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Tandem Mass Spectral Library


The National Institute of Standards and Technology is responsible for an evaluated, tandem mass spectral library as an extension of the NIST/EPA/NIH Mass Spectral Library and the NIST Peptide Mass Spectral Libraries. The principal purpose of the library is to provide reference mass spectral data for the identification of compounds through the fragmentation of their ions generated by electrospray ionization. In conjunction with separation by liquid chromatography, this technique is widely used to identify components in many complex practical fluids and tissues, such as disease-related metabolites, drugs, and environmental contaminants. This database is available from distributors for testing and integration with existing instrumentation (http://chemdata.nist.gov/mass-spc/msms-search/).


Intended Impact

Modern mass spectrometers used in the field of metabolomics are capable of profiling hundreds of molecules in a single experiment. Each of these molecules is isolated and fragmented to form a mass spectrum. Therefore, interpretation of these tandem mass spectra is a critical step in the experimental workflow. Since metabolite mass spectra represent physical properties of these molecules, standard interpretation of these mass spectra and their full fragmentation identification has the potential to improve the success rate of all discovery experiments in metabolomics.


Biological mass spectrometry is a critical tool in the search for new markers of disease. These markers will be used as targets for tomorrow's diagnostics and therapeutics. NIST researchers are using their expertise in building mass spectral libraries to compile a library of consensus mass spectra of metabolites and other important compounds. Developing a comprehensive library of high quality tandem mass spectra is critical for establishing and advancing this technology.


  • Develop a tandem mass spectral library of all biologically relevant metabolite ions
  • Provide the library in a form that is easily searchable using software tools
  • Update and maintain the library as a reference data resource

Research Activities and Technical Approach

The mass spectrometers used to identify metabolites and other small molecules have improved greatly over the past ten years. While hundreds of compounds may be detected in a single experiment, identification of these compounds depends on the availability of libraries of standard reference mass spectra of all those compounds. Mass spectral libraries are built from measured spectra of known compounds and enable the use of sensitive search algorithms. The use of these algorithms and libraries (1) will lead to a higher percentage of identified spectra at the same level of reliability and (2) will greatly increase the robustness of the metabolite identification step.

The data for this project is both being generated 'in-house' at NIST and collected from several outside sources. To date, this mass spectral library contains >120,000 spectra for >15,000 ions of >7,000 compounds of biological and environmental relevance (including metabolites, bioactive peptides, amino acids and small peptides, sugars and glycans, lipids and phospholipids, drugs, pesticides, surfactants, and various contaminants). The spectra in the libraries have the features of being experimentally validated, critically evaluated, and annotated with great detail.

The metabolite library has been used in the profiling of complex biological reference materials such as human plasma. A website (http://srmd.nist.gov) has been designed to provide interactive access to experimental data produced at NIST and by its customers organized by SRM.

Additional Technical Details:


Building a High Quality and Comprehensive Tandem Mass Spectral Library. X. Yang, P. Neta, Y. Simón-Manso, L. Kilpatrick, Y. Liang, S. E. Stein. Poster presented at the 2012 International Conference of the Metabolomics Society.

Methods for Building High Quality and Comprehensive MS/MS Libraries.  X. Yang, P. Neta, Y. Simón-Manso, Y. Liang, L. Kilpatrick, J. Roth, M. L. A. De Leoz, W. Mi, S. E. Stein. Poster presented at the 60st ASMS Conference on Mass Spectrometry and Allied Topics, June 2012.

Developing qualitative LC-MS methods for characterization of Vaccinium berry Standard Reference Materials. M. S. Lowenthal, M. M.Phillips, C. A. Rimmer, P. A. Rudnick, Y. Simón-Manso, S. E. Stein, D. Tchekhovskoi, K. W. Phinney. Anal. Bioanal. Chem. 2013, in press. (DOI 10.1007/s00216-012-6346-3)

Major Accomplishments:

  • A large metabolite mass spectral library has been developed
  • A metabolite version of NIST MS Search 2.0 is available (Fig. below)
  • A website has been launched for distribution of the libraries and software (http://chemdata.nist.gov/mass-spc/msms-search)


(Zoom in picture)

End Date:


Lead Organizational Unit:


Related Programs and Projects:


Dr. Stephen E. Stein
phone: (301) 975-2505
fax: (301) 975-3670