Recently, I got this question on how to import GMD mass spectral reference libraries into the Automated Mass Spectral Deconvolution and Identification System (AMDIS). As I think this might be interesting for other people as well, I copy the question and my answer below:
Hi,I am XXX in YYY lab at ZZZ university. I have just downloaded the following library GMD_20111121_VAR5_ALK_MSL.txt from Golm Metabolome DB. Because I would like to use it AMDIS software.
However, the extension file of the library is in TXT and I need to converte it to MSL. I will appreciate a lot if you could tel me how to do it.XXX
PS. I tried to rename the extention but it did not work in AMDIS
Thank you very much for using the Golm Metabolome Database (GMD).
Please use the Amdis software to convert the downloaded file into a library. I try to list all necessary steps in the following
- Open Amdis :)
- Click Library ==> Build One Library (this option is only available if a data file is open)
- Click Files
- Click Load Library Select the file downloaded from the GMD, you might need to change file type to "all files *.*" to see your file with file extension .txt
- The import is now starting and as a result you should see a list of 2,594 imported spectra
- Click Files
- Click "Save Library As"
- Give a appropriate file location and name and use the file extension msl The file is now exported and a ".cid" file (compound identification library) is generated, this is a crucial step
- Click Exit to close the Library Window
- Click Analyse ==> Analyse GC/MS Data...
- Click Target Library
- Select Page "Libr."
- Select "Target Compounds Library"
- Click "Select New"
- Select the new generated file, not the file downloaded from the GMD Click Save Click Run
If you any problem with the library please don't hesitate to drop me a line.
Your feedback is highly appreciated.