GNPS Public Spectral Libraries


Library Name View Description
All GNPS Library Spectra View This contains all available spectra available publically for search at GNPS. All interactively explore fragmentation with our new visualizations.
GNPS Library View The GNPS library contains natural product compounds from user contributions.
FDA Library Pt 1 View Approved drug library from Selleckchem Part 1 run by Sirenas MD.
FDA Library Pt 2 View This set of reference compounds generated by the Dorrestein Lab contains 535 FDA natural product compounds complements part 1.
PhytoChemical Library View 140 compounds from the Prestwick Phytochemical Library generated by the Dorrestein Lab.
NIH Clinical Collection 1 View 327 compounds from the NIH Clinical Collection 1 generated by the Dorrestein Lab. Further information about the collection can be found here .
NIH Clinical Collection 2 View 164 compounds from the NIH Clinical Collection 2 generated by the Dorrestein Lab. Further information about the collection can be found here .
NIH Natural Products Library Round 1 View 1256 compounds from the NIH Natural Products Library generated by the Dorrestein Lab. Further information about the collection can be found here .
NIH Natural Products Library Round 2 Positive
Negative 		The NIH Natural Products Library Round 2 was generated by the Dorrestein Lab (UC San Diego) from 4,545 compounds from the NIH ‘ACONN’ Natural Products Library provided by Ajit Jadhav (NIH/NCATS) . The 2018 release contains fragmentation spectra collected on qTOF MS in positive (3,386) and negative (1,863) ionisation mode. The 2020 release includes additional MS/MS entries for the positive ionisation mode on qTOF (806) and Q-Exactive mass spectrometers (1,315) that were obtained using the Ion Identity Networking workflow. The spectral library was created by Louis-Felix Nothias, Mingxun Wang and Robin Schmid (UC San Diego).
Pharmacologically Active Compounds in the NIH Small Molecule Repository View 1460 compounds from the Pharmacologically Active Compounds in the NIH Small Molecule Repository generated by the Dorrestein Lab.
Faulkner Legacy Library provided by Sirenas MD View 127 compounds from the Faulkner natural product legacy library.
EMBL Metabolomics Core Facility (EMBL MCF) View Standards run by EMBL Metabolomics Core Facility (EMBL MCF)
Pesticides Positive
Negative 		Pesticide MS/MS spectral library (204 compounds) generated by the Dorrestein Lab and the CNRS for the 3D-Plant2Cells project, funded under the European Commission Horizon2020 program (MSCA project 704786). Standards were run on Q-Exactive and Maxis (q-TOF) tandem mass spectrometer in both positive and negative ionisation mode.
Medicines for Malaria Venture Pathogen Box Positive
Negative 		400 compounds analyzed on an Agilent 6538 Accurate Mass QTOF LC/MS in Positive/Negative ionization mode by Sirenas LLC. Funding generously provided by the Bill and Melinda Gates Foundation.
LDB Lichen Database Positive
Negative 		MS/MS spectra of 241 small molecules isolated from lichens collected in the chemical library of S. Huneck (Berlin Garden and Botanical Museum) provided by Harrie Sipman and Robert Lücking. The spectra were produced by three different LC-MS machines, ie and Agilent 6530 qToF (Pierre Le Pogam, University of Paris-Sud, University of Paris-Saclay, Joel Boustie, University of Rennes 1), a Waters Xevo G2-XS qToF (David Rondeau, Thomas Delhaye, University of Rennes 1) and a Thermo Q-Exactive Orbitrap (Jean-Luc Wolfender, Pierre-Marie Allard, University of Geneva). The LDB currently contains more than a thousand spectra across different machines, including diverse adduct spectra in addition to the [M+/-H]. The most common scaffolds in lichens are represented : depsidones, dibenzofuranes, pulvinic acids, paraconic acids, chromones, quinones, xanthones, monoaromatic compounds, quinones, xanthones and chromones. These spectra are not single energy but the consensus of spectra produced at different energies. For Agilent, these were 10, 25 and 40 eV in ESI-, (and also 2.5, 5.0 and 7.5 eV for the more fragile depsides), and 5, 20 and 35 eV in ESI+ or APCI+ for terpenes. For Waters, the collision energies were 10, 20, 30 and 40 eV in ESI- and ESI+. The Thermo spectra were acquired using Normalized Collision Energy (NCE) based on the measured m/z value and three energies : 15, 30, 45 eV.
