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Title: Viewing mzXML files on MAC
Post by: willpoway on April 15, 2012, 09:35:23 AM

I need to find freeware application to view mzxml files (TICS, XICS, MS) for lcms data from MassLynx (Qtof) on MAC.

Thanks

Title: Re: Viewing mzXML files on MAC
Post by: Jan Stanstrup on April 15, 2012, 12:28:41 PM

How about http://http://mzmine.sourceforge.net? You of course need to convert the waters' raw files first. But beware that there are some issues with that: http://http://metabolomics-forum.com/viewtopic.php?f=25&t=191

Title: Re: Viewing mzXML files on MAC
Post by: hpbenton on April 16, 2012, 10:19:52 AM

Any of the open source programs will open up the mzXML, including xcms (note not xcms online). There is a list of softwares here:
http://masspec.scripps.edu/metabo_scien ... stools.php (http://masspec.scripps.edu/metabo_science/dataanalysistools.php)
I would also add openMS to this list. http://open-ms.sourceforge.net/ (http://open-ms.sourceforge.net/)

If you use xcms the command in R would be something like the following:

Code: [Select]

xr<-xcmsRaw("C:/Folder With my data/Name of my file.mzXML")
plotSurf(xr)
plotTIC(xr)
plotEIC(xr, m=c(200.1,200.2)

If you check out the xcms forum and look at the FAQ's there is some example code to do some overlays and other cool plots. :)

Metabolomics Society Forum

Software => XCMS Online => Topic started by: willpoway on April 15, 2012, 09:35:23 AM