Friday, 11 May 2012

How to import the GMD refenrence library into NIST MS Search

I got this question asked today and thought this is worth be documented. I only have version 2.0 of the NIST ms search software at hand, but I assume that the way to import the reference library is pretty similar in later versions.
  1. Start the program.
  2. Click Librarian on the tab control at the bottom.
  3. Create a library by clicking the most right button in the toolbar.
  4. Type an appropriate library name - "GMD".
  5. Close the dialog by clicking OK. The click on the Import button, left in the toolbar.
  6. Select the msp-file downloaded from the GMD. Make sure to first select "All files" in the file type menu.
  7. In the option check "include Synonyms" Click "Import All".
  8. The import is starting.
  9. You can cancel the library matching process.
  10.  The GMD reference library is imported and ready for use.


  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. Dear Rahul,
      Thank you very much for using the Golm Metabolome Database!
      The files available for download on the GMD download page are identical with respect to metabolites and spectra. However, they differ in the given retention index (combination between two differernt column polarities and retention index markers based either on alcanes or fames). Last but not least, the exported files differ in the file formats. For the NIST MS-Search software please use one of the downloads tagged as File-type 'MSP' and choose the the chromatography variant most similar to the GC-system utilised in your laboratory.

      Best regards!