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The NIST 11 Mass Spectral Library
(NIST11/2011/EPA/NIH) (previously NIST 08/NIST08/2008)

Notice to licensed NIST 11 users
  • A free 2012 update to the MS/MS sub-library can be shipped upon request if you have an older 2011 CD.
  • Please register to receive e-mail notifications when future updates to your NIST and/or Wiley MS libraries are available.
> Search NIST Compounds Online
Figure: EI spectra, structure, and corresponding data for a sample compound in the NIST database.

Four-page brochure of NIST 08 (PDF)

One-page NIST 11 bruchure (PDF)

--The fully-evaluated, most widely used mass spectral reference library. Compiled by the National Institute of Standards and Technology (NIST).

Summary: The NIST 11 mass spectral database, the successor to the NIST 08, is a fully evaluated collection of electron ionization (EI) mass spectra. It also contains a growing set of MS/MS spectra and GC data. It is the product of more than two decade, comprehensive evaluation and expansion of the world's most widely used mass spectral reference library by a team of experienced mass spectrometrists in which each spectrum was examined for correctness.

NIST 11 Components

NIST 11 is not just a mass spectral library. It contains these components:

  • (UPDATED) Electron ionization (EI) mass spectral library - 243,893 carefully evaluated spectra of 212,961 unique compounds, with identifications, nearly all with chemical structures. You may search names of NIST compounds online.
  • (UPDATED) MS/MS library - 10,065 ion trap spectra for 9,194 different ions of 4,628 compounds, and 85,344 collision cell spectra (qtof and tandem quad) spectra for 7,172 different ions of 3,877 compounds. (Also available separately, as the NIST MS/MS Database.)
  • (UPDATED) Gas Chromatography (GC) data library - 346,757 Kovats retention index values for 70,835 compounds (38,648 in the EI library), covering both polar and non-polar columns. Includes retention indices with GC column conditions and literature citations. (Also available separately, as the NIST GC Database.)
  • (UPDATED) NIST MS Search software - software for searching (identifying) compounds from their mass spectra and for browsing mass spectral libraries. Also includes MS interpretation programs for analyzing mass spectra on the basis of chemical structure, molecular formula, isotopic patterns, and more.
  • (UPDATED) AMDIS software - software for deconvoluting gas/liquid chromatograms
  • (UPDATED) Documentation - Approximately 50 page printed and electronic manual on setup and basic usage. Additional information is in the help files.

Libraries are formatted the binary format suitable for use alone or by the NIST MS Search software (and AMDIS). Additional instrument-specific formats (e.g. Agilent ChemStation and MassHunter) are available separately to permit library searching directly within your GC/MS or LC/MS data system.

With each purchase, we ship a CD (installs software, libraries, and documentation) and a printed manual.

Online Search (NIST)

To check for compounds in the NIST library, you may search names of compounds online.

Summary Statistics

Statistics for NIST 11 and earlier versions are given below.

  NIST 11 NIST 08 NIST 05 NIST 02
EI Spectral Library:
Number of EI Spectra
243,893(*) 220,460(*)
(with separable collection of 717 spectra of 672 salts)
190,825(*) 174,948
Number of Unique Compounds 212,961 192,108 163,198 147,198
Kovats Retention Index 346,757 index values for 70,838 compounds (38,648 in the EI library) 224,038 index values for 44,008 compounds (21,847 in the EI library), now on both polar and non-polar columns. 121,112 index values for 25,893 compounds (12,452 in the EI Library), on only non-polar columns. NONE
MS/MS Library 95,409 spectra (10,065 ion trap spectra of 9,194 different ions of 4,628 compounds; 85,344 collision cell spectra (qtof and tandem quad) of 7,172 different ions of 3,877 compounds)[#] (121,586 spectra in 2012 update) 14,802 spectra of 5,308 precursor ions (3,898 cations and 1,410 anions). 5,191 spectra of 1,943 different ions (1,671 positive and 341 negative) NONE
NIST MS Search software v. 2.0g (2011-05) v. 2.0f (2008-08) v. 2.0d (2005-04) v. 2.0a (2002-07)
AMDIS software v. 2.70 (2011-05) v. 2.65 (2006-12) v. 2.62 (2005-03) v. 2.1 (2002-07)
Release Date June 2011 August 2008 June 2005 July 2002

(*) plus quality improvements

See also What's New in NIST 11.

Electron Ionization (EI) mass spectral library - NIST 08

Note: the following description reflects NIST 08 (see What's New in NIST 11 for more recent changes).

This is a "fully evaluated" collection of electron ionization (EI) mass spectra. It is the product of a more than two decade, comprehensive evaluation and expansion of the world's most widely used mass spectral reference library by a team of experienced mass spectrometrists in which each spectrum was examined for correctness. This has lead to thousands of selections, deletions and modifications to produce an optimal reference library of compound identification by spectrum matching and library searching. Each spectrum has been carefully evaluated, and all decisions regarding selection or deletion were made only after agreement of two experienced mass spectral evaluators, as described in presentations at major conferences. While computer methods assisted in finding chemical identification errors and inconsistencies, and revealed certain varieties of mass spectral errors, manual interpretation was the principal basis for this evaluation effort.

The Electron Ionization (EI) mass spectral library consists of 220,460 spectra of 192,108 unique compounds, each with related data and (nearly always) chemical structure.

Besides spectra, typical data include name, formula, molecular structure (.mol), molecular weight, CAS number, contributor name, list of peaks, synonyms, and estimated retention index.

Name: 1-Decanol
Formula: C10H22O
MW: 158 CAS#: 112-30-1 NIST#: 227969 ID#: 17833 DB: mainlib
Contributor: Japan AIST/NIMC Database- Spectrum MS-NW-4441
10 largest peaks: 
55 999 |43 988 |56903 |70894 |41776 |
69 725 |83 549 |57462 |84397 |42371 |
1.Decyl alcohol
4.n-Decyl alcohol
5.Alcohol C10
6.Alfol 10
7.Capric alcohol
8.Caprinic alcohol
...22 other names...