GNPS Matches to NIST14 View 5,763 High confidence matches to NIST14 MS/MS library spectra.
GNPS Collections Miscellaneous View Miscellaneous reference compounds run specifically for GNPS-Collections
GNPS Collections Bile Acid Library 2019 View Reference MS2 spectra for 21 commercial bile acids and 4 synthesized amino acid conjugated bile acids run in positive and negative mode, including spectra of observed adducts.
GNPS Sigma's Mass Spectrometry Metabolite Library (MSMLS) View This library contains 863 MS/MS from molecules in Sigma's Mass Spectrometry Metabolite Library. MSMLS is a collection of high quality small biochemical molecules that span a broad range of primary metabolism. These standards consisted of lipid-like molecules and water-soluble sugar compounds. The chemical standards were run on a Q-Exactive in positive and negative mode.
PSU Sigma's Mass Spectrometry Metabolite Library (MSMLS) View This library contains 576 MS/MS spectra using small molecules from IROA's Mass Spectrometry Metabolite Library of Standards (MSMLS). These standard MS/MS spectra were generated from SCIEX 5600 TripleTOF with positive and negative mode at Metabolomics facility The Pennsylvania State University
Dereplicator Identified MS/MS Spectra View MS/MS spectra identified in GNPS Public data automatically by dereplicator tool. Searching various compound databases, including marinlit, etc. and best matching MS/MS spectra with significant p-values.
Pacific Northwest National Lab (PNNL) Lipids View Positive
View Negative 		MS/MS spectra from 1790 Lipids provided by Thomas Metz's group at the Pacific Northwest National Lab (PNNL), collected in positive/negative ionisation mode and multiple collision energy. Most compounds were annotated using LIQUID tool in real samples.
MIADB Spectral Library View MS/MS spectra from 172 monoterpene indole alkaloids provided by Mehdi Beniddir and coll. (Universite Paris-Sud, Universite Paris-Saclay).
Compounds were collected from the chemical libraries of Universite Paris-Sud, Universite Paris-Descartes, Institut de Chimie des Substances Naturelles, Université d'Angers, Muséum national d'Histoire Naturelle (France), Universite de Liege (Belgium), University of Malaya, (Malaysia), Institut of Chemical Research of Catalonia (Spain).
For each compound an average MS/MS spectrum of three collision energies (30, 50 and 70 eV) was obtained, in the positive mode, using mono-charged molecular or pseudomolecular ions.
IQAMDB IsoQuinoline and Annonaceous Metabolites Database View MS/MS spectra of 220 isoquinoline alkaloids and some further annonaceous metabolites provided by Beniddir, Le Pogam and coll. (Universite Paris-Saclay, France). The spectra were generated using an Agilent 6546 qTof (Universite Paris-Saclay). Compounds were collected from the in-house chemical libraries of Universite Paris-Saclay (France), accumulated during decades of phytochemical investigations on annonaceous plants by Pr. M. Leboeuf and co-workers, and also from the Universite of Angers (France), and the Amazonas State University (Manaus, Amazonas, Brazil). The most common isoquinoline scaffolds are comprised in the library: benzylisoquinolines, bisbenzylisoquinolines featuring diverse assembly modes, protoberberines, berberines, proaporphines, aporphines, morphinanes, promorphinanes, benzophenanthridines, protopines, cularines, spirobenzylisoquinolines etc.
Sam Sik Kang Legacy Library View MS/MS spectra of 233 phytochemicals (184 positive and 153 negative) from Prof. Sam Sik Kang (Seoul National University)'s legacy chemical library. The spectral library was created by Sang Hee Shim (Seoul National University) and Kyo Bin Kang (Sookmyung Women's University).
HCE Cell Lysate Lipids Spectral Library View The spectra correspond to cell lipids extract of Human Corneal Epithelium cell. This lipids belong to phospholipids and sphingolipids classes.
Lipids of human conjonctivals cells (IOBA-NHC) View This library contains 200 MS/MS spectra of lipids from human conjonctival cells (IOBA-NHC cell line). The lipids belong to the sphingolipids, glycerophospholipids and glycerolipids subclasses.This library was generated by Orlane Lectez, Romain Magny and Nicolas Auzeil from Université de Paris on a Waters Synapt G2 mass spectrometer operated in positive and negative ion mode in the Olivier Laprevote Lab.
