Mass Dynamics now operates exclusively on pre-processed, tabulated data from DDA and DIA quantitative workflows and is compatible with output files from leading tools such as MaxQuant, DIA-NN, Spectronaut, and Bruker ProteoScape. Users can also upload custom tabular outputs, using our mapping interface to align required fields for statistical analysis, visualization, knowledge integration, and dataset querying.
Rather than processing raw files directly, we ensure flexibility by decoupling from specific instrument formats and enabling streamlined downstream analysis. As such, we fully support workflows involving Thermo or Bruker raw files processed via DIA-NN, Spectronaut, Proteome Discoverer, and ProteoScape pipelines, which are fully supported through this tabular upload approach.
Why we take this approach
-
Instrument-agnostic: By focusing on tabular outputs, we avoid locking users into a single vendor format and keep pace with new hardware (e.g., timsTOF, Thermo Astral) as soon as upstream tools can export a table.
-
Reproducibility: The original search/quantification parameters stay in your pipeline of choice; Mass Dynamics adds statistics, QC, and collaboration layers on top.
-
Flexibility: Labs can swap search engines or update methods without changing their downstream analysis workflow inside Mass Dynamics.