Estimated non-polar retention index (n-alkane scale): 
Value: 1258 iu
Confidence interval (Alcohols):  41(50%) 176(95%) iu

The NIST EI Library focuses on:

  • Drugs, metabolites, and poisons,
  • Pesticides and fungicides,
  • Organics present in soil, water and air,
  • Aminoacids, di- & tri-peptides,
  • Common sample contaminants,
  • Common analytical derivatives of the above

Here is a breakdown by mass:

The best quality spectra are placed in the Main Library; and good-quality, alternate spectra are provided in the Selected Replicates Library.

NIST 08 includes a separable collection of 717 spectra of 672 salts and low-volatile substances not expected to be measurable by GC/MS (nist_salts). Here's a breakdown by mass:

To check whether certain compounds or classes of compounds exist within the NIST 08 database, you may do an online search of compounds in the NIST 08 database.

NIST spectra have been obtained from thousands of sources. Major sources include

# Spectra, Name
29410 A.A.Kutin, Moscow, Russia
28787 Zaikin V.G., Borisov R.S., L.N.Kulikova, TIPS RAS / RPFU / Russian
..... Friendship University / Topchiev Inst.Petrochem.Synth., Moscow, Russia
26548 Chemical Concepts
13336 Japan National Institute of Advanced Industrial Science and Technology
..... (AIST) / National Institute of Materials and Chemical Research (NIMC)
..... Database- Spectrum MS-IW-1026/MS-NW-9250
9594  NIST Mass Spectrometry Data Center
7657  Div. of Experiment Therapeutics, Walter Reed Army Institute of Research
..... (WRAIR), Washington DC
5586  National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK),
..... National Institutes of Health (NIH), Bethesda, MD
4163  A.T.Lebedev, Moscow State University
2683  ASES Database, Dalian Institute, P.R. China
2376  Carl Djerassi, Dept. Chemistry, Standford University, Stanford Calif.
2360  Asinex Ltd, Moscow, Russia
2205  D.Henneberg, Max-Planck Institute, Mulheim, Germany
2182  Institute of Organic Chemistry, Novosibirsk, Russia
1789  A.Mazepa, Phys.-Chem.Institute, Odessa, Ukraine
1528  Humboldt-Universitat zu Berlin, Department of Chemistry, Analytical Group
1481  A.Pleshkova, Nesmeyanov Inst.Org.Elem.Cpds, Moscow
1091  Organic Synthesis Lab, MSU, Moscow
1066  William W. Christie, Mylnefield Lipid Analysis, Invergowrie, Dundee,
....  Scotland, UK

MS/MS Library

Note: the following description reflects NIST 08 (see What's New in NIST 11 for more recent changes). The MS/MS Library can also now be purchased separately if you'd like the MS/MS data only.

Most of the MS/MS spectra have been measured on ion trap and collision cell instruments using electrospray ionization, although spectra from a number of other instrument types and ionization methods are represented. Spectra have been provided by contributors, measured at NIST and extracted from the literature. In view of the relatively small size of the library, it is intended primarily to serve as a 'starter set'. It also documents spectrum variations between instruments classes at different conditions. We have found that at sufficiently high signal-to-noise measurement conditions, modern instruments are capable of providing very reproducible, library searchable spectra. While collision energy can be an important variable, spectra varies in an understandable way depending on compound and instrument class and conditions. This Library is provided in formats equivalent to the Electron Ionization Library but with new fields added to describe the instrument and analysis conditions. A small number of MS1 spectra are also included for reference purposes. These generally contain the ions used for MS/MS.

The search software permits the examination of all MS/MS spectra - these are available as a selectable library, with the name 'nist_msms'. A new MS/MS tab has been added to the MS Search Software to view that data.

Figure: MS/MS search tab in NIST11. Spectra organized by positive/negative charge, mass, compound name, and conditions.

Further information on the MS/MS sub-library (some of this is from the 2008 and 2011 versions but is still useful):

Gas Chromatography (GC) Data Library

Tip: You probably have heard of the NIST MS Database. But have you heard of the NIST GC Database? The GC Database is also available separately at very low cost, so you can provide it to each of your chemists to run on their desktops.

Gas phase retention data for compounds common to the EI and NIST Retention Data collection are provided with links to the EI library. This involves 192,108 Kovacs indices and corresponding GC column conditions and literature citations for 21,847 compounds, an increase of over 50% from the previous version. Data include both non-polar and polar columns. Most values were abstracted from the open literature and then compared to replicate values (average of 10 per compound) and estimates to find and remove errors. We also continue to provide estimates of retention indices for most compounds in the library using an extension of a method developed earlier for boiling points [2-3].

GC data includes

  • Column
  • Type
  • Stationary phase
  • Dimensions
  • Support (for packed)
  • Temperature
  • Carrier gas
  • Retention index
  • Reference Citation

Here's typical GC data included for a compounds (decanol):

Estimated non-polar retention index (n-alkane scale): 
Value: 1258 iu
Confidence interval (Alcohols):  41(50%) 176(95%) iu

Retention index 
1. Value: 1256 iu
Column Type: Capillary
Column Class: Standard non-polar
Active Phase: CP-Sil PONA GB
Column Length: 100 m
Carrier Gas: He
Column Diameter: 0.25 mm
Phase Thickness: 0.25 um
Data Type: Linear RI
Program Type: Ramp
Start T: 140 C
End T: 230 C
Heat Rate: 5 K/min
Start Time: 10 min
End Time: 25 min
Source: Cunicao, M.M.; Lopes, A.R.; Ccco, L.C.; Yamamoto, C.I.;
Plocharski, R.C.B.; Miguel, M.D.; Junior, A.G.; Auer, C.G.; Miguel,
O.G., Phytochemical and antibacterial evaluation of essential oils
from Ottonia Martiana Miq. (Piperaceae), J. Braz. Chem. Soc., 18(1),
2007, 184-188.

...152 additional retention index citations follow...

The GC data is useful not only for the GC retention index values but also for the GC column conditions and cited literature that goes with it.

[1]. Babushok, V.I., Linstrom, P.J., Reed, J.J., Zenkevich, I.G., Brown, R.L., Mallard, W.G., Stein, S.E., Development of a database of gas chromatographic retention properties of organic compounds. J.Chromatog. A, 2007, 1157, 414-421.
[2]. Stein, S.E., Brown, R.L. Estimation of normal boiling points from group contributions. J.Chem.Inform.Comput.Sci., 1994, 34, 581-587.
[3]. Stein, S.E., Babushok, V.I., Brown, R.L., Linstrom, P.J., Estimation of Kovats retention indices using group contributions. J.Chem.Inf.Modeling, 2007, 47, 975-980.

