FLASHQuant performs MS1-level label-free quantification data analysis in top-down proteomics with an automatic overlapping signal resolution method.

Check it out on Github!

Now binary installer files for all platforms are available here: (Please use the latest version)

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  • Input: Centroided MS1 scans (*.mzML)
  • Output: Quantified proteoforms in a tab-separated file (*.tsv); optionally, OpenMS LC-MS features output (*.featureXML)
    • for each proteoform, mono-isotopic/average mass, retention time range, charge range, different types for quantity values, and isotope cosine similarity score are provided.
  • Parameters can be found by running FLASHQuant using the “–helphelp” option.

Consensus FeatureGroup (putative proteoform) detection

FLASHQuant executes per LC-MS run; thus, we provide an additional simple tool for detecting consensus feature groups (i.e., jointly detected proteoforms) among multiple scans (i.e., technical replicates) named ConsensusFeatureGroupDetector. Retention time and mass tolerance can be adjusted with parameters.


FLASHQuant and (consecutive) ConsensusFeatureGroupDetector can be executed easily with the GUI, FLASHQuantWizard.

To learn how to run the programs, please check FLASHDeconv page for details.