m/z sort assumption violated

January 05, 2015, 09:09:53 AM

Hi,

I have the same problem as many people have had, and I found posts relevant to this topic but was not able to get the code to work. So I have HILIC UPLC-MS data. I tried running xcms but received this error saying that m/z sort assumption was violated. I tried running the following code but I got no output and no .CDF files were corrected; can you please advise me on what I should do next:

## Notes: This program will check the m/z vector for a single file for sort violation
## If a sort violation is found the m/z vector is reorganised along with the Intensity
## vector. Finally a new CDF file is made which is fixed.
## !!!NB!!! : Parallel version does not report progress

require(xcms)
checkAllcdfs<-function(Ftype="mzXML", nSlaves=1){
AllCDFs<-list.files(recursive=TRUE, pattern=Ftype, ignore.case=TRUE, full.names=TRUE)
if(nSlaves >1){
if(require(snow)){
cl <- makeCluster(nSlaves, type = "SOCK")
}
clusterEvalQ(cl, library(xcms))
unlist(clusterApply(cl, AllCDFs, checkCDFfile))
stopCluster(cl)
} else{
sapply(AllCDFs, checkCDFfile)
cat("n")
}
}

checkCDFfile<-function(file, type=".mzXML"){
cat("n")
cat(paste("Loading File:", file, sep=""))
xr<-xcmsRaw(file, profstep=0)
for(i in 1:length(xr@scanindex)){
scan<-getScan(xr, scan=i)
if(is.unsorted(scan[,"mz"]) == TRUE){
cat(" x ")
newfile<-sub(type, "-Fixed.mzdata", file, ignore.case=TRUE)
write.mzdata(xr, newfile)
file.copy(file, sub(type, ".OLD", file, ignore.case=TRUE))
unlink(file)
rm(list=ls())
gc()
return(1)
}
if(i == length(xr@scanindex)){
cat(" O ")
rm(list=ls())
gc()
return(0)
}
}
}

Re: m/z sort assumption violated

Reply #1 – January 05, 2015, 01:56:18 PM

Basically I can get this code to work for correcting individual .CDF files, but how can I loop this code through all of my .CDF files?

> xr<-xcmsRaw("mh141210xg2_sccs_00101.CDF", profstep=0)
> write.mzdata(xr, file="mh141210xg2_sccs_00101.CDF")

Thanks so much for your help!
-Majda

Re: m/z sort assumption violated

Reply #2 – April 01, 2016, 06:35:00 AM

Hi,

There is now an automatic fix in https://github.com/sneumann/xcms/tree/f ... assumption
which I'll pull into a Bioconductor version after the next release in April.

Yours,
Steffen