How to Contribute to ReDU

Required Items

> Data (.mzXML or .mzML) uploaded to MassIVE and made public
> ReDU-compliant sample information uploaded to corresponding MassIVE accession

Step-by-step Instructions

Step 1 - Data

1A - Convert to Open-Source File Formats

1B - Upload Data to GNPS/MassIVE and Create a MassIVE ID

  • Data can be uploaded to MassIVE or GNPS using a FTP client. A free account is necessary.
  • Launch the "Submit your data" workflow (MassIVE) to create a MassIVE ID
  • The title must beginning with "GNPS - "
  • We encourage the upload of vendor-specific raw data, e.g. .raw (Thermo) and .d (Bruker and Agilent), in addition to open-source file formats (.mzXML, .mzML, or .mgf).
  • You will receive an email when the workflow has completed.
  • Details on dataset creation can be found here.

1C - Prepare the MassIVE ID

  • The MassIVE ID must be made publicly avaliable by clicking the "make public" button.
  • Please click the "convert spectra" button to expedite inclusion in ReDU.

Step 2 - Sample Information

2A - Make a copy of the Sample Information Template

  • Navigate to the ReDU Sample Information Template
  • One template is required per MassIVE ID.
  • Save a copy of the sample information template by going to "File - Make a copy" into a personal google drive

Sample Template_Copy

2B - Fill the Sample Information Template

  • Fill in sample information using drop-downs when applicable (grey columns at the end of the template are automatically entered using formulae).
  • It is highly recommended to fill the template in Google Sheets to ensure validation.
  • When copying and pasting from another spreadsheet, please copy + special paste so as to not chance the cell formulae or formatting.
  • ReDU uses a controlled vocublary - the accepted terms are listed in the "ReDUMS2_controlled_vocabulary" tab per column. If you require terms that are not avaliable, please raise an issue on GitHub.

Sample Template_Fill

2C - Download the Sample Information Template

  • When complete, delete all extra rows of the template.
  • Download from Google Sheets as a tab separated text file using "File-Download as" and selecting "Tab-seperated values..."

Sample Template_DeleteRows

Step 3 - Validation

3A - Validate your Sample Information File

  • Navigate to the ReDU Sample Information Validator
  • Drag-and-drop or select your sample information file into the validator.
  • A message will indicate if the files passes or not.
  • Non-adherant information is displayed in the "Sample Information Validation Errors" panel - the row, column, and the accepted terms are listed.
  • If errors occur, then please correct the non-adherant information in the template and repeat from 2C

Sample Validate

3B - Rename the Sample Information File

  • Upon passing the validator, rename the file to be exactly "gnps_metadata.tsv"
  • The filename must be gnps_metadata.tsv - this step is critical
  • It is suggested to make a seperate directory on your computer to store each MassIVE IDs sample information template

Step 4 - Upload the validated Sample Information file named "gnps_metadata.tsv"

  • Navigate to the MassIVE ID created
  • Click on the "add files" button
  • Use the Drag-and-Drop upload option to add the validated sample information file named "gnps_metadata.tsv"
  • Place the validated sample information file into the "Supplementary file" folder and submit the update

That is it! Double check that your data make it into the ReDU file selector.


  • GNPS/MassIVE is search multiple times per day to find new or updated sample information files so it may take some time for your data to appear.
  • If corrections or updates are necessary, please make them accordingly and upload the new validated sample information file named "gnps_metadata.tsv". ReDU will automatically import the most recent version of the "gnps_metadata.tsv" file (files cannot be deleted by users from MassIVE).
  • Any conflict between identically named files will result in their exclusion.
  • The filename in the sample information file must match the data uploaded to MassIVE (.mzML or .mzXML) - we do not support vendor-specific formats.