I am performing LCMS/MS analysis of rat liver tissue. Output files are in .mzxml format. I am trying to analyze these files in XCMS (offline software) using R programming language but I am not able to make a correct path when uploading these files.
You should first verify the structure of the file; i.e., its format. Ensure that the format is understood by you, and importable by R. As for path, if you mean from one machine to another, such as over a network, an network administrator should be able to give you exact answers, and get you quickly on your way. If by path you mean that the analysing equipment is not connected to the internet, then you need to find alternative means, like floppy disk or thumb drive, etc.
Hi, a good easy to use tool for LS-MSMS is http://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp
if you are/know an advanced R user, that is the way to go
http://www.bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcmsMSn.pdf
http://www.bioconductor.org/packages/release/bioc/vignettes/mzR/inst/doc/mzR.pdf
http://nppns.fcfrp.usp.br/workshop_data/data/probmetab_newV03.pdf
Chandra,
Laurent Gatto is one of the great proponents of the use of R in the analysis of MS data. He has written this recent review article:
Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):42-51. doi: 10.1016/j.bbapap.2013.04.032. Epub 2013 May 18.
Using R and Bioconductor for proteomics data analysis.
(also interesting, if it is not proteomics data you are looking at). You might also want to look up other work that he has published.
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