The NIST 26 Mass Spectral Library
& Search Software (NIST 2026/2023/2020/EPA/NIH)

• EI library adds 35K more compounds with retention indices.
• MS/MS tandem library grown to 51K compounds, all at multiple fragmentation energies and conditions. 33% more compounds. 35% more spectra. 3.2M spectra.
• NIST MS Search 4.0 (new release) made significant enhancements to its metadata and software, such as full chromatogram analysis and multilevel analysis such XIC-based. See What's New.
• Upgrade discount for any previous versions

• EI library adds 40K more compounds with retention indices, most selected, measured, and evaluated by NIST.
• MS/MS tandem library grown to 3.2M spectra of 68K compounds at multiple fragmentation energies and conditions. 33% more compounds and 35% more spectra.
• NIST MS Search 3.0 (new release) made significant enhancements to its software.

• Please see Update Registration to receive e-mail notifications when future updates to your NIST and/or Wiley MS libraries are available.

Main scope of changes:

• The NIST 23 MS/MS Tandem library has grown to ~50,000 compounds (2.4M spectra) - all at multiple fragmentation energies and conditions.
• NIST 23 EI library (GC/GS) has added spectra of 40,000 compounds with their retention indices to their EI Library, most of them selected by, measured and evaluated at NIST.
• NIST has made significant enhancements to their metadata and their software, Mass Spectral Search 3.0.

New features of the program and database are:

• Major Spectrum Type choice (EI, Tandem, Peptide, All) helps to suppress display of search parameters most probably not used.
• Name search sorting has been increased from 16 to 249 characters; the list of names has been split into two panes: compound list in the upper pane and spectrum list in the lower pane. All spectra derived from a selected compound are shown in the spectrum list (EI: replicate, derivatives, stereoisomers; Tandem: energy, instrument, fragmentation type).
• A list of 'Other Databases' (compound references) for each compound has been significantly extended. See file Other_DBs.xlsx
• Added a new search method - Partial Spectrum Search - for searching with abbreviated spectra.
• All retention indices are displayed in the EI hit list. They are used for EI search with RI match factor correction. If experimental data is not available for a compound, a reliable AI predicted value is used in its place.
• Hovering a mouse pointer around a peak in a spectrum plot displays peak annotation.

Changes to the program (compared to MS Search v2.4 / NIST 20):

• Term "In-source/EI with accurate ion m/z" replaced with "HiRes No Precursor"
• "Penalize rare compounds" EI library search option has been retired.
• PubChem InChiKey search has been replaced with Google search.
• Major mass spectral text file extension has been changed from .MSP to .MSPEC. Extension .MSP is still recognized.

Features added to recent versions (NIST 20 MS Search v.2.4 and earlier):

• Major expansion of coverage of analytically important compounds of all classes, based on documented importance of each compound.
• For the first time ever, almost all spectra measured and fully evaluated entirely at NIST.
• Modernized and enhanced evaluation procedure allowing for multiple evaluations of spectra.
• Enhanced comparison of replicate spectra and 'best of replicates' selection. The entire library is now based on chemical structures using the NIST-developed InChIKey representation.
• Enhanced quality control using greatly improved MS Interpreter program that links ions to originating structures in the precursor molecule.
• Enhanced method for assisting the examination of results having many spectra generated by Tandem spectra. See "What's New in MS Search Program" topic in MS Search help for more details.

