Using NIST Search Program with Vendors’ Programs

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NIST has greatly facilitated the utilization of the NIST Version 2 library search software package with a wide variety of  other vendors' data processing packages as shown below.

I have developed FREE classes to show the identification of unknowns with NIST search by EI and MS/MS (tandem) spectra:

Free Classes NIST Search

Manufacturers’ Instructions for Interfacing:

As I mentioned above, the program can be easily interfaced to an instrument manufacturer’s data system.  I have included below a simple descripition that I wrote and a more detailed one from David Sparkman, a NIST contractor.


Also specific information for commercial mass spec data systems are listed below:

Shimadzu GCMSsolution Software

The advanced options of the NIST search and AMDIS deconvolution software are available to users via an add-in to the GCMSsolution software.  This is very well documented in their Shimadzu AMDIS Deconvolution "Quick Operation Guide" (Appendix 3, pp 48-51) available upon request from Shimadzu.

See some screenshots from the Guide in the following link

Link to Screehshots from Shimadzu manual  

This enables options in the NIST software such as:

  • Powerful deconvolution of complex GC/MS chromatograms
  • Searching up to 127 libraries in a combined search
  • e.g. , the combined library of NIST and Wiley (>1.1 million total spectra) can be searched in ~ 2 seconds
  • Assignment and use of extensive GC retention indices
  • Searching libraries for model compounds by similar and exact structure
  • Using MS Interpreter to explain EI fragmentation patterns for both user and commercial library spectra
  • Advanced hybrid EI search which greatly extends the standard EI search for unknown characterization

I still think their users would appreciate an approach of sending directly to NIST search as I have proposed.

Proposed Direct Send to NIST Search

There are two other approaches:  1)  Convert a Shimadzu GC-MS data(i.e. .qgd) to .mzData and import the .mzData file to NIST MS Search without going through AMDIS  2)  Import mzData  into AMDIS, switching file type to "All Files (*.*).

See Shimadzu Video

JEOL/Mass Mountaineer


Agilent ChemStation:
NIST Manual (Appendix 2, p 72-74)
Iowa State Users' Guide

Agilent MassHunter:

Thermo Xcalibur (Nominal Mass):
NIST_User Manual (Appendix 4, pg. 78)

Thermo FreeStyle (Accurate Mass, D. Sparkman):
NIST_Thermo_FreeStyle Brief

Thermo Trace Finder (Accurate Mass, Deconvolution)

Waters MassLynx:

I occasionally had problems getting MassLynx to work, see attached fix:

Agilent LC-MSD software:

ACD Software:


Wsearch: This program exports spectra to NIST search and supports many different file formats.

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