NIST MS Search Software - NIST 08

Note: the following description reflects NIST 08 (see What's New in NIST 11 for more recent changes).

Figure: NIST MS Search software

The updated, full-featured NIST MS Search Program for Windows has a full range of integrated tools.  The new updated version of this widely used, full-featured software is designed for identifying compounds from their mass spectra and for exploring mass spectral libraries.  It also contains tools for deconvoluting gas/liquid chromatograms and interpreting mass spectra.

Tip: If you've used older versions of NIST MS Search, here's a few new features of MS Search in NIST08 that you might not know about.
  • Library Searching via Multiple Search Modes
    • Chemical Identity
    • Structure Similarity
    • Impurity Reduction
    • Neutral Loss
    • Four Peak Types
  • Library Building
  • GC/MS Deconvolution
  • MS Interpretation
  • Chemical Substructure Analysis
  • Chemical Substructure Identification
  • Molecular Weight Estimation
  • Chlorine/Bromine Analysis
  • Isotope/Formula Generator
  • Integration with multiple Instrument Data Systems


This software provides a flexible means of accessing data in the NIST and User libraries including:

  • chemical identification by optimized, documented spectrum-matching methods,
  • analyzing mass spectra of compounds not in the library using library data,
  • finding spectra with pre-selected characteristics,
  • viewing spectra by name, formula, CAS registry number, molecular weight, or ID number,
  • User library building and maintenance, and
  • integration with a number of commercial GC/MS data systems and spectral analysis tools.
Windows Organization

When the program is first started, seven tiled windows appear on the screen (the Desktop), each with its own data and behavior.  The behavior of any Window may be modified by making it active (clicking on it) and then pressing the AdjustWin button at the bottom of the Desktop.  As you become familiar with program operation, you may wish to change the dimensions of some Windows or even close some of them to create a custom Desktop.  When the program is restarted, it will begin with the most recent Desktop.  To save a window-arrangement Desktop for future use, select Desktop from the Menu Bar and then Save As from the resulting Menu.  Prior Desktops may be restored using one of the predefined names or your own name.  Such arrangements describe the geometry and type of information shown in each Window, not the actual data contained in it.  To restore a previous hit list, select it from the list at the top of the Hit List Window.

Library Searching - Identify unknown compounds and substructures using fully documented and optimized procedures, or search by a wide range of compound and spectral properties.

Library Building - Maintain your own libraries, add your own chemical structures and search using the same optimized procedures developed for NIST.

Flexible User Interface - Set multiple Desktop configurations with up to seven independently configured windows to examine search results and match your needs.

Use with Your Instrument Data Systems - Direct transfer between a number of commercial data systems and the NIST Search Program.

Adding User-Drawn Structures
Users may import their own chemical structures with selected user spectra.  This is done in the Tools/Librarian section of the program by connecting a user-drawn structure in standard MOL-file format with a user spectrum.  Such structure-drawing programs are widely  available (for example, ISIS/Draw may be freely downloaded from  As before, if a user spectrum is given its CAS registry number and the Main Library has a structure for it, this structure will automatically be shown with user spectra unless the user has attached an imported structure to the spectrum.

Aids for Automation and Reporting
A variety of methods for automated searching and reporting of results are available.  From the File menu selection, if Print automation is on, printing will follow each library search.  A set of print options is also available from the "User Search Options" Window (select Search, then User spectrum).  This is of particular use when using this NIST Program with other data acquisition programs.

Automated Mass Spectrometry Deconvolution and Identification System (AMDIS)

The AMDIS software extracts pure component spectra from complex GC/MS or LC/MS data files and searches against specialized libraries or the NIST library.  This module was developed at the national Institute of Standards and Technology (NIST) for the critical task of verifying a major international treaty, the Chemical Weapons Convention. After two years of development and extensive testing it is now being made available to the general analytical chemistry community. AMDIS can operate as a "black box" chemical identifier, displaying all identifications that meet a user-selectable degree of confidence. Identification can be aided by internal standards and retention times. Libraries can be built directly from analyzed data files or from spectra in the NIST/EPS/NIH Database. AMDIS can also serve as a preprocessing tool for the GC/MS data files, automatically performing noise reduction for all components. It permits traditional library searching for any selected component. A flexible interface is provided to assist the analysis of complex matrices.

Included as a separate utility, AMDIS attempts to reconstruct original mass spectra for individual components in arbitrarily complex GC/MS and LC/MS reconstructed total ion current (RTIC) chromatograms; and, if a target library is provided, can directly identify target compounds.  AMDIS is especially useful when an RTIC chromatographic peak represents multiple components.  Regardless of each component's concentration, pure mass spectra are deconvoluted for analyses.  AMDIS was developed by NIST for the Defense Weapons Agency (Department of Defense) for verifying compliance with a major international treaty (Chemical Weapons Convention) ratified by the United States Senate in 1997.  In order to meet the rigorous requirements for this purpose, AMDIS was tested against more than 30,000 GC/MS data files accumulated by the EPA Contract Laboratory Program without a single false-positive for the target set of known chemical warfare agents.  While this level of reliability may not be required for all laboratories, this shows the degree to which the algorithms have been tested.

AMDIS has been designed to reconstruct "pure component" spectra from complex RTIC chromatograms even when components are present at trace levels.  For this purpose, observed chromatographic behavior is used along with a range of noise-reduction methods.  AMDIS is distributed with specialized libraries (environmental, flavor and fragrance, and drugs and toxins), that were derived from the NIST Library.  AMDIS has a range of other features, including the ability to search the entire NIST Library with any of the spectra extracted from the original data file.  It can also employ retention index windows when identifying target compounds and can make use of internal and external standards maintained in separate libraries.  A history list of selected performance standards is also maintained.

