FLASHDeconv: Ultra-fast high-quality deconvolution enables online processing of top-down MS data

Top-down (TD) proteomics has gained a lot of momentum for in-depth protein characterization and protein species analytics. The complex structure of TD spectra makes deconvolution necessary to easily interpret the spectra. Deconvolution is a transformation of the spectra from the m/z domain to a mass domain in order to disentangle different analyte charge states and is thus a key step for successful top-down analysis. While several methods for deconvolution have been suggested, they still have issues with runtime and often yield artifacts. Here we present FLASHDeconv, an ultra-fast high-quality deconvolution algorithm for TD MS spectra based on a novel algorithmic idea for spectrum transformation, which achieves runtimes of few milliseconds per spectrum.



The current version is only beta version.


FLASHDeconv installation files (for windows *.exe, for mac *.dmg, and for linux *.deb) are found in here.



FLASHDeconv basic parameters are found by simply running FLASHDeconv.

  • -in: input file or directory (only *.mzML files are currently accepted)
  • -out: output file prefix; two files (*.tsv and *.m) are generated. *.tsv file is tab delimited file and *.m file is matlab script file containing mass, nominal mass, retention time, and aggregated intensity.
  • -minC: minimum charge of peaks (default: 5)
  • -maxC: maximum charge of peaks (default: 30)
  • -minM: minimum mass of peaks (default: 500)
  • -maxM: maximum mass of peaks (default: 50000)
  • -tol: tolerance in PPM (default: 5)


FLASHDeconv advanced parameters are found by running FLASHDeconv with –helphelp option.

  • – minInt: minimum intensity of peaks (default: 100)
  • -minCCC: minimum number of peaks of continuous charges per mass (default: 4)
  • -minCC: minimum number of peaks of distinct charges per mass (default: 6)
  • -minIC: minimum continuous isotope count (default: 3)
  • -maxIC: maximum isotope count (default: 100)
  • -maxMC: maximum mass count per spec (will be deprecated)
  • -minIsoScore: minimum isotope cosine score (default: 0.75)
  • -minCDScore: minimum charge distribution score (default: 0)


Running FLASHDeconv:

Currently no GUI is prepared. Only runnable on command line.

The mandatory options are -in and -out options. Basic parameters could be adjusted by the user according to instrumental setup.

For example if one wants to deconvolute /User/me/data/mydata.mzml and get the result /User/me/out/myoutput.tsv,

one could run FLASHDeconv by typing as follows in the directory where FLASHDeconv is installed,

./FLASHDeconv -in /User/me/data/mydata/mzml -out /User/me/out/myoutput

In /User/me/out/ directory, myoutput.tsv and myoutput.m files will be generated.


Output file:

Two output files (*.tsv and *.m) are generated currently.

  1. *.tsv file contains information such as mono isotopic mass, nominal mass, retention time, aggregated intensity, and corresponding peaks per spectrum.
  2. *.m file contains a large matrix where each column corresponds to a single deconvoluted mass, and each row contains mono isotopic mass, nominal mass, retention time, and aggregated intensity of the mass.