Added by Mingxun Wang, last edited by Mingxun Wang on Feb 16, 2015  (view change)


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Table of Contents

User Contributed Spectra

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.

Please note: Only letters, numbers and underscores are allowed in the filenames.  Spaces and special characters are NOT allowed.

Input Spectrum Formats

mzXML, non-zlibbed 32-bit is accepted. Standard MGF files are accepted.

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

Library Quality Levels

For a description of the different library levels, please click here.

Contributing Spectra

Adding Spectra

From the GNPS Splash Page here, 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.

Selecting Input Spectrum

Select an input spectrum file. Accepted files formats are mzXML and MGF, however mzXML is strongly preferred.
To upload spectrum files please refer to this file uploads page.

Selecting Spectral Library

Select the gnps_library/gnps_library.mgf. This is the default public library. If you do not know what you are doing, do not change this. 

Annotation Fields

Sample Parameters
Field Desc. Default Required
Ion Source Source of Ions LC-ESI Yes
Instrument Mass Analyzer Instrument 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
Field Desc. 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 Yes
Charge Charge of Precursor 0 will read from spectrum file Yes
Advanced Annotation

For commercial compounds, CAS number should be included.

For published MS/MS data, the PubMed ID for the publication should be included.

For Exact Mass, please calculate the exact mass of the structure without adducts.  This allows multiple adducted forms of a compound to be identified in the spectral libraries by searching with the exact mass.

Field Desc. 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

Validating 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.

Adding Spectra After Data Analysis

Users can perform data analysis on uploaded data. For further information, please see the molecular networking page.
If a spectra is discovered to be from a particular compound and users wish to add it to a library directly from the data analysis page it is possible. This is only possible from the View All Clusters view after users have clicked on a cluster.

Click on the quality of the library you wish to add to and it will take you to the input form.