Added by Louis Felix Nothias, last edited by Louis Felix Nothias on Oct 30, 2016  (view change)


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ili Workshop: link to the template: feature_table_with_coordinates.csv


Exploring MS/MS data with the GNPS Data Analysis workflow

Step 1- Create an account

Go to GNPS main page in an other window ( and create your own account.

Step 2- Find a MS/MS dataset on MassIVE (Mass spectrometry Interactive Virtual Environment)

A) Go to GNPS ( and access the MassIVE datasets repository.

B) Search for the MassIVE datasets named "GNPS Workshop". Explore its content, and copy the MassIVE ID number.

Step 3 - Access to the Data Analysis workflow

Go to back GNPS main page ( and open the Data Analysis workflow.

Step 4 - Configure and launch the Data Analysis workflow

A) Indicate a Title.

B) Clic on Spectrum Files (required).

C) Go to the Share Files spreadsheet and import the data of the "GNPS workshop" MassIVE datasets with the Import Data Share (use the MassIVE ID).

D) Go back to the Select Input Files spreadsheet.

E) Add the files from the datasets peak/TIPS review/Biotin into Spectrum Files G1.

F) Add the files from the datasets peak/TIPS review/Tryptamine spectra into Spectrum Files G2.

G) Modifiy parameters to meet high-resolution mass spectrometry: Precursor Ion Mass Tolerance (0.02), Fragment Ion Mass Tolerance (0.02), Min Pairs Cos (0.6), Minimum Matched Fragment Ions (2), Minimum cluster size (use 1)

H) Validate the selection with Finish Selection button.

J) Launch the Data Analysis workflow using the Submit button.

Step 5 - Visualize the Data Analysis workflow output

A) Return to GNPS main page ( and go to the Jobs page.

B) Explore the spectral library annotations by clicking on view All Library Hits.

C) Go back to the Status Page.

D) Clic on the View Spectral families and visualize the network 1.

E) Map on the molecular network, the parent mass, and the LibraryID.

F) Visualize a first MS/MS spectrum by left-clicking on one node. Visualize a second MS/MS spectrum by right-clicking on a second node.

Copy the link of the Data Analysis results webpage using Add Comment below