Added by Mingxun Wang, last edited by Mingxun Wang on Nov 20, 2014  (view change)

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Challenge Spectra

One of the goals of GNPS is to develop and improve the annotation of molecules detected by mass spectrometry. However, there are many MS/MS that have been observed but lack a complete identification and structure. Since it is infeasible for a single lab to invest the time and effort to identify all interesting MS/MS spectra that are observed, we provide a mechanism to challenge the community to aid in identifying these known unknowns. We created these challenge spectra to promote community collaboration for solving structures or partial structures of the most interesting unidentified MS/MS spectra observed. The user can directly specify and upload a challenge spectrum or select an interesting spectrum with a single click while analyzing a molecular network. The user is required to provide a description as to why this is an interesting spectrum as well any metadata such as UV or NMR that can aid in structure elucidation.

Browsing Challenge Spectra

From the GNPS splash page here, users can reach the public link to browse all challenge spectra here.

Users will be presented with a view almost identical to browsing libraries, but this time, the name is a description on the interest of the particular unknown spectrum.

Adding Challenge Spectra

Adding by Form

Challenge spectra can be added from the splash page, but click the appropriate link here in a very similar way to adding identified spectra.

Users will reach an import form similar to this:

Adding from Network

Users can also add challenge spectra from a molecular networking. When viewing the View by Cluster with IDs view, users can click the +Challenge link.

Users will be taken to another link where they can choose an exact raw spectrum to be added to the challenge spectra by clicking the "+Challenge" link to prepopulate a form. Users can then fill out the appropriate metadata.

Browsing Challenge Spectra

To browse challenge spectra, users can begin on the GNPS splash page (http://gnps.ucsd.edu/ProteoSAFe/static/gnps-splash.jsp) and click on the browse challenge spectra link:

http://gnps.ucsd.edu/ProteoSAFe/gnpslibrary.jsp?library=GNPS-LIBRARY#%7B%22Library_Class_input%22%3A%2210%22%7D.

This page is very similar to the browse libraries page, where each row represents individual challenge spectra:

Annotating Challenge Spectra

Users are able to re-annotate and promote the challenge spectra be identified as a bronze spectrum by clicking the annotate and promote to bronze button.