GNPS API Overview¶
GNPS Library Spectra¶
All Public Library Spectra at GNPS¶
This gets you all spectra but without peaks.
https://external.gnps2.org/gnpslibraryjson
All Public Library Name List at GNPS¶
https://external.gnps2.org/gnpslibrary.json
Browse all spectra
https://external.gnps2.org/gnpslibrary
Download as JSON
https://external.gnps2.org/gnpslibrary/ALL_GNPS.json
Example JSON Format
[
{
"spectrum_id": "CCMSLIB00000579358",
"source_file": "Training_001.mgf",
"task": "03c206430208430c887ca025ea6c3641",
"scan": "1",
"ms_level": "2",
"library_membership": "CASMI",
"spectrum_status": "1",
"peaks_json": "[[164.033997,32294.500000],[179.057495,129907.101562]]",
"splash": "null-null-null-null",
"submit_user": "lfnothias",
"Compound_Name": "Theophyllin",
"Ion_Source": "LC-ESI",
"Compound_Source": "Commercial",
"Instrument": "Orbitrap",
"PI": "CASMI",
"Data_Collector": "CASMI2016",
"Adduct": "M-H",
"Scan": "-1",
"Precursor_MZ": "179.057",
"ExactMass": "0.0",
"Charge": "1",
"CAS_Number": "N/A",
"Pubmed_ID": "33919",
"Smiles": "CN1C2=C(NC=N2)C(=O)N(C)C1=O",
"INCHI": "\"InChI=1S/C7H8N4O2/c1-10-5-4(8-3-9-5)6(12)11(2)7(10)13/h3H,1-2H3,(H,8,9)\"",
"INCHI_AUX": "N/A",
"Library_Class": "1",
"SpectrumID": "CCMSLIB00000579358",
"Ion_Mode": " Negative",
"create_time": "2016-05-24 18:27:20.0",
"task_id": "03c206430208430c887ca025ea6c3641",
"user_id": "null",
"InChIKey_smiles": "ZFXYFBGIUFBOJW-UHFFFAOYSA-N",
"InChIKey_inchi": "None",
"Formula_smiles": "C7H8N4O2",
"Formula_inchi": "",
"url": "https://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=CCMSLIB00000579358",
"annotation_history": [
{
"Compound_Name": "Theophyllin",
"Ion_Source": "LC-ESI",
"Compound_Source": "Commercial",
"Instrument": "Orbitrap",
"PI": "CASMI",
"Data_Collector": "CASMI2016",
"Adduct": "M-H",
"Scan": "-1",
"Precursor_MZ": "179.057",
"ExactMass": "0.0",
"Charge": "1",
"CAS_Number": "N/A",
"Pubmed_ID": "33919",
"Smiles": "CN1C2=C(NC=N2)C(=O)N(C)C1=O",
"INCHI": "\"InChI=1S/C7H8N4O2/c1-10-5-4(8-3-9-5)6(12)11(2)7(10)13/h3H,1-2H3,(H,8,9)\"",
"INCHI_AUX": "N/A",
"Library_Class": "1",
"SpectrumID": "CCMSLIB00000579358",
"Ion_Mode": " Negative",
"create_time": "2016-05-24 18:27:20.0",
"task_id": "03c206430208430c887ca025ea6c3641",
"user_id": "lfnothias"
}
]
}
]
As MGF
https://external.gnps2.org/gnpslibrary/ALL_GNPS.mgf
Example MGF Format
BEGIN IONS
PEPMASS=407.186
CHARGE=1
MSLEVEL=2
SOURCE_INSTRUMENT=LC-ESI-qTof
FILENAME=Plate1_1_20_GG1_01_16488.mzXML
SEQ=*..*
IONMODE=Positive
ORGANISM=GNPS-SELLECKCHEM-FDA-PART2
NAME=Bortezomib (Velcade) [M+Na]
PI=Dorrestein
DATACOLLECTOR=Garg_Neha
SMILES=C1=CN=CC(=N1)C(N[C@H](C(N[C@H](B(O)O)CC(C)C)=O)CC2=CC=CC=C2)=O
INCHI=N/A
INCHIAUX=N/A
PUBMED=N/A
SUBMITUSER=negarg
LIBRARYQUALITY=1
SPECTRUMID=CCMSLIB00000077995
SCANS=1211
95.886879 236.0
131.058121 188.0
144.823196 204.0
...
