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GNPS API Overview

GNPS Library Spectra

All Public Library Spectra at GNPS

https://gnps-external.ucsd.edu/gnpslibraryjson

All Public Library Specta at GNPS with Peaks and Annotation History

https://gnps-external.ucsd.edu/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://gnps-external.ucsd.edu/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://gnps-external.ucsd.edu/gnpslibrary/ALL_GNPS.msp

Single Library Spectrum

https://gnps.ucsd.edu/ProteoSAFe/SpectrumCommentServlet?SpectrumID=<Library Accession>

Example

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>

Example

Structure Conversion

Conversion to Smiles

https://gnps-structure.ucsd.edu/smiles?inchi=<inchi string>

Example

Conversion to InChI

https://gnps-structure.ucsd.edu/inchi?smiles=<smiles string>

Example

Conversion to InChIKey

https://gnps-structure.ucsd.edu/inchikey?smiles=<smiles string>

Example

Conversion to exact mass

https://gnps-structure.ucsd.edu/structuremass?smiles=<smiles string>

Example

Conversion to formula

https://gnps-structure.ucsd.edu/formula?smiles=<smiles string>

Example

Structure Classyfire

If you have Smiles

https://gnps-structure.ucsd.edu/classyfire?smiles=<smiles string>

Example

If you have InChI

https://gnps-structure.ucsd.edu/classyfire?inchi=<InChI string>

Example

If you have InChI Key

https://gnps-classyfire.ucsd.edu/entities/<InChI Key>.json

Example

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.

Structure Image

https://gnps-structure.ucsd.edu/structureimg?smiles=<smiles string>

Example

ReDU

Per File Sample Information Query

https://redu.ucsd.edu/filename?query=<File full path in MassIVE>

Example

Page Contributions

Ming Wang


Last update: June 29, 2020 23:10:54