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NEW NIST 2017 mass spectral library - Upgrade discount for any previous version 

NIST 17 - The successor to NIST 14 (2014)

  • Electron ionization (EI) mass spectra
  • Tandem MS/MS spectra
    (ion trap and collision cell)
  • GC method and retention data
  • Chemical structures and names
  • Software for searching and identifying your mass spectra

The NIST Library is known for its high quality, broad coverage, and accessibility. It is a product of a three decade, comprehensive evaluation and expansion of the world's most widely used and trusted mass spectral reference library compiled by a team of experienced mass spectrometrists in which each spectrum was examined for correctness.

System requirements

This MS search program is a 32-bit Unicode application and thus requires Windows XP, Vista, or Windows 7, 8, 8.1, 10. Total installed size is approximately 3.0 GB.

NIST17 release contains

306,622 EI spectra for 267,376 compounds
NIST 17 MS/MS libraries (nist_msms and nist_msms2) with 652,475 spectra of 123,881 ions for 15,243 compounds (65% increase)
GC Methods/Retention indices library (nist_ri) with 99,400 compounds;   72,361 compounds in the Main library have retention index data.

History of the releases:

Release  Number of     Number of      Number of       Number of
Year     spectra (EI)  compounds (EI) spectra(MS/MS)  compounds (RI)

1993       74,828         62,235                   -                -
1998     129,136       107,866                    -                -
2002     174,948       147,198                    -                -
2005     190,825       163,198                5,191           25,728
2008     220,460       192,108              14,802           44,008
2011     243,893       212,961              95,409           70,835
2012                                               121,586
2014     276,248       242,466            234,284           82,868
2017     306,623       267,376            652,475           99,400

New features of the program and the NIST17 database are:

- Significant expansion of coverage of metabolites and designer drugs in the EI library, as well as the application of new computer-assisted evaluation methods for removal of low quality spectra.

- Greatly expanded NIST 17 MS/MS Library. Spectra include metabolites, peptides (biologically active peptides and all di-peptides and tryptic tri-peptides), contaminants, metabolites, lipids and more.

- A new search type, the 'Hybrid Search' for all spectrum types, enable finding many more similar compounds in the hit list. It requires a precursor mass.

- A new neutral loss search is available that eliminates restrictions on the maximum loss considered.

- Improved algorithms for scoring high mass accuracy searches that account for sparse spectra.

- Peaks shifted in the 'Hybrid Search' are shown before and after shifting.

- New filters for tandem mass spectra to limit hits by charge, precursor type, instrument, msn, and mass accuracy.

- An 'InChI' presearch that limits identification to compounds with the same structure as the search spectrum.

- Searching by exact precursor m/z.

- See "What's New in MS Search Program" topic in MS Search help for more detail.

What's New in MS Search Program?

The basic software of the NIST MS Search Program for Windows Version 2.3 is unchanged.

The following features were added to the current version 2.3, distributed with NIST 17 as compared to ver. 2.2, distributed with NIST 14.

HiRes MS/MS Hybrid Search

EI Hybrid search

presearch for EI Loss search

Types of Any Peak search: HiRes peak and HiRes loss

InChIKey presearch for all Library spectrum searches (finds all spectra, which have the same first InChIKey segment as the search spectrum, and compares them to the search spectrum)

Indexing old libraries for EI Hybrid and EI Loss, HiRes Any peaks Peak and Loss searches, InChIKey presearch (to index an MS/MS library for HiRes MS/MS Hybrid search, rebuild it with the library converter Lib2NIST.)

MS/MS Precursor m/z search

Precursor type constraint

Spectrum polarity filter

New Library Search output columns selection control for all Library spectrum searches.

Update list of libraries may be performing without exiting MS Search (Tools menu)

Movable column headers in Hit Lists and Spec List and a new column selection method located in Properties of a list, Items to Display.


The following features were added to the current version 2.2, distributed with NIST 14 as compared to ver. 2.0g, distributed with NIST 11 or with NIST 12 MS/MS library.

Using Retention Index in library searching: RI deviation of a hit from the search spectrum is used to penalize the Match Factor.

Indexing older user libraries to use saved in them RI values for library searching

Displaying relevant RI values in the hit list

New definitions of derivatives are used for finding replicate spectra

Displaying derivative precursor in the Lib. Search hit list

Displaying additional MS/MS information in hit lists

Editing accurate peak m/z, intensities, peak annotations and compound RI in the built-in mass spectrum editor

All small molecule mass spectra in NIST libraries have InChIKeys linked to PubChem. These InChIKeys may also be used for searching compound information on the Web or for exact structure search in libraries.

