Can anyone suggest a workflow, how to evaluate GC-MS data? I would like to make untargeted analysis, but I have some problems with deconvolution algorithms in MassHunter. At the beginning I evaluated every peak manually, but now I wanted to make the process more accurate.
Thank you for your help.
You can try using AMDIS to do a quick analysis of your injections of GC-MS. The AMDIS software is free and very easy to use for deconvolution. I think that automatic algorithms do not seem as good as doing things manually. You tell me how it went if you try with this software. In this link you can find it
http://chemdata.nist.gov/dokuwiki/doku.php?id=chemdata:downloads:start
Good Luck
You may want to try out the free and open source software OpenChrom (http://www.openchrom.net). It is designed for workflows you describe. The newest version can directly read Masshunter GC/MS files (nominal mass MS), you only need to install the Masshunter converter (free) after installation of OpenChrom. Connectors to AMDIS and to NIST MS Search can also be installed as free plug-ins. Files can be batch-processed and saved as files including all conducted processes (peak detection and integration etc.). If you have problems to get started with the software, check out the Wiki pages (https://wiki.openchrom.net/index.php/Main_Page) or contact the OpenChrom team to get assistance.
I hope this helps.
http://www.openchrom.net
https://wiki.openchrom.net/index.php/Main_Page
Dear Dalma,
I´m using MassHunter for analysing my SPME-GC-MS data, too. In my case the deconvolution tool is working very well. It is able to separate 2 volatiles eluting simulaneously with a broad hexanoic acid peak into three distinct well integrated peaks. Have you played around with the deconvolution parameters to get a better separation? One disatvantage of the deconvolution tool is, it needs hours to calculate the peaks for more than 3 chromatograms ot once. But if you let the program calculate over night, it´s fine. Afterwards, I have to check the integrated peaks by hand. If you don´t find the "perfect" deconvolution parameters which are working for each compound perfectly, you have to re-check the peaks always by hand. For evaluation of peak areas, no computer is as well as a human brain. I know, it is the most boring work you could imagine, but I fear there is no way out.
Cheers,
Nadine
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