Some noteworthy features of the program and database in recent versions:

• 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.
• MS/MS browsing window and MS/MS library
• New type of mass spectrum search: MS/MS Identity search for searching for MS/MS spectra in MS/MS libraries. The updated Lib2NIST converter is a tool for creating MS/MS libraries. To create a MS/MS library, run Lib2NIST and check "MS/MS spectra only" option. For this search to work, the MS/MS spectra must contain precursor m/z values.
• Derivatives for GC/MS can be represented as their precursor molecules using a large number of derivative types.
• Retention indexes in some of Main and Replicates libraries spectra. Automatic Retention Index estimation from chemical structure (right-click spectrum text window, select Properties, Retention Indices). Polar columns were new to the 2008 release.
• Structural replicates display (in addition to usual CAS number matching) in Main and Replicate libraries, including a new feature: displaying derivatives and a wider range of tautomers. 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. The Structure similarity search algorithm has been changed: now it includes homologue recognition that generates a match factor of 1000 for homologs. You will need to rebuild structure search databases in user libraries (as you usually need to do after editing a user library containing structures.)
• Searching in the Contributor/Comment spectral records and extracting tagged fields into the displayed spectrum text information.
• Drag and Drop - Data can be dragged and dropped between windows. Point mouse to the name of the compound in the spectrum plot window, press and hold the left mouse button, drag the spectrum and drop it into Spec List or Compare Window.
• User Library Structures - This feature has been present for some time, but many are unaware of it.
• Compare Views - There are a number of different ways for you to 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.
• Thermodynamics-based MS Interpreter program version 3.0. This program now works for both low and high mass accuracy spectra and permits using a mouse to select parts of a chemical structure for mass and formula determination and analysis.

Library improvements

• Major expansion of coverage of analytically important compounds of all classes, based on documented importance of each compound.
• For the first time ever, almost all spectra measured and fully evaluated entirely at NIST.
• Modernized and enhanced evaluation procedure allowing for multiple evaluations of spectra.
• Enhanced comparison of replicate spectra and 'best of replicates' selection. The entire library is now based on chemical structures using the NIST-developed InChIKey representation.
• Enhanced quality control using greatly improved MS Interpreter program that links ions to originating structures in the precursor molecule.

Search software improvements

(Note: Version 3.0 features are not yet listed here.)

The following features were added to version 2.4 (2020), distributed with NIST 20 as compared to ver. 2.3, distributed with NIST 17.

For Tandem Spectrum Searching

• These greatly aid the examination of hit lists containing many spectra that may arise from the same compound (using any type of search):
  • New columns in hit lists (selectable from Properties menu): Precursor Ion, Instrument, Energy
  • Filter button (refine hit list using Instrument and Precursor Ion Type settings).
  • Constraints have been enhanced to correspond to Filter button
• When searching with high mass accuracy spectra, the NIST low resolution library (lr_msms_nist) is searched using wide m/z tolerances (unit mass resolution)
  • This ensures that compounds with only low resolution spectra can be found when searching with high mass accuracy spectra.
  • If searching with low resolution spectra, simply specify a wide m/z product ion tolerance for searching any library.

GC Retention Index

• New artificial intelligence predicted values roughly twice as accurate as earlier version
• RI columns optionally shown in hit lists for any EI search.

In the Librarian tab, a replace button was added. This replaces a spectrum in a selected library without changing its ID number.

The MS Interpreter included with NIST 2020 has been greatly improved from prior versions. It processes EI and positive and negative ion tandem spectra of any mass accuracy.

New features of the NIST 17 program and database are:

• EI Library Expansion: 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.
• MS/MS Library Expansion: 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.
• New 'Hybrid Search' search type for all spectrum types, enable finding many more similar compounds in the hit list. It requires a precursor mass.
• 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.
• Searching by exact precursor m/z.

For Electron Ionization Mass Spectra (Low Resolution)

• A new EI Hybrid Search (Similarity/Hybrid). Hybrid searching uses both the logic of normal searching plus the logic of neutral loss searching. It uses the same algorithm as MS/MS Hybrid search with unit charges and Nominal MW instead of Precursor m/z.
  