Importing and displaying Glycan structures in KCF format; adding them to mass spectra in a user library

In-source/EI with accurate ion m/z spectra - High resolution mass spectra

  • Import of ‘in-source’ tandem spectra, or EI with accurate ion m/z spectra, which do not include a defined m/z of the precursor ion. To import these spectra, select  "in-source / EI (accurate m/z)" in Spectrum Import Options.
  • In-source/EI with accurate ion m/z spectra have accurate ion peak m/z and intensities. The accuracy is set in Spectrum Import Options.
  • In-source/EI with accurate ion m/z spectra may be searched in In-source/EI with accurate ion m/z and/or MS/MS library with the new In-source HiRes search (ion peak m/z tolerance down to  0.015 ppm or 6x10-5 m/z units), Similarity Simple, Identity Normal or MS/MS Presearch OFF search options. For this purpose, adding Reverse Search option may useful.
  • In-source/EI with accurate ion m/z spectra may be added to a user library. Currently, in-source/EI with accurate ion m/z spectra added with NIST MS Search to a user library may be searched with In-source HiRes search only with Presearch OFF option. Rebuld the library with Lib2NIST to get in-source HiRes search benefits.

A number of new features have been added to the version distributed with the 2012 release of NIST MS/MS Libraries.

A new MS/MS search for small molecules

  • Improved ability to identify compounds with a few dominant peaks – a common situation for Tandem MS.
  • More robust scoring for spectra acquired on imperfectly-tuned instruments

New Mass Spectrum Import Options

  • Control the number of decimal places in the input m/z
  • Set peak intensity threshold
  • Set Prepend/Overwrite/Ask automatic mass spectrum import option
  • Import in-source or EI spectrum with accurate ion peak m/z and intensities.
  • Import MS/MS and in-source spectra from JCAMP files (October 2012, nistms32.dll version or later)

Note that the following features were added to the previous version  (distributed with NIST 11, version 2.0g)

A new Exact Mass Search and similar to it Exact Mass Constraint allow searching for an exact mass of a precursor using its mass or formula or m/z of the precursor ion.  This search and constraint take into account the presence or absence of an electron, adducts or losses; accepts uncertainty in ppm or millimass units; and allows searching for isotopic or monoisotopic peaks.

Ability to use accurate mass to search exact fragment ion mass values in NIST libraries mainlib, replib, and nist_msms using Exact Mass in the Any Peaks Search.

Display of the exact mass with any spectrum that has an associated chemical formula.

Manage and search as many as 127 separate MS libraries instead of 16, which was the limit in previous versions.

Optional display of columns in Hit Lists containing the number of synonyms and the number of other databases in which the hit appears.  The hit list can be sorted according to the values in these columns.

Maximum number of spectra in a database has been increased from 786,420 to 1,048,560.

Full compatibility with most recent NIST Peptide MS/MS libraries.

Copy selected lines from Hit List or Spec List into Windows Clipboard as tab-delimited Unicode text; this may be conveniently pasted into Excel.

Spectra in the MSP text format can be imported from the Windows clipboard into the Spec List via a Right Mouse button (RMB) menu option.

Searching for words in mass spectrum text information window (use context menu).

Optional exclusion of Homologues from the results of Structure Similarity search.

Import spectra from mzXML and mzData files.

Multiple CAS Registry numbers for a spectrum.  A small fraction of spectra in NIST 14 has more than one CAS r.n.  Each CAS r.n. may be found in the CAS Number search.

Tags for searching in Spectrum Text Info have been added to Tags in Comment constraint

New MS/MS Instrument Type Constraint

An alternative peak matching method to improve the reliability of the score when searching noisy MS/MS spectra.

When a Tag from the "Comment" field is displayed separately, its display in the "Comment" field is suppressed.


Combining fragment-ion and neutral-loss matching during mass spectral library searching:  

A new general purpose algorithm applicable to illicit drug identification
Arun Senthan Moorthy, William Edward Wallace, Anthony José Kearsley, Dmitrii V Tchekhovskoi, and Stephen E. Stein
Anal. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.analchem.7b03320 • Publication Date (Web): 20 Nov 2017