GCMS data.. Problems in processing? Please help!!!

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

Re: GCMS data.. Problems in processing? Please help!!!

Reply #1 – 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

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

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