As of version 2.65, AMDIS reads data files in the following formats:

  • Agilent ChemStation (*.D)
  • Agilent MS Engine (*.MS)
  • Bruker (.MSF)
  • Finnigan GCQ (*.MS)
  • Finnigan INCON (*.MI)
  • Finnigan ITDS (*.DAT)
  • HP ChemStation (*.D)
  • HP MS Engine (*.MS)
  • INFICON GCMS (*.acq)
  • JEOL/Shrader (*.lrp)
  • Kratos Mach3 (*.run)
  • MassLynx NT (*.*)
  • Micromass (*.)
  • mzXML/mzData (*.*) (new in NIST11)
  • NetCDF (*.CDF)
  • PE Turbo Mass (*.raw)
  • Shimadzu MS (*.R##)
  • Shrader/GCMate (*.lrp)
  • Varian MS (*.MS)
  • Varian SMS (*.sms)
  • Varian XMS (*.xms)
  • Xcalibur Raw (*.raw) - requires Xcalibur be installed

AMDIS may also be downloaded separately.

Note: The above description reflects NIST 08 (see What's New in NIST 11 for more recent changes).

Additional NIST MS Tools: Mass Spec Interpreter

Figure: NIST MS interpreter

This utility enables the user to examine neutral losses, isotope patterns and possible chemical formulas along with computer assisted chemical structure/spectral analysis. Starting with Version 1.5, the program has offered a unique means of interpreting spectra of compounds not identified in the Library by the User spectrum search.  This is most useful when no acceptable matching spectra are found in a User spectrum search of the NIST Library.  At this point, by selecting Substructure Information from the Tools menu, the current hit list is analyzed and statistical information on the composition of the unknown is derived from the hit list.  For instance, the probability that any of a range of substructures are present or absent are listed (phenyl, acid, ester group, double bond, heteroatom, etc.) along with an estimate of the molecular weight and chlorine/bromine content (the latter is based only on the spectrum itself).

This tool was developed to aid NIST evaluators in their analysis of mass spectra.  In one integrated program, it permits a wide range of calculations on a mass spectrum using--if available--a proposed chemical structure.  Spectra and structures are associated in the library facility of the Windows Search Program discussed above, and the program is activated from the Tools menu.  Peaks in the spectrum originating as a logical fragment of the molecule are marked, and corresponding fragments may be highlighted.  It also allows the analyst to keep track of important neutral losses, both from the parent or a derived ion, and to readily compute possible formulas for any peak or neutral loss and isotopic patterns as desired. Observed isotopic clusters can be compared to theoretical predictions subject to a number of user-specified constraints.

Figure: NIST Formula and Isotopic Pattern Generator

New in NIST11

NIST11 consists of

  • The 2011 release of the NIST/EPA/NIH Electron Ionization (EI) Mass Spectral Database.
  • The NIST MS/MS Database.
  • The NIST GC Methods and Retention Index Database.
  • A new version of the NIST Mass Spectral (MS) Program (v.2.0g).
  • Enhanced versions of MS Interpreter and AMDIS are also included with NIST11.
NIST11 expands in three main areas:
  • EI Database expanded (~10%) and improved.
  • MS/MS database expanded by 6x.
  • Updated search software & utilities with new features.

The NIST/EPA/NIH Database of Electron Ionization Mass Spectra now contains 243,893 carefully evaluated spectra for 212,961 compounds, an increase of nearly 10% from the 2008 version. This includes 23,433 new spectra of metabolites, drugs of abuse, derivatives of common compounds and many more, all measured specifically for this library. Other major enhancements have been made to the prior version including many replacements with higher quality spectra, a thorough review of chemical names and merging of the previous salts library into the main library.

The NIST Database of MS/MS spectra has undergone an even greater enhancement. The new collection more than doubles the number of compounds represented. Further, most spectra have been acquired on both ion trap and qtof/triple quad instruments, thereby increasing the number of spectra by over a factor of six compared to the 2008 version. Spectra for the latter instrument classes have been acquired over a wide range to energies to ensure matching regardless of instrument collision settings. Also, when available, high mass accuracy spectra are stored. New spectra include metabolites, peptides (biologically active peptides and all di-peptides and tryptic tri-peptides), contaminants, lipids and more. The near-final version contains 9,934 ion trap spectra for 9,138 different ions of 4,649 compounds, and 91,557 collision cell spectra (qtof and tandem quad) for 6,939 different ions of 3,774 compounds.

There have been a number of enhancements made to the NIST MS Search Program; not the least of which is the addition of an Exact Mass Search and the ability to sort Hit List by the number of synonyms and other databases (non-mass spectral databases) in which the compound can be found. Features introduced in NIST08, like the ability to use the EI Database and the Substructure Identification Tool in the interpretation of CAD spectra and the ability to display isomers and derivatives as replicate spectra, have been retained and are still available. Figure 1 shows one view of the new look of the Hit List window and Text Information window in the Lib Search Window of MS Search v.2.0g.

The NIST MS Search Program, since its introduction as a Windows version (v.2.0), has evolved into a power tool for not only the matching of spectra of unknown compounds against spectra for that compound in the EI and MS/MS Databases, but also the identification of unknowns encountered in toxicology, forensic, quality control, flavor and fragrances, environmental and many other fields through their mass spectra, regardless of the type of ionization or the analyzer used to determine the abundances of ions sorted according to their m/z values. The EI Database contains much more than just the mass spectra of compounds. It contains a primary and in many cases multiple synonyms including common and trade names. It contains names of other databases where specific compounds can be found, the name of the contributor, the compound��™s elemental composition, its nominal and exact mass, and the compound��™s chemical structure.

The NIST MS Search Program can be an invaluable tool in GC/MS method development through the use of the GC Method/RI Database, exposed in the NIST MS Search program. This utility can also be enhanced by the addition of the new NIST GC Method/RI Search Program, which can be used by itself in the GC laboratory. The NIST MS Search Program has evolved out of the needs of those in the NIST Mass Spectrometry Data Center that use it and the Databases on a daily basis. Many user suggested enhancements have been add to the Program which is distributed with NIST11.

Figure 1. Library Search Window of NIST MS Search provided with NIST11 with the Exact Mass Constraints dialog box overlaid. Note the Exact Mass field in the displayed Hit List spectrum and the two new columns for the number of synonyms for the compound and the number of other databases (non-mass spectral) containing the compound.

The following is lists a number of new features available in the NIST MS Search Program v.2.0g. Only by exploring, using the Help available in the Program and looking at the electronic manual that is provided will it be possible to begin to see all the features and benefits. Only through extensive utilization and practice will it be possible to see the entire picture available with the NIST MS Search Program.

