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Which files to upload to Mass Dynamics

Mass Dynamics automatically recognizes pre-processed data from popular processing software, including MaxQuant, Spectronaut, DIA-NN and Bruker ProteoScape (TIMS-DIA-NN), and guides you through a few quick steps to complete your upload to Mass Dynamics. 

Where Mass Dynamics does not detect the file type, you are able to map uploaded files or get assistance from the Mass Dynamics team.

Learn more

Regardless of the data format, refer here for a complete overview of the upload process.

 

MaxQuant

Mass Dynamics recognises DDA protein level TMT and LFQ MaxQuant processed results, with the extended ability to handle fractionated samples. 

Refer here to learn which files are required. 

Pre-processed DIA

Our system will autodetect the following:

  • For DIA-NN output, refer here to learn which files are required
  • For Bruker ProteoScape (TIMS-DIA-NN), refer here to learn which files are required
  • For Spectronaut output, refer here to learn which files are required.

Other file formats will not be auto-detected; however, you can still map uploaded files or send these to our support team so that they can assist you with uploading the data and setting up your experiment in Mass Dynamics.


Uploading a folder:

Note: where your files are contained in a folder, we recommend uploading the entire folder. Our system will extract the necessary information and ignore any unnecessary files in the folder.

 

All other file types

Where you wish to upload a file type that is not automatically detected by Mass Dynamics, you will be given the following options:

  • Use the MD Format as described here
  • Manually map your files as described here
  • Assisted upload (via our Support Team)

 

MD Format 

If you choose this option, Mass Dynamics expects two files - one containing protein intensities and one containing peptide intensities - formatted as described here. Once you select these files, Mass Dynamics automatically detects the MD format and streamlines the upload process, allowing you to move straight into setting up your experiment design.

 

Mapping files:

If you choose this option, our system will guide you through a few questions about the location of your protein intensities data and any protein metadata. After you have provided this information, you will be able to continue your file upload. 

 

Assisted upload:

Our experts can help you upload your data and set up your experiment in Mass Dynamics. You can learn more here.