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Spectral Libraries

Bruker Metabolomics Spectral Libraries

Create deeper metabolomics insights through correct compound identification with tailored spectral libraries

Confident Identification

Dedicated Libraries for Bruker Mass Spectrometry instruments



MS/MS Spectral libraries

Spectral libraries for high confidence in compound identification

High quality MS/MS spectra measured for reference compounds on Bruker Mass Spectrometry instruments.
MS/MS spectra matching, and accurate precursor information allow for identification of known compounds.
Knowledge Gain
Understand more about the compounds detected in your samples.
Bruker MS/MS spectral libraries contain information on hundreds of thousands of compounds.


Bruker Metabolomics Spectral Libraries

Bruker MetaboBASE® Personal Library 3.0

Mass spectral libraries containing relevant endogenous and exogenous metabolites enable you to match to experimental MS/MS spectra for automatic dereplication. The number of compounds contained in these spectral libraries is an important factor and has continuously grown over recent years, enabling the identification of an increasing number of known metabolites.

This is reflected for example by the new version of the Bruker MetaboBASE® Personal Library 3.0. It contains: 

  • MS/MS spectra of over 100,000 synthetic or isolated standards derived from the well-known METLIN(*) compound library, including di- and tri-peptides, in addition to endogenous and exogenous metabolites to study changes that occur in biological systems. These data have been acquired on QTOF instruments. Data from over 14,000 have been acquired on Bruker QTOF instruments.
  • In-silico generated MS/MS spectra for more than 233,000 compounds in this library, paving the way for a faster tentative identification of relevant targets which are not yet available as pure reference standards.
All spectra were measured in positive and negative mode at different collision energies, and poor-quality spectra were discarded. Collision energies of 10, 20 and 40 eV have been used for the in-silico library, 10/25 and 25/50 eV for the others.
Supplemental spectral data includes InCHi, SMILES, and CAS identifiers and synonyms for most substances. Database IDs and hyperlinks to external databases, including HMDB, METLIN, and PubChem, let you quickly bring identified metabolites into a biological context.

The Bruker MetaboBASE® Personal Library 3.0 has been provided by well-known Prof. Gary Siuzdak and Dr. Paul Benton.

*METLIN™ is a trademark of THE Scripps Research Institute.

Note: the Bruker MetaboBASE® Personal Library 3.0 is only supported by MetaboScape® 4.0 and higher.

Bruker HMDB Metabolite Library 2.0

It is not only the number of spectra that matters, though also the quality of the data contained in the libraries, which is highly important for confident identification.
All spectra contained in the Bruker HMDB Metabolite Library 2.0 were manually inspected to remove noisy spectra and contaminant peaks. The masses of precursor and fragment ions were corrected to match the theoretical mass values and isotopic pattern distributions.

The second version of this spectral library provides more than 6000 MS/MS spectra for more than 800 compounds selected from the Human Metabolome Data Base (HMDB) plus Retention time information. Data for the Bruker HMDB Metabolite Library 2.0 was acquired using pure reference standards. All compounds were measured on an impact series QTOF high-resolution mass spectrometer using 5 different collision energy levels.

Retention time information for reversed phase LC for approximately 600 metabolites adds further orthogonal information for increasing confidence in identification of metabolites found in, for example, urine, blood and other biofluids.

The T-ReX Elute Metabolomics-kit: RP is a dedicated Reversed-Phase LC column kit for enabling matching retention times to corresponding values in Bruker HMDB Metabolite Library 2.0. It also contains methods and Standard Operation Procedures (SOPs) for LC-MS/MS data acquisition and is part of the complete

T-ReX LC-QTOF solution for simplified non-targeted metabolomics.

The Bruker HMDB Metabolite Library is exclusively provided by Bruker and was generated in collaboration with Prof. Liang Li and Prof. David Wishart and their teams at the University of Alberta, Canada.

Bruker MetaboBASE® Plant Library

Spectra were created using commercial standards and putatively identified metabolites found in the model legume plant, Medicago truncatula. This enables identification of metabolites in plants and food research. The Bruker Sumner MetaboBASE® Plant Libraries also contains 228 spectra for 84 compounds extracted identified by MS and NMR.

