Community Curated MS/MS Spectral Libraries

GNPS provides a platform for users to contribute their own annotated MS/MS spectra to the spectral libraries. There are several requirements for annotation: 1) the compound must be of known structure and 2) the MS/MS must be of sufficient quality to support the annotation of the compound. By contributing these spectra, users will expand the spectral libraries and allow dereplication of these compounds within other datasets.

Library Quality Level

The spectral libraries are categorized based upon quality of the data. The level indicates both the quality of the MS/MS spectra as well as the trust worthiness of the annotations. These reflect both quality of the MS/MS spectra as well as the trust worthiness of the annotations.

Quality Level Description Quality Number
Gold Synthetic, Complete structural characterization with NMR, crystallography or other standard methods as defined in the publication guidelines for Journal of Natural Products, Privileged users 1
Silver Isolated or lysate/crude, Published data showing presence of molecule in the sample 2
Bronze Any other putative, complete or partial annotation 3
Challenge Unknown Identity, open to community to help annotate 10

By default, users will have access to Bronze, but approval is required to contribute to silver and gold libraries. To obtain training and access please email Mingxun Wang.

Adding Single Spectra

Input Formats

mzXML, mzML, and mgf file formats are accepted.

Additionally, spectra to be added to the library should be centroided. Profile data is not processed correctly by our algorithms.

Adding Spectrum

From the GNPS Splash Page, users can click on

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to be brought to the Add Single Annotated Spectrum workflow. By default, users will contribute bronze quality reference spectra. Permission is required to contribute higher quality spectra to the gold and silver workflows.

Select an input spectrum file.

NOTE: do not change the spectral library that is selected.

Annotation Fields

Sample Parameters

Field Description Default Required
Ion Source Source of Ions LC-ESI Yes
Instrument Mass Analyzer qTof Yes
Ion Mode Ionization Mode Positive Yes
Compound Source Sample source of compound Commercial Yes
Principle Investigator PI overseeing compound acquisition and analysis N/A Yes
Data Collector Individual Collecting Data N/A Yes

Annotation

Field Description Default Required
Scan Spectrum Scan of Spectrum 0 Yes
Adduct Adduct of Ion fragmented in MS2 M+H Yes
Compound Name Compound Common Name N/A Yes
Precursor MZ Experimental Precursor MZ for Compound 0 (will read from spectrum file if 0) Yes
Charge Charge of Precursor 0 (will read from spectrum file if 0) Yes

Advanced Annotation

Field Description Default Required
CAS Number Chemical Abstracts Service compound identification number N/A No
Pubmed ID Pubmed ID where compound or data was published N/A No
Exact Mass Compound Exact Mass 0 No
Smiles Smiles Structure N/A No
Inchi Inchi Structure N/A No
Inchi Aux Inchi Auxiliary Structure N/A No

Guidance on Providing Names to the Annotations in GNPS

Source Structure Structural Position of Analog Mass Shift of Analog Guidance Example
Chemical Standard Full Structure Known Known N/A please annotate with the common name and provide the SMILES and Inchi in the corresponding text fields. 7-Methylxanthine
Your Data Full Structure Proposed Proposed based on MS/MS N/A please annotate with the common name and provide the SMILES and Inchi in the corresponding text fields (a bronze star rating will indicate a putative status) 7-Methylxanthine
Your Data Incomplete Structure Proposed Cannot based on MS/MS N/A please annotate with the common name and indicate the position is unknown using "X" (X)-Methylxanthine
Your Data No Structure Information No Position Information Mass shift provided via Molecular Networking please annotate with the common name of the chemical it is connected to and indicate mass shift. Mass shift indicated by nominal mass followed by putative formula difference (if the formula difference is unknown please enter "X"). No SMILES or Inchi should be provided. Caffeine +14(CH2)
Caffeine +52(X)

Validation Spectra Selection

To validate the input file and scan a user has selected, there is a plotting section that will attempt to plot the spectrum selected.

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To plot the spectrum, click "Plot It!". Additionally, if users would like to see the annotation with a peptide fragment highlights, users can enter a peptide in the Peptide field, but this will not be stored in the annotation.

If the plotting succeeded and a spectrum appears, then the selection for the spectrum is done correctly.

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If there was an error, check the original file was converted correctly and the scan number is not 0.