Metabolomics Society Forum

Software => R => XCMS => Topic started by: rahulkapoore on December 06, 2012, 04:06:05 PM

Title: GCMS data.. Problems in processing? Please help!!!
Post by: rahulkapoore on December 06, 2012, 04:06:05 PM
Hello there,

I have a GC-MS data from Thermo finnigaan quardrupole instrument in Xcalibur format. I have managed to convert the data to MZXML format. However I am confused which files to upload in Dataset 1 & 2. I have 3 Biological replicates. Within each Biological replicate I have 4 different conditions & for each condition I have 3 technical replicates. Could you please assist me in how to divide this data,  when it comes to uploading the data in 2 data sets in XCMS. Other query is, what parameters should I select for above instrument. I want to do Peak alignment, normalisation of my data with internal standard. So finally I want to compare the differences between 4 conditions that I have kept in my experiment. I want to see how metabolites concentration have changed across all 4 conditions. Is it possible to easily trace those metabolites which are showing drastic changes across 4 conditions. Can you suggest any better way to analyse data of this type using XCMS.

Many thanks in advance
Title: Re: GCMS data.. Problems in processing? Please help!!!
Post by: carlos on April 25, 2013, 11:19:54 AM
Hi!

I'm also starting to use xcms for GCMS data, and browsing in the forum I bumped into someone recommending this thread in the old forum:
https://groups.google.com/forum/?fromgr ... OPu70yYTnM (https://groups.google.com/forum/?fromgroups=#!topic/xcms/gOPu70yYTnM)

It has a lot of useful information and code snippets. Also, there is another package for processing GCMS data that uses AMDIS:
http://www.bioconductor.org/packages/2. ... lagme.html (http://www.bioconductor.org/packages/2.11/bioc/html/flagme.html)

Because apparently using xcms for GCMS data can be tricky, due to the EI fragmentation. If you found other parameters or if you have some tips on GCMS data processing, I would really appreciate some help.

Hope this helps,


Carlos