The recent addition of Collisional Cross Section (CCS) values acquired on a Bruker timsTOF instrument for more than 150 compounds enables matching of orthogonal information derived from trapped ion mobility separation. This allows the identification of compounds based on CCS values in addition to precursor mass and isotopic pattern, retention time, and MS/MS spectra.The spectral libraries contain spectra acquired at multiple collision energies and were acquired in ESI negative-ion mode. For most compounds the molecular formula, structures in *.mol format, InChI, and SMILES are provided.


Bruker NIST 2020 Mass Spectral Library

The Bruker NIST 2020 Mass Spectral Library is a product of the National Institute of Standards and Technology (NIST), redistributed by Bruker. The library contains the complete NIST package and covers compounds from Marbofloxacin antibiotic, Naphthalene E&L, APCI, Luteolin glucoside flavone, Retinoic acid metabolite, Fuc-GM1(d18:1/16:0) glycolipid, and more. It is subdivided into several spectral libraries:

  • The NIST/EPA/NIH Mass Spectral Library: This release contains 350,704 electron ionization (EI) spectra (306,643 compounds, 43,774 replicate spectra) – an increase of 39,729 more compounds than NIST17
  • The Gas Chromatography Retention Index and Methods Library: This contains 447,289 retention indices (RI) values for 139,382 compounds, an increase of 40K compounds. Further 114,629 compounds with both RI & MS are included
  • The NIST Tandem Mass Spectral Library of small molecules: This contains 1,320,389 spectra of 185,608 precursor ions from 30,999 chemical compounds
For detailed description please refer to NIST20: Updates to the NIST Tandem and Electron Ionization Spectral Libraries at
Beside the original NIST Search Software to evaluate and use the library (MS Interpreter and Hybrid Search). The small molecule high resolution accurate mass (HRAM) MS/MS library is formatted in a Bruker-specific format to be directly readable by the software MetaboScape® 2021 and higher, and DataAnalysis version 5.2 and higher. It contains MS/MS spectra of 27840 compounds acquired in high resolution accurate mass (HRAM) mode.


Bruker Metabolomics Spectral Libraries

From samples to knowledge: create deeper metabolomics insights through correct compound identification

The metabolome consists of a complex mixture of small molecules covering a wide dynamic range. As the number of detectable substances continues to grow to include mammalian, microbial, and plant-based endogenous and exogenous metabolites, identification is essential to fully understand the biological context of metabolomic data. 

Therefore, the annotation of previously described known target metabolites, known as dereplication, becomes critical and must be both automatic and conclusive.
Meaningful insights in a biological context can only be obtained if compounds are identified with high confidence. This confidence is obtained by matching different criteria stored in databases and spectral libraries containing relevant endogenous and exogenous metabolites.

Information which can be derived from high quality LC-MS/MS data  acquired on your Bruker QTOF instruments and matched to spectral libraries for confident identification includes accurate precursor mass and isotopic pattern, MS/MS spectra and retention time information, as well as CCS values. MetaboScape® enables matching this information according to user definable threshold levels. The graphical Annotation Quality “AQ” representation enables the analyst to readily evaluate their confidence for each annotation automatically generated in MetaboScape®.


Annotation Quality symbol

Integrated Solutions for Fast & Confident Metabolite Dereplication

Several complementary spectral libraries are supported in the fully integrated MetaboScape® workflow solution for automated and positive identification of known compounds. These metabolite libraries include Bruker HMDB Metabolite Library, Bruker MetaboBASE® Personal Library, Bruker MetaboBASE® Plant Library, Bruker NIST Spectral Library, and further public as well as custom libraries.   

These spectral libraries are stored on your PC, providing local search capabilities to provide both performance and throughout and to eliminate privacy concerns.


Bruker Metabolomics Spectral Libraries

Spectral Library search

For the identification of metabolites, all available information needs to be collected. This includes the comparison of fragment spectra from pure standards to acquired spectra from Metabolomics samples. The specific fragment masses and intensity distribution contribute valuably to metabolite identification.

The spectral library content is queried using the MetaboScape® software or Bruker DataAnalysis (unless not otherwise noted). Both run on local PCs and provide private search capabilities. Additionally, both software solutions are designed to create custom libraries of proprietary compounds, and to export them to an ASCII format. This allows sharing libraries with colleagues in an open source format.

Spectral Library editor

Building own MS/MS spectral libraries is easily possible with the Bruker library editor. Extend the coverage of existing compound spectra or complement existing information with further reference measurements from e.g. varying collision energies. Library spectra measured at multiple collision energies ensure the automatic and high confidence identification of a wide range of metabolites.


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