  A few articles mentioning hydrid search:

  • Combining Fragment-Ion and Neutral-Loss Matching during Mass Spectral Library Searching: A New General Purpose Algorithm Applicable to Illicit Drug Identification
  • The Hybrid Search: A Mass Spectral Library Search Method for Discovery of Modifications in Proteomics
  • Introduction of NIST 17—A Major Update of Mass Spectral Libraries and Software—at the 65th ASMS Conference on Mass Spectrometry and Allied Topics
• Presearch for EI Similarity/Neutral Loss search

For Tandem (MS/MS) and High Resolution Mass Spectra

• HiRes MS/MS Hybrid Search

  Search for an MS/MS spectrum in a library of MS/MS spectra. Uses the logic of normal searching and the logic of neutral loss searching. Only library spectra with the same precursor charge as that of the search spectrum are considered. If a search spectrum precursor charge is missing, it is set to +1. If "Peptide" check box in MS/MS tab of Library Search Options is selected, product ion charges from library spectrum peak annotations are used. Otherwise, all product ion charges are set to 1 or 2 in case precursor charge is 2 or greater. Neutral loss searching is done after changing library spectrum peaks' m/z values so that they have the same neutral losses with respect to the search spectrum precursor as they had with respect to the library spectrum precursor in the original library spectrum. This changed spectrum is compared to the search spectrum; found peak matches are included in the dot product. If a library spectrum peak matches different search spectrum peaks in both direct and neutral loss searches, its intensity is split between these two matches to maximize the dot product and keep total library spectrum intensity unchanged.

  The changed library spectrum product ions' m/z are calculated by adding (M_S - M_L)C_M/C_P, where M is precursor m/z, C is charge, subscripts are: S - in search spectrum, L - in library spectrum, M - in both precursors, P - in product ion.

  

• Types of Any Peak search: HiRes peak and HiRes loss
  
• Display additional MS/MS information in hit lists
• Edit accurate peak m/z, intensities and peak annotations in the built-in mass spectrum editor
• MS/MS Precursor m/z search
• Precursor type constraint. Restrict MS/MS spectra in search results to specific precursor types, exclude isotopic precursors, display MS3 and higher spectra in addition to MS2. Works with NIST 17 nist_msms library. Rejects spectra which do not have correct Precursor type syntax. This is in addition to other filters for MS/MS spectra to limit hits by charge, precursor type, instrument, msn, and mass accuracy.
  
• Spectrum polarity filter
  

For all Mass Spectra

• An '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.

  InChIKey - Restrict search to only molecules with the first segment of InChIKey being the same as that of the search spectrum or a user supplied InChIKey. Use this presearch when the chemical structure or InChIKey of the search spectrum is known. To use this presearch, a library must be indexed by InChIKey. An older library may be indexed by selecting (Re)Index InChIKey from Tools menu. The search and found compounds do not have to have mass spectral peaks: hits with score=0 are included in the hit list. This allows to search nist_ri library. To retain all hits (up to 400) use Identity Normal, Quick, or Similarity Simple search. Other searches impose certain conditions on the library spectra thus excluding hits.

• When a spectrum is associated with a structure in the Spectrum Information dialog box of the Librarian tab view, the InChI Key is automatically associated with the spectrum.
  
• Columns in any Hit List can be positioned as desired.
• Update list of libraries may be performed without exiting MS Search.
  
• Indexing old libraries for EI Hybrid, EI Loss, HiRes Any-peaks Peak and Loss searches, and InChI presearch. This includes third party libraries like the Wiley Registry.
  • Structure Search Database Builder updates user library structure indexation.
  • (Re)Index Exact Mass creates index files for Exact Mass Search
  • (Re) Index Accurate m/z creates index for Any Peaks Accurate m/z and Accurate Loss peak types
  • (Re)Index EI Hybrid Search create index for EI Hybrid Search presearch and EI Neutral Loss search presearch
  • (Re)Index InChIKey creates index for InChIKey presearch
  • (Re)Index RI creates a file for using RI with a library.
• A new version of MS Interpreter allowing for high accuracy mass spectra and exact masses for fragment ions.
  • High Mass Accuracy Spectrum Import and Display
  • Zoom Control [keyboard shortcuts]
  • Manual fragment selection
  

