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

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

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.

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.

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