Mass Dynamics can accept most file types and automatically detect files from most popular software.
Where Mass Dynamics does not detect the file type, you are able to map uploaded files or get assistance from the Mass Dynamics team.
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MaxQuant
Our system will autodetect the following:
- TMT (protein only) and LFQ data-dependent acquisition (DDA) experiments.
- A minimum of 2 conditions, 3 replicates per condition
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.
Recommended files:
- proteinGroups.txt
- summary.txt
Uploading these MaxQuant output files will enable Mass Dynamics protein level differential expression statistics and to understand your experimental design.
Please ensure that these files are named as originally produced by MaxQuant.
Optional files:
- evidence.txt
-
modificationSpecificPeptides.txt
-
msms.txt
- parameters.txt
- peptides.txt
All users are highly encouraged to provide these optional files, which will enable an improved quality control report for label-free quantification experiments.
Please ensure that all file names are provided as originally produced by MaxQuant.
All optional files need to be included to receive an enhanced quality control report.
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 contained in the folder.
Pre-processed DIA
Our system will autodetect the following:
- A minimum of 2 conditions, 3 files per condition
- For DIA-NN or Bruker ProteoScape output, 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:
- Map the files - as described here
- Assisted upload (via our support team)
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.