Some other noteworthy features that are not new but you might not be aware of:

• MS/MS browsing window and MS/MS library
• New type of mass spectrum search: MS/MS Identity search for searching for MS/MS spectra in MS/MS libraries. The updated Lib2NIST converter is a tool for creating MS/MS libraries. To create a MS/MS library, run Lib2NIST and check "MS/MS spectra only" option. For this search to work, the MS/MS spectra must contain precursor m/z values.
• Derivatives for GC/MS can be represented as their precursor molecules using a large number of derivative types.
• Retention indexes in some of Main and Replicates libraries spectra. Automatic Retention Index estimation from chemical structure (right-click spectrum text window, select Properties, Retention Indices). Polar columns were new to the 2008 release.
• Structural replicates display (in addition to usual CAS number matching) in Main and Replicate libraries, including a new feature: displaying derivatives and a wider range of tautomers. 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. The Structure similarity search algorithm has been changed: now it includes homologue recognition that generates a match factor of 1000 for homologs. You will need to rebuild structure search databases in user libraries (as you usually need to do after editing a user library containing structures.)
• Searching in the Contributor/Comment spectral records and extracting tagged fields into the displayed spectrum text information.
• Drag and Drop - Data can be dragged and dropped between windows. Point mouse to the name of the compound in the spectrum plot window, press and hold the left mouse button, drag the spectrum and drop it into Spec List or Compare Window.
• User Library Structures - This feature has been present for some time, but many are unaware of it.
• Compare Views - There are a number of different ways for you to 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.
• Thermodynamics-based MS Interpreter program version 3.0. This program now works for both low and high mass accuracy spectra and permits using a mouse to select parts of a chemical structure for mass and formula determination and analysis.

EI, MS/MS, and GC RI libraries have all undergone substantial enhancements in the 2014 release (see also statistics at the top of this page).

1. EI MS Library: Spectra for nearly 30,000 new compounds have been added since the 2011 version, with increased attention to adding metabolites (plant and human), drugs, and compounds of industrial and environmental importance. Emphasis has been put on spectra for a wider range of derivatization methods. Extensive improvements in chemical names, structures and replicate spectra have also been made, with particular attention to improving naming for derivatives.
2. Tandem MS/MS Library: The number of compounds from the 2012 version has increased by 30% to 9,345 (a 60% increase from 2011 version). With an increased focus on adding all possible precursor ions, this had led to an increased in the number of precursor ions by a factor of three relative to the 2012 version with a near doubling of the total number of spectra to 232K. All new spectra were acquired at high accuracy and resolving power, over a range of energies, and in both collision cells (beam type) and ion traps (up to MS3) in both positive- and negative-ion mode, when appropriate. A large proportion of these new compounds are metabolites, both from plants and humans. Spectra include metabolites, peptides (biologically active peptides and all di-peptides and tryptic tri-peptides), contaminants, lipids and more. Advanced noise removal processes have improved the quality of a number of spectra that appeared in earlier versions. Each spectrum contains extensive annotation, and now user libraries can be created with the same degree of annotation.
   • The MS/MS library now also includes more than 5,000 glycan (native and fluorescently-labeled) spectra of over 100 compounds (a tenfold increase over the previous release), shown in standard "cartoon" format shown below.
     
3. GI RI Library: RI data are provided for over 82,000 compounds, an increase of over 12,000 compounds from the 2011 version. More than 56K of these compounds have spectra in the EI Library. The total number of experimental RI values and GC Methods in this release is 387,463, which is an increase of over 10% from NIST 11. The detail of the GC Methods allows for the reproduction the analysis that resulted in the reported RI value and to see the original citation from which the data were derived. As with the previous release, it is possible to do a string search for text in the Text Info pane of a spectrum display to find keywords in titles or column types (RMB menu, Find selection). As has been the case for the last two releases the GC Method/Retention Index Library is also available without the mass spectral data and is provided with its own Search Program.