  • 1. The NIST MS Search Program v.2.0g which accompanies NIST11 has had an Exact Mass Search added to the list of Other Searches. It takes into account the presence or absence of an electron, adducts; accepts uncertainty in ppm or millimass units, and allows searching for isotope peaks or monoisotopic peaks. This has been enabled for both molecular ions AND product ions.
  • 2. An Exact Mass Constraint has been added to a Spectrum Search, Sequential Search, and Any Peaks Search. This Constraint (Figure 1) has the same properties as the Exact Mass Search.
  • 3. The MS Interpreter program now enables high mass accuracy for both molecular ions AND product ions.
  • 4. Any mass spectral database in the NIST MS Search Program��™s format (including all user libraries, the Wiley Registry, and Wiley��™s boutique libraries like MPW, DD20XX, FFNS, the Agilent DRS libraries, etc.) can be indexed to allow use with the Exact Mass Search or Exact Mass Constraint.
  • 5. As long as a chemical formula is associated with a mass spectrum, not only is the nominal mass (MW) displayed but the Exact Mass is also displayed in the spectrum��™s Text Information window.
  • 6. Optionally displayed columns in Hit Lists (MS Search and Other Search) have been added for the number of synonyms and the number of other databases that a compound from the NIST EI Database is in; the Hit List may be sorted according to the contents of these columns (Figure 1).
  • 7. Sort Hit Lists alphabetically (This was a feature in the MS Search Program in NIST08.)
  • 8. Sort Spec List alphabetically or by number. (New to NIST11)
  • 9. Toggle between Tab views (Lib. Search, Other Search, Name, Compare, Librarian, and MSMS Windows) using Crtl-Tab or Ctrl-Shift-Tab.
  • 10. The NIST MS Search Program will now accommodate as many 127 separate databases instead of 16, which was the limit in previous versions of the NIST MS Search Program.
  • 11. The NIST MS Search Program will now accommodate up to 1,048,560 spectra in a database instead of 786,420 spectra allowed in the previous version.
  • 12. NIST11, like NIST08, is fully compatible with Microsoft® Vista™ and Windows 7™.
  • 13. Tags in Comments Field: The concept of Tags (described below) was added to v.2.0f of the NIST MS Search Programs. Tags in the Comments field of a spectrum can be searched. With respect to the spectra in the mainlib and/or replib Databases, when using the Sequential Search, by typing a text string in the dialog box as shown in Figure 2, the Contributor field will be searched. All spectra contributed by a single source can be identified in this way. This feature is continued v.2.0g and even further enhanced.
  • 14. When clicking the Right Mouse button in a Text Information window to display the popup window, there is a Find option that allows the window to be searched for a specific text string. This is particularly useful with GC Method/RI records that are associated with spectra in the NIST/EPA/NIH Database.
  • 15. One or more items from any Hit List may be copied into the Windows Clipboard as tab delimited Unformatted Unicode text and pasted into Excel™. The copying may be done from the Right-Mouse-button Menu or by pressing Ctrl-K (possibly subject to change) with the spectrum (spectra) highlighted. To select all the spectra in a Hit List, press Ctrl-A (a feature from NIST08). Note: Plain ASCII text, which may be obtained using Paste Special/Unformatted text, would not have proper Greek letters.
  • 16. Tags (Field titles) in User Library & Spec List Spectra A Tag is the name of a Field heading that will be displayed with the Text Information of a User Library or Spec List spectrum and can optionally appear in the line below the Plot of the spectrum. Text is designated as Tag in the Comments field of a User Library or Spec List spectrum with the Spectrum Edit function of the Librarian Window by entering the Field title (a line of characters without spaces) followed by an =. Following the = is the contents of Field. This can be a line of characters without spaces, a number or a text string with open and close quotation marks (“”). For example, the following may be entered in the Comments field of the Spectrum Information dialog box of a Spec List or a User Library spectrum:
    Structures were provided by O. David Sparkman Contributor="University of the Pacific Mass Spectrometry Facility" Instrument="Agilent 5975 Inert XL MSD w/7890 GC" Tune="Standard Spec w/ PFTBA" ScanRange=35-400 GC_column="30 m x 250 �µm with 0.3 �µm film thickness of BD-5" OvenTemp="50 C 5 min. to 250 C @ 5 C/min" Synthesized="Matt Cutis"

    Figure 2

    As shown in Figure 5, the information preceding each equal sign (=) will be displayed as a Field title in the Text display of the spectrum and can optional be displayed with the Plot of the spectrum. The information following the equals sign (=) will appear following the Field header. Entry of Field contents (string) must conform to the rules above. In order for this display to occur, the Field titles must be registered in the Display comment field options dialog box shown in Figure 4 (View/Comment fields options). When the Tags have been entered into the Comment Field Options dialog box, they will not be displayed in the Comments field of the Text Information window. Figure 5 shows a spectrum (Plot and Text) with added Field headers.

    When a search is done of a User library that contains Tags (Field titles), it is possible to Constrain that search based on the Tag (Field title) and the partial or whole contents of the Tag (Field title). More specific details on the use of Tags as Constraints are in MS Search Help and Manual.

    Figure 3

    Figure 4

    Figure 5
  • 17. Display of Spectra of Derivatives as Replicate Spectra: One of the major new features with NIST MS Search (v.2.0f) in NIST08 was the ability to display spectra of derivatives as replicate spectra. If a spectrum of 1-octanol is in a Hit List and the mainlib or mainlib and replib databases have spectra of trimethyl silyl, pentamethyldisilyl, and/or acetate derivatives of 1 octanol, these would be listed as replicate spectra. When the replicates are displayed, actual replicates of compounds found in the replib database would be designated with an R. The spectra of the derivatives would be designated with either an m (in the mainlib database) or an r (in the replib database). This display feature is defaulted in MS Search 2.0f. To turn this feature off or modify it, use the Replicates Display Options dialog box called by Options/Replicates. This feature which first appeared with NIST08 has been enhanced for NIST11.
  • 18. The MS/MS in EI option in the Spectrum Similarity Search is used with spectra of unknowns obtained by fragmentation process, EI or Collision Activated Decomposition (MS/MS spectra) for the determination of the probability of the Presence and Absence of substructures using the NIST companion Substructure Identification Tool. The MS/MS in EI option accesses neutral losses in the sample spectrum. A search against the neutral losses of the spectra in the NIST EI Database is then carried out. A Hit List containing EI spectra which have exhibited the same or similar neutral losses from the molecular ion of compounds in the EI Database is generated.

