlab.com/stanstrup-work/snippets/-/blob/master/ms%20data%20conversion/msconvert_par.R

That will convert multiple files in parallel.