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

Multiple files are generated for DIA analyses where you have used DIA-NN or Bruker ProteoScape (TIMS DIA-NN) to pre-process your raw data. These include:

  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 from DIA-NN or Bruker ProteoScape:

  1. Login to app.massdynamics.com
  2. Click on 'Create an experiment'Screenshot 2023-06-22 at 9.45.01 am
  3. Upload or drag files  
  4. For DIA-NN, upload the following files:
    1. The main report.tsv file,
    2. The report.pg_matrix.tsv
    3. The report.pr_matrix.tsv
    4. The log.txt file

  5. For ProteoScape TIMS DIA-NN, only upload the following files:
    1. The main report.tsv file
    2. The log.txt file

  6. Follow the prompts to complete the upload 

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


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