    Figure 6. A spectrum obtained by MS/MS using the protonated molecule at m/z 248 obtained by electrospray as the precursor ion.
    Each spectrum in the EI Database is indexed according to substructures of the compound that generated the spectrum. Substructures are features such a functional group, heteroatoms, the number of rings-plus-double bonds (R+dB), etc. Figure 6 is a mass spectrum acquired using MS/MS in a 3D Quadrupole Ion Trap of a precursor ion with m/z 248 formed with positive-ion electrospray. This spectrum was searched using the NIST MS/MS in EI option Spectrum Similarity Search in the MS Search Program and the NIST11 EI Mass Spectral Database. The resulting Hit List (not of spectra of similar compounds but of EI spectra that exhibited the same natural losses as the CAD spectrum) was then analyzed using the Substructure Identification Tool. A portion of the Results are shown in Figure 7.

    The Substructure Identification Tool indicated that there were probabilities ≥90% that the unknown contained one are more atoms of oxygen, had a R+dB count greater than five, that it contained both a methyl and a methylene group and that there was a substructure with both connected to one another, and a carbonyl group. There were probabilities >85% that the unknown contained one or more atoms of nitrogen, that there was an aromatic ring and a heterocyclic ring with nitrogen, a carbon oxygen bond, and many other substructures.

    Figure 7

    The probability of the absences of substructures showed a >90% probability that there was not a phenyl carbonyl or phenyl methoxy, a dialkyl ether, an oxygen in a ring, benzyl moiety, an alkyl-aryl ether, or an aryl nitro group. Using these reported presences and absences it was not too difficult to establish a probable structure as shown to the left. Not only can the Substructure Identification tool be used in the evaluation of CAD (MS/MS Spectra), it can also be used in the identification of unknowns using spectra when there is no spectrum for the unknown in a database.

  • 19. When performing Other Searches such as Molecular Weight, Sequential, and Formula Searches it may be desirable to change or include Constraints to limit the number of hits. This may need to be done for several iterations. To facilitate this, now when one of the Searches is requested the Search dialog box opens with Constrains tab display rather than the options tab (See Figures 8 and 9).

    Figure 8. (left) Search Dialog Box Displayed on Opening in NIST08. Figure 9. (right) Search Dialog Box Displayed on Opening in NIST11.
  • 20. A possibility to turn off Homolog hits in a Structure Similarity Search has been added. This is a new feature in the Library Search Options dialog box
  • 21. Spectra in the MSP text format can be imported from the Windows Clipboard into the Spec List via a Right Mouse button Menu option.
  • 22. In the new mainlib-11 a relatively small number of compounds have more than one CAS registry number. These compounds may be found by the usual CAS r.n. search; a new file registry2.in6 in the NIST11 Main and Replicate Library-folders is required. If the registry2.in6 file is not present, then a regular CAS search is performed thus providing backward compatibility. The current version does not display these extra CAS r.n.��™s; although, they are present as invisible synonyms.
  • 23. The NIST MS Search Program can import centroided spectra from mzXML and mzData MS and MS/MS files.
  • 24. An alternative peak matching method has been added to improve the reliability of the score when searching noisy MS/MS spectra.
  • 25. The NIST MS Search Program is fully compatible with most recent NIST Peptide MS/MS Libraries.
  • 26. A chemical structure in the MOL file format can be inserted from the Windows clipboard into the Spec List in Librarian or Lib Search Window via a right-mouse-button menu command allowing for a Structure Similarity Search.
  • 27. A chemical structure in the MOL file format located on the Windows Clipboard can be attached to the plot in Search Spectrum window displayed in the Lib. Search Window. The result may be subsequently sent to Spec. List and added to a user library (this undocumented feature was in the version of the MS Search Program distributed with NIST08 software).
  • 28. Comments on the Compare Window and its undocumented abilities are to be added.

New in NIST 08

NIST 08 made the following major changes since NIST 05.

Electron Ionization (EI) Library: The new library consists of 220,435 spectra of 192,262 compounds an increase of 15% over the previous version. NIST has, at the same time, continued to improve overall library quality by re-measuring and reexamining thousands of spectra. For example, it has been provided consistent identification for hundreds of salts and created a separable collection of low-volatile substances not expected to be measurable by GC/MS (717 spectra of 672 salts). Thousands of spectra of common derivatives and contaminants measured at NIST or by close collaborators have been added. As before, all compounds are represented by both names and chemical structures.

GC Data Library: Includes 224,038 Kovacs indices for 21,847 compounds, an increase of over 50% from the previous version. Data include both non-polar and polar columns (NIST 05 had only non-polar columns). Most values were abstracted from the open literature and then compared to replicate values (average of 10 per compound) and estimates to find and remove errors.

MS/MS Spectra: This release greatly expands our collection of MS/MS spectra by 250% to 5,308 different precursor ions. A large fraction of the new spectra are for contaminants and metabolites.

Some enhancements were also made to the MS Search Software, such as

  • Displays replicate spectra of derivatives/parent, tautomers, and optical isomers.
  • Optimized MS/MS Identity search in MS/MS libraries
  • MS/MS search can employ exact m/z values
  • Search & display of user-defined data

New in NIST 05

NIST 05 made the following major changes since NIST 02.

EI Library: This now contains 190,825 spectra of 163,198 different chemical compounds. In addition to the new spectra, important quality improvements have been made in both spectra and compound identification information. The binary format has not changed from the 2002 version, although several new files have been added that associate equivalent compounds and link individual compounds to the retention index library (see below).

GC Data: This is a new addition, containing 121,112 Kovats Retention Index values for 25,893 compounds on nonpolar columns, 12,452 of which are compounds represented in the Electron Ionization Library. Full annotation is provided, including literature source and measurement conditions. These are provided in a format accessible by our Search Program.

MS/MS Library: This is a new addition, containing 5,191 spectra of 1,943 different ions (1,671 positive and 341 negative ions).