Updated Software: A number of major new features have been added to the search software. The most significant are

1. EI MS Library:
   • Optional use of retention index (RI) in browsing and library searching. The RI can be displayed in the hit list and/or used for penalize the Match Factor in library searches.
     
     Indexing of older user libraries allows RI values saved in them to be used for library searching.
     
     Spectra imported into the Librarian tab can be assigned an RI value via the Edit function for library searching purposes.
   • Simplified derivative identification. Names of derivative compounds have been extensively simplified to the underivitized precursor compound plus the derivative name (e.g. "L-Alanine, TMS derivative"). Derivative structures optionally can also be displayed as the underivitized precursor compound with the derivative name. (This is settable from View > Derivative Parent menu in the Lib Search tab.)
     
     The simplified names for derivatives also help in the hit list.
2. Tandem MS/MS Library (most data from ESI)
   • Additional information has been added to compound names in the Tandem MS library that show the precursor ion, instrument and energy.
     
   • Displaying additional MS/MS information in hit lists
     
   • Search scoring for spectra with few dominent peaks—a common situation in Tandem MS—has been improved in 2012.
3. All Libraries
   • The InChI chemical identifier has been added to each compound (in EI, GC/RI, and small molecule MS/MS libraries) - clicking on it optionally bring up a NIH (PubChem) entry for the compound. to PubChem. These InChIKeys may also be used for searching compound information on the Web or for exact structure search in libraries.
     
   • The spectrum editor and spectrum-import function have undergone significant enhancements to improve the development of user libraries. It is now capable of editing accurate mass data, adding certain field headers and contents, RI, and limited annotation of peaks. As existed in the previous version, it is still possible to use Comments Tags (see Help file) to add non-specific field headers and contents. The Other Names (Synonyms) of the dialog box is used to add Field Headers and the contents for those fields.
     
   • Structure chirality features are now supported. This has been the case for user libraries in past releases, but is now also the case for the mainlib and replib of the EI Library, currently to a limited extent.
     
   • Import of High resolution mass spectra (In-source tandem or EI with accuracy m/z)
     The Spectrum Import function has a significant change. In prior versions of MS Search, spectra were imported only as integer m/z values MS Search v.2.2 provides far more control, including accurate m/z value imports with a specified number of decimal places for EI and in-source CAD spectra as well as spectra obtained using MSMS techniques.
     (left NIST 2011 2.0g; right NIST 2014 2.0, similar to 2012 2.0g)
     • Import of "in-tandem" spectra, which do not include a defined m/z of the precursor ion. To import these spectra, select "In-source spectra" in Spectrum Import Options.
     • In-source spectra have accurate ion peak m/z and intensities. The accuracy is set in Spectrum Import Options: ion peak m/z tolerance down to 0.015 ppm or 0.00006 m/z units.
     • Importing and displaying Glycan structures in KCF format.
     
     (This is further described in Accurate Mass Capabilities in NIST14 Search Software[*] by James Little.)
   • A new In-source HiRes Identity Search for in-source/EI spectra with accurate m/z value ions was developed. This search is done against a user library containing in-source/EI accurate m/z-value or MS/MS spectra using libraries built with Lib2NIST. Search Options are set for MS/MS and In-source/EI with accurate m/z values in Spectrum Search Options dialog box that are located in MS/MS tab. Unlike the Identity MS/MS Search, this search does not compare precursor ion m/z values.
     
     • In-source spectra may be searched in In-source and/or MS/MS libraries with the new In-source HiRes search, Similarity Simple, Identity Normal or MS/MS Presearch OFF search options. For this purpose, adding Reverse Search option may useful.
     • In-source spectra with accurate m/z may be added to a user library. Currently, these may be searched with In-source HiRes search only with the Presearch OFF option. Rebuild the library with Lib2NIST to get in-source HiRes search benefits.

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.

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'ade;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.

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 Kovats 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

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 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.

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.