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1
Other / Tandem MS/MS .d files and Proteowizard
Hi Everyone,

I am trying to convert Agilent .d files to .mzXML files using ProteoWizard (for eventual use in xcms).  When viewing the .d files in SeeMS, the MS Level column only contains '2' data.  When converting the files to .mzXML with MSConvert and using in xcms, I receive errors that there is no MS1 data.  Does anyone have experience reading .d files obtained with tandem MS/MS with the ProteoWizard set of tools?  When viewing the chromatograms in MassHunter, precursor ions are clearly distinguished from fragments, so I am not sure why the Proteowizard tools fail to recognize the MS1 scans. 

Thanks.
2
XCMS / fillPeaks error: subscript out of bounds
Hi everyone,

Has anyone encountered the following error?

Error in buf[bufidx[imz[1]:imz[2]], iret[1]:iret[2],drop=FALSE]: subscript out of bounds
In addition: warning message:
In FUN(X[[1L]],...):
(corrected) retention time vector length mismatch for file

The previous steps seemed to work well (xset<-xcmsSet(mslevel=2);xset1<-group(xset);xset2<-retcor(xset1);xset3<-group(xset2);xset4<-fillPeaks(xset3))

Thanks.