Posted by: tvasailor | August 28, 2011

Using NIST Search Program with Data Processing and Drawing 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 and structural drawing packages as shown at the bottom of the post.


The NIST software includes a data processing program, AMDIS:

Handouts and YouTubes on Using AMDIS

We use AMDIS, but also use the NIST search with a variety of other data processing programs.  I have included some links with instructions to setting up several of these programs below.

David Sparkman indicated that sometimes problems are noted in transferring spectra from a manufacturer’s data processing to the NIST search for processing.  This can often be fixed by deleting the AUTOIMP.MSD file found in the same directory as the installed NIST search software.  The file will then be created correctly when starting the transfer of the spectrum from the manufacturer’s program to the NIST search.

Interfacing to Manufacturers’ Data Processing and Drawing Programs:

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 is also listed below:

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)


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.

Shimadzu GCMSsolution Software

Shimadzu does not export directly, but by exporting as netCDF file which is then processed using AMDIS and sent to NIST search, see video link

Shimadzu GCMSsolution Software

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 (*.*).

Various Structural Drawing Packages:


Using NIST as Corporate Database/Archive:


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