Latest new features in the program and database:

  • New MS/MS browsing window and new MS/MS library
  • New Retention index library and retention indexes in Main and Replicates libraries (Retention index library contains only structures, no spectra). Automatic Retention Index estimation from chemical structure (rigth-click spectrum text window, select Properties, Retention Indices.)
  • New structural replicates display (in addition to usual CAS number matching) Select matching method in Options, Replicates.
  • Structure searching - the program will find all chemical structures similar to the structure of the search spectrum. The searching can be done using structural data from the NIST MS database, from the user database or from a structure drawn in most chemical drawing packages. A structure may be exported to chemical drawing software. Structure similarity search algorithm has been changed, now it includes homologues recognition which, if successful, makes match factor 1000. You will need to rebuild structure search databases in user libraries (as you usually need to do after editing a user library containing structures.)
  • Drag and Drop - Data can be dragged and dropped between windows.
  • User Library Structures - This feature has been present for some time, but many are unaware of it.
  • Compare Views - There are a number of new ways that you can visually compare two spectra.
  • Direct interaction with a number of chemical drawing packages - the clipboard can be used with some of them, most can be used by use of intermediate files.
  • The NIST MS Search program takes advantages of many normal Windows conventions. Look at the context sensitive options on the right mouse button click and on buttons at the top of the window.
  • New, thermodynamics-base MS Interpreter program version 2.0 replaces the previous version. A spectrum with a structure may be sent to MS Interpreter by right-clicking the windows with a mass spectrum and structure and selecting Send To, MS Interpreter.

New in NIST 02 and previous versions

NIST 02 made the following major changes since NIST 98 and previous versions.

The previous version (NIST 98) provided for a 75% increase in coverage and this latest release (NIST 02) provides for an additional 35% increase in coverage.  This was accomplished primarily by the addition of complete, high quality spectra either measured specifically for the library or taken from major practical collections, including:

  • Chemical Concepts - including Prof Henneberg's industrial chemicals collection
  • Georgia and Virginia Crime Laboratories
  • TNO Flavors and Fragrances
  • AAFS Toxicology Section, Drug Library
  • Association of Official Racing Chemists
  • St. Louis University Urinary Acids
  • VERIFIN & CBDCOM Chemical Weapons

NIST 02 contains spectra of more than 147,000 compounds along with associated chemical identification data including chemical structures, synonyms, and other of relevant information. The best quality spectra are placed in the Main Library; and good-quality, alternate spectra are provided in the Selected Replicates Library, bringing the total number of spectra to about 175,000. This release represents the largest increase in both quality and coverage in the 25-year history of the NIST/EPA/NIH Mass Spectral Database--and for the first time that it can be stated that the library has been fully evaluated.  The objective of this effort was to provide the best possible reference library for compound identification by mass spectral library searching.

System Requirements - NIST11

Operating system requirements:

  • Windows 2000, XP, Vista, 7, and Windows 8 (both 32 and 64-bit editions of XP, Vista, 7, and 8) are fully supported.
  • Windows 3.x, 95, 98, Me, and NT 3.x are not compatible with NIST11 (at least the standard version; ChemStation format might work).
  • Windows NT 4 is partly compatible with NIST11: Only NIST MS Search, which provides access to the NIST 11 MS Library would work. The NIST11 version of AMDIS is not compatible with Windows NT 4.0. The latest version of AMDIS known to be compatible with Windows NT 4.0 SP1 and NIST11 MS Search is version 2.64 (build Jan 13, 2006). The user would also need
    • Adobe PDF Reader to access the NIST11 Manual
    • WinNT4Sp3+MSIE4.0/4.01/4.01SP1+hhupd.exe or WinNT4Sp6+MSIE4.01SP2 or later version of IE to access NIST MS Search HTML Help.
    • Windows NT 4.0 SP1 and WinNT4Sp3+MSIE4.01Sp1+hhupd.exe under MS Virtual PC 2007 are the earliest versions of Windows that NIST11 has been tested.

System Requirements - NIST08

Complete installation (libraries, NIST MS Search program, and AMDIS) requires ~400 MB of free hard disk space. The MS search program requires Windows NT 4.0, Windows 2000, XP, or Vista.

Note for old ChemStations (B1701BA): the error about $_ undefined can be resolved by replacing $_(number, string) with string in the ChemStation macros. Contact us for instructions if you run into this.

Note for Windows NT 4: You may need to download the older AMDIS version 2.63. Running 2.66 on NT 4 gives the error "AMDIS_32.EXE - Entry Point Not Found - The procedure entry point MonitorFromPoint could not be located in the dynamic link library USER32.dll".

Demo Version - NIST 08

Download NIST 08 Demo. The demo differs from the full version of NIST 08 mainly in that it contains a very small subset of the database. Also, this is a demo of only the standard version of NIST (does not contain native formats in the ChemStation and multiformat versions of NIST). Note: a demo version of the newer NIST 11 release is not available, but the software looks and operates similarly.

Note: In order for your MS data system to recognize the demo version, you may need to edit the file "c:\windows\win.ini" (or "c:\winnt\win.ini") to change the line "[NISTMSDEMO]" to "[NISTMS]".

Download AMDIS 2.71 (July 2012) (free) (a somewhat older version of this is included in demo and need not be downloaded separately)


  • 2012 Update to MS/MS library available.
  • 2012-07 - AMDIS 2.71 posted
  • 2011-12-28 - An updated ChemStation macro (NISTSrch.mac) is available to avoid interference in situations where both ChemStation and another search system (e.g. Xcalibur or Masslynx) are used simultaneously on the same computer (by reusing the file). [download ZIP] (contains NISTSrch.mac and install instructions).


Part No. Description Quantity
In Stock
Price Quantity
to order
New Licenses:
741010 Standard Version (Search Programs + Libraries in NIST format) 3$2295.00[*B][*B] 3 or more: 5% off; 10 or more: 7% off.
741010HP ChemStation Version (Search Programs + Libraries in NIST Format + Libraries in Agilent ChemStation .L Format) 2$2595.00[*B][*B] 3 or more: 5% off; 10 or more: 7% off.
741010MF Multiformat Version (Search Programs + Libraries in NIST Format + Libraries in Multiple Additional Native Formats) 0[*L]Standard lead-time for out-of-stock items is approximately two weeks depending on the item. $3750.00
741010UG Standard Version (Search Programs + Libraries in NIST Format, UPGRADE from any previous version of NIST) 9$1295.00[*B][*B] 3 or more: 5% off; 10 or more: 7% off.
741010HPUG ChemStation Version, UPGRADE (Search Programs + Libraries in NIST Format + Libraries in Agilent ChemStation .L Format, UPGRADE from any previous version of NIST) 1$1495.00[*B][*B] 3 or more: 5% off; 10 or more: 7% off.
741010MFUG Multiformat Version, UPGRADE (Search Programs + Libraries in NIST Format + Libraries in Multiple Additional Native Formats; UPGRADE from any previous version of NIST) 0[*L]Standard lead-time for out-of-stock items is approximately two weeks depending on the item. $2550.00

Which version to buy? Contact us if you have any questions if unsure.

