Thursday, 22 March 2012

How to integrate mass spectral refenrence libraries into AMDIS

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:
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.

PS. I tried to rename the extention but it did not work in AMDIS
Dear XXX,
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.

Best regards



  1. Hello Jan,

    I am a final year PhD student at The University of Sheffield, England. I am working on improving the metabolome coverage of Chlamydomonas reinhardtii by hyphanated MS based techniques like GC-MS & LC-MS.

    I am using AMDIS & NIST 11 database for my GC-MS analysis. I have GC-EI-Quardrupole-MS (Thermo-finnigan).

    I have used GOLM database before, but I need to format my laptop for some reason so today I went to download GOLM database to again, but I see there were too many libraries available to download.

    Could you please suggest me which one I should download based on above information I have given. I want to cover as many metabolites as possible to improve the metabolome coverage through GC-MS technique.

    I will really appreciate if you could guide me on which library is best suitable in my case which I can integrate with NIST & AMDIS. or else do i have to use more than one library to meet my research requirements.

    Currently I am in my final phases of my PhD, so I will really appreciate if you could help me on this issue.

    Thanking you in advance.

    1. The library files are text files formatted as follows: in the filename "GMD_20111121_VAR5_ALK_MSL.txt ", you have "Golm Metabolome Database_(probably a date)_GC/MS Column Type_Retention Index Standard_Library File Format.txt"

      AMDIS can read the MSL library file format, so you can just pretty much follow the instructions in this here blog post, boy howdy.

      Oh - and thank you for the blog post, this was really helpful. GOLM FOR THE WIN

  2. Hi Jan,

    I have followed the detailed instructions (Thank you!) above and downloaded the Q_LYS_NS library accordingly. I have two questions:

    1) When I saved the library as a .MSL file a .CID file was created, but its size was 0KB - does that make sense?

    2) When you say "Select the new generated file, not the file downloaded from the GMD" you mean the .MSL file? Or the .CID file?

    Thank you,

    1. Hi Rose,
      The .CID file contains only very simple information from the .MSL, basically a list of compound names. It's usually small however 0KB seems a bit dodgy. When importing library into AMDIS you always choose .MSL. Hope it helps.