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Messages - majah

1
XCMS / Re: m/z sort assumption violated
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
2
XCMS / m/z sort assumption violated
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)
      }
  }
}
3
XCMS Online / Re: Parameters: Cannot Extract Particular Mass
Hi,

it has been a while since I posted. I just have a quick question regarding the "minPtsAboveBaseLine" option, and if it is available for tweaking in the online XCMS version at this time? This is important for some features I would like to be able to extract using XCMS.

Thank you!

Majda
9
XCMS Online / Re: XCMS peak picking
Yup, that is what I used and I don't believe it is oversaturated. I am having this issue with some of our masses of interest not being extracted but they are when I use Mass Lynx. I don't understand XCMS well enough yet to be able to "intelligently" tweak parameters, but I have tried playing with them..but still nothing in terms of getting the masses I am interested in.
10
XCMS Online / Re: Parameters: Cannot Extract Particular Mass
Hi Paul,

I played with parameters and set s/n=5, but still nothing, I cannot get the mass to come through in XCMS. The peak looks normal, yes!
That particular mass has relatively abundant counts in 30% of samples. So it really should be coming through.

I really don't know what other parameters to tweak so that I can get it to come through? Any suggestions?

Thank you so much for your help!

Majda
12
XCMS Online / Re: XCMS peak picking
Hi Ralf,

sorry I never saw that you posted this reply back in May. I am still having the same issue with a mass not being extracted in XCMS but it does come through using Mass Lynx.

The instrument we are using is UPLC-ESI-QTOFMS. Can you tell me please what XCMS parameters you think I should try to tweak in order for cotinine to come through?

THank you very much!

Majda
13
XCMS Online / Stored Datasets Error
Hello,

I am trying to use some stored datasets for a new job I am creating, but only when I click on Data 1 "select stored dataset" does it show me my stored datasets. Data 2 shows that I have no stored datasets--is this a bug?

Thank you.
Majda
14
XCMS Online / Re: Parameters: Cannot Extract Particular Mass
Hi Paul,

Thanks so much for your reply, and your answer definitely helps.

My parameters are already set so that I can capture as much stuff as possible. When I use Marker Lynx, my ion comes through. So if I were to change signal/noise threshold (which is currently set at 10) what do you suggest I put it at?

Thank you very much!

Majda