Summary of the different NIST versions:

  • The standard version of NIST (741010). Is recommended for most users (except for Agilent ChemStation, MassHunter, and Shimadzu). It includes the NIST library formatted in NIST format, which is the native format understood by the NIST MS Search program, which integrates with a number of data systems (e.g. Varian Saturn, Finnigan Xcalibur, Waters MassLynx version >= 4.0). GC/MS, LC/MS, and MS spectra from many data systems can also be imported indirectly into AMDIS (see above) and then library searched via the AMDIS-NIST MS Search program integration.
  • The Agilent version of NIST (741010HP) is recommended primarily to Agilent (ChemStation or MassHunter) users. It includes everything in the standard version plus NIST formatted in the Agilent .L library format for library searching directly from Agilent software (e.g. Data Analysis, PBM search). A few additional older formats (e.g. the old Finnigan GCQ/Varian ITS40/ .LBR format and the VG MASSLAB/Lab-Base/MassLynx .IDI/.IDB/.PDB/.PDI format) for other data systems are also included in this package.
  • The Multiformat version of NIST (741010MF) is recommended for Shimadzu GCMSSolution users in particular. It includes everything in the standard and Agilent versions of NIST plus the following additional native formats: Shimadzu GCMS Solution, Waters MassLynx, and Thermo Spectral ID.
  • Other formats may be available upon request.

Instructions by MS manufacturer:

  • Agilent ChemStation (or MassHunter) - The Agilent version of NIST is recommended for GC/MS ChemStation or MassHunter, as this provides the most seamless integration with Agilent data systems. This version includes a copy of the NIST library formatted in the Agilent library format (*.L) with structures, for searching by Agilent's PBM library search routines. Also, Agilent ChemStation (*.D) and MS Engine (*.MS) can be imported into AMDIS using the standard version of NIST. For LC/MS ChemStations (which don't use the .L library format), the standard version of NIST will work just as well.
  • Thermo (Finnigan) - The standard version of NIST can be used with Xcalibur, which integrates directly with the Xcalibur data system. Also, Xcalibur Raw (*.raw), Finnigan GCQ (*.MS), INCOS (*.MI), ITDS (*.DAT) can be imported into AMDIS using the standard version of NIST. The NIST library in the Thermo Spectral ID is available in the multiformat version of NIST.
  • Varian Saturn - The standard version of NIST can be used. Also, Varian (*.MS), SMS (*.sms), and XMS (*.xms) can be imported into AMDIS using the standard version of NIST.
  • Waters MassLynx - The standard version of NIST is recommended, at least for MassLynx versions > 4.0. On search, the spectra is automatically transferred into the NIST MS Search window for library searching. (Older MassLynx versions only support the native MassLynx library format, which is available in the multiformat version of NIST and Agilent/Other version. In fact, newer MassLynx versions continue to support this method as well, but the information displayed has been reported to be more limited than with NIST MS Search--e.g. in terms of information displayed, search time, and 8-digit CAS number limit.) MassLynx NT (*.) can also be imported into AMDIS using the standard version of NIST.
  • Waters Empower - Contact us for details. Please tell us what version of Waters Empower you are using.
  • Shimadzu: NIST in the native Shimadzu GCMSSolution library format is available in the multiformat version of NIST, allowing searching (.qgd) directly from the Shimadzu software. The native Shimadzu library format has only been tested on recent 2.x versions of GCMSSolution software. Chemical structure diagrams are not included in the native Shimadzu format itself, though you can still browse structures in the NIST MS Search software. Alternately, using only the standard (or any other) version of NIST, it is possible to import old Shimadzu QP5000/QP5050 "CLASS-5000" software MS (*.R*) files into NIST AMDIS, for searching instead from the NIST MS Search software, but this approach does not work with the newer .qgd files without first converting the .qgd to .cdf (e.g. using MASSTransit).
  • PE TurboMass (*.raw) files can be imported into NIST MS Search via AMDIS using the standard version of NIST. NIST MS Search may also be directly integrated with the PE TurboMass software (but call us for instructions). Also, NIST in TurboMass library format (.IDI/.IDB/.PDB/.PDI), where TurboMass will do the library searching without MS Search, is included the Agilent/Other version of NIST (and it is also in the multiformat version of NIST). Agilent/Other version of NIST is recommended for maximum flexibility.
  • Bruker .MSF files can be imported into AMDIS using the standard version of NIST.
  • INFICON GCMS (*.acq) can be imported into AMDIS using the standard version of NIST.
  • JEOL/Shrader/GCMate (*.lrp) can be imported into AMDIS using the standard version of NIST. Shrader also has direct interfaces into the standard version of NIST. Contact us for details.
  • Kratos Mach3 (*.run) can be imported into AMDIS using the standard version of NIST.
  • Micromass (*.) can be imported into AMDIS using the standard version of NIST.
  • Others/NetCDF (*.cdf) can be imported into AMDIS using the standard version of NIST. NetCDF is a vendor-neutral format supported by a number of data systems and GC/MS format conversion software (e.g. GC/MS File Translator and MASSTransit).

(The above list is somewhat of a moving target. Please drop us an e-mail if anything here is incomplete.)

Site licensing: A few site licensing options are available, typically for at least half a dozen nodes.

Other databases available: The NIST 08 is a strongly validated and extensively used MS library of general compounds recommended for most all users. Users looking for a larger library or libraries dedicated to certain classes of specialty compounds may wish to augment their NIST database with one of the Wiley MS libraries.

SIS Catalog Cross Reference
Page #Part Numbers
A93 - NIST MS Library and Software 741010, 741010HP, 741010HPUG, 741010MF, 741010MFUG, 741010UG
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