What files do I need to upload for Bruker ProteoScape (TIMS DIA-NN) or DIA-NN processed results?

For DIA analyses where you have used Bruker ProteoScape (TIMS DIA-NN) or DIA-NN to pre-process your raw data, multiple files are generated. There are multiple output files typically produced by DIA-NN, including:

  1. The main report.tsv
  2. A report.log.txt
  3. Matrix files, such as:
    1. report.unique_genes_matrix.tsv
    2. report.pg_matrix.tsv
    3. report.pr_matrix.tsv
  4. report.stats.tsv, and
  5. report.pdf

Follow the steps below to upload pre-processed DIA output:

  1. Login to app.massdynamics.com
  2. Click on 'Create an experiment'Screenshot 2023-06-22 at 9.45.01 am
  3. Click on Pre-processed DIAScreenshot 2023-06-22 at 9.41.47 am
  4. Upload the following files:
    1. The main report.tsv file
    2. The log.txt file
  5. Follow the prompts to complete the upload

If you wish to upload the other output files, such as the matrices files (e.g. report.pg_matrix.tsv), then head to the 'Other' tab and follow the instructions for Option 1: Create a generic upload .tsv file.

If you need support in uploading your data, you can follow these instructions to leverage our assisted upload service.


Like to read more about how we store and handle your data? Please check out Security and Privacy information here