Nutri-Metabolomics View Positive View Negative This library is made with Orbitrap LTQ-XL mass spectrometer. Scan for full scan was of 30,000 while, MSMS were acquired at 7500 resolution. The CID of 35 eV was applied. References for operational conditions of Orbitrap and LC columns are here: DOI 10.1007/s11306-015-0935-z and DOI: 10.1002/mnfr.201901137.
This library consists of different analytical standards which were purchased form Sigma Aldrich for Fondazione Edmund Mach (Italy), for Nutri-metabolomics research.
Compounds that are included in this library are: small phenolic acids, organic acids, fatty acids, carnitines, indoles, some aroma compounds, endogenous human metabolites. They were purchased for two purposes: i) the confirmation at level I of some metabolites, ii) look for matching substructures between biomarkers in studies and analytical standards.
GNPS Sciex Library View The Sciex dataset contains authentic standards from different compound libraries and single reference standards were used. Specifically, the Agilent LC/MS Pesticide Comprehensive mix, Sigma Aldrich Bile Acid/Carnitine/Sterol Metabolite Library of Standards, Sigma Aldrich Fatty Acid Metabolite Library of Standards and Sigma Aldrich Acid Metabolite Library of Standards were used. Standards were dissolved in suitable solvents and mixed in 43 mixtures in such way to avoid overlap of isomeric and isobaric substances. Standard mixtures were analyzed using a Sciex Exion AD liquid chromatography system coupled to a Sciex X500R QTOF-MS. Separation was achieved on a Phenomenex Kinetex F5 column (150 mm × 2.1 mm ID, 2.6 μm particle size) with a gradient from eluent A (100 % H 2 O + 0.1 % formic acid) to eluent B (100 % acetonitrile + 0.1 % formic acid) using the following gradient: 100/0 at 0 min, 100/0 at 2.1 min, 5/95 at 14 min, 5/95 at 16 min, 100/0 at 16.1 min, and 100/0 at 20 min. Column temperature was set to 30 ◦ C and flow rate to 200 μL/min. Data was acquired by data dependent acquisition of MS/MS spectra using a collision energy ramp from 20 to 50 eV. The MS was automatically recalibrated every five injections in MS1 and MS/MS mode.
Berkeley Lab MS/MS spectral library View Berkeley Lab MS/MS spectral library of endogenous metabolites v0.1 (24,563 spectra) compiled and analyzed by the Northen Lab and DOE JGI with funding from the United States Department of Energy Office of Biological and Environmental Research under Contract No. DE-AC02-05CH11231 to Lawrence Berkeley National Laboratory.
Propogated Library - IIMN-based Library View Spectral library entries extracted from experimental datasets by the IIMN workflow. Ion Identity Molecular Networking connects ions of the same molecule. Note: This library is by default not selected for search in GNPS and must be explicitly selected.
Massbank Spectral Library (3rd Party) View ESI Positive MS/MS spectra from Massbank.
Massbank EU Spectral Library (3rd Party) View MS/MS spectra from Massbank EU that are not included in Massbank JP.
Massbank NA Spectral Library (3rd Party) View MS/MS spectra from Massbank NA that were not present in Massbank JP.
ReSpect Spectral Library (3rd Party) View ESI Positive MS/MS spectra from ReSpect for Phytochemicals.
HMDB Spectral Library (3rd Party) View MS/MS spectra from HMDB.
CASMI Spectral Library (3rd Party) View MS/MS spectra from the CASMI challenges 2014 and 2016. The CASMI is an open contest on the identification of small molecules.
Sumner Spectral Library (3rd Party) View The Bruker MetaboBASE Plant Library contains ~1300 spectra of ~300 plant metabolites, including flavonoids, phenolics, sapogenins and organic acids. This library was generated by Prof. Lloyd W. Sumner and Drs. Dennis Fine and Daniel Wherritt from the Plant Biology Division of the Noble Foundation, Ardmore, OK, USA.

Recent GNPS-Community Library Additions


Copyright © 2023. Last modified: 2023-10-30. Version 1.3.16-GNPS.