1402.281494 144.0
END IONS
As MSP
https://external.gnps2.org/gnpslibrary/ALL_GNPS.msp
All GNPS Spectra and Structure as a Table¶
https://external.gnps2.org/gnpslibraryfornpatlastsv
Single Library Spectrum¶
https://gnps.ucsd.edu/ProteoSAFe/SpectrumCommentServlet?SpectrumID=<Library Accession>
Experimental or Library Spectrum by USI¶
Access a JSON or csv version of a spectrum by any Universal Spectrum Identifier.
https://metabolomics-usi.gnps2.org/json/?usi1=<USI HERE>
https://metabolomics-usi.gnps2.org/csv/?usi1=<USI HERE>
json example for mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00000579622
csv example for mzspec:GNPS:GNPS-LIBRARY:accession:CCMSLIB00000579622
GNPS Jobs¶
Job Results API¶
GNPS job results page in JSON format:
https://gnps.ucsd.edu/ProteoSAFe/result_json.jsp?task=<task id>&view=<view name>
Job Status API¶
GNPS job status page in JSON format:
https://gnps.ucsd.edu/ProteoSAFe/status_json.jsp?task=<task id>
Job Parameters¶
GNPS job parameters page in XML format:
https://gnps.ucsd.edu/ProteoSAFe/ManageParameters?task=<task id>
Structure Conversion¶
Conversion to Smiles¶
https://structure.gnps2.org/smiles?inchi=<inchi string>
Conversion to InChI¶
https://structure.gnps2.org/inchi?smiles=<smiles string>
Conversion to InChIKey¶
https://structure.gnps2.org/inchikey?smiles=<smiles string>
Conversion to fingerprint¶
https://structure.gnps2.org/structurefingerprint?smiles=<smiles string>
Conversion to exact mass¶
https://structure.gnps2.org/structuremass?smiles=<smiles string>
Compare to Adduct m/z¶
https://structure.gnps2.org/adductcalc?smiles=<smiles string>&mz=<experimental mz>
Conversion to formula¶
https://structure.gnps2.org/formula?smiles=<smiles string>
Structure Classyfire¶
If you have Smiles
https://structure.gnps2.org/classyfire?smiles=<smiles string>
If you have InChI
https://structure.gnps2.org/classyfire?inchi=<InChI string>
If you have InChI Key
https://gnps-classyfire.ucsd.edu/entities/<InChI Key>.json
Additionally, in case the inchikey is not classified, you can provide smiles or inchi arguments for
us to push to the Wishart servers to classify.
ClassyFire
ClassyFire is tool from the Wishart Lab - check it out here. Here is the recommended citation: Feunang, Yannick Djoumbou, Roman Eisner, Craig Knox, Leonid Chepelev, Janna Hastings, Gareth Owen, Eoin Fahy et al. "ClassyFire: automated chemical classification with a comprehensive, computable taxonomy." Journal of cheminformatics 8, no. 1 (2016): 61.
Structure Natural Product Classifier (NP Classifier)¶
If you have Smiles
https://npclassifier.gnps2.org/classify?smiles=<smiles string>
Example JSON Output
{
class_results: [
"Purine alkaloids"
],
superclass_results: [
"Pseudoalkaloids"
],
pathway_results: [
"Alkaloids"
],
isglycoside: false,
fp1: [
0,
0
...
],
fp2: [
0,
0,
...
]
}
NPClassifier
NPClassifier is A Deep Neural Network-Based Structural Classification Tool for Natural Products - check it out here. For citation: Kim, Hyun Woo, Mingxun Wang, Christopher A. Leber, Louis-Félix Nothias, Raphael Reher, Kyo Bin Kang, Justin JJ van der Hooft, Pieter C. Dorrestein, William H. Gerwick, and Garrison W. Cottrell. "NPClassifier: A deep neural network-based structural classification tool for natural products." Journal of Natural Products (2020). https://doi.org/10.1021/acs.jnatprod.1c00399. Checkout the tool index for a large scale workflow for batch classification.
Structure Image¶
https://structure.gnps2.org/structureimg?smiles=<smiles string>
Structure Similarity¶
https://structure.gnps2.org/structuresimilarity?smiles1=<smiles string>&smiles2=<smiles string>
Warning
Please make sure you are URL encoding your SMILES/InChI strings or else the web server on the other end won't understand your request.
Structure External Resource information¶
https://external.gnps2.org/structureproxy?smiles=<smiles string>
Chemical Translation Service
This API uses the Chemical Translation Service made by the Fiehn Lab - check it out here. For citation: Gert Wohlgemuth, Pradeep Kumar Haldiya, Egon Willighagen, Tobias Kind, Oliver Fiehn, The Chemical Translation Service—a web-based tool to improve standardization of metabolomic reports, Bioinformatics, Volume 26, Issue 20, 15 October 2010, Pages 2647–2648, https://doi.org/10.1093/bioinformatics/btq476.
Warning
Please make sure you are URL encoding your SMILES/InChI strings or else the web server on the other end won't understand your request.
ReDU¶
Per File Sample Information Query¶
https://redu.ucsd.edu/filename?query=<File full path in MassIVE>
Page Contributions¶