How do I map files when uploading to Mass Dynamics?

The upload experience automatically recognizes pre-processed data from popular processing software, including MaxQuant , Spectronaut, DIA-NN and Bruker ProteoScape (TIMS-DIA-NN). You can learn more about what files to upload here.

When our system doesn't automatically recognize the data being uploaded, you will be guided to specify a few criteria to map your data files before the dataset creation, avoiding the need to re-format files before upload.

Steps to map files

1. Go to the Dataset Upload page and choose the file(s) or folder(s) to upload. Click 'Next' and follow the instructions. 

2. When prompted, choose the file containing protein intensities and select the columns containing sampe names. Currently, Mass Dynamics can only map protein intensities for wide tables, i.e. where sample names are found in the column headers. 

3. Then, select the table containing the protein metadata and assign the appropriate columns to each metadata field.

4. Once the intensities and metadata mapping is completed, follow the steps to upload the experiment design, sample metadata, and assign the dataset name.

5. Click "Create Experiment" and wait until your files upload.

6. Get started with analyzing your data! 

Alternatively, you can also leverage the Mass Dynamics team to help you upload your files to Mass Dynamics. Follow the instructions here.