FLASHDeconv: Ultrafast, high-quality feature deconvolution for top-down proteomics

Feature deconvolution is the determination of intact protein masses in native/top-down proteomics and currently suffers from long runtimes. We present FLASHDeconv, an algorithm based on a simple transformation of mass spectra, which turns deconvolution into the search for constant patterns thus greatly accelerating the process. We show equal or higher deconvolution quality and two to three orders of magnitude faster execution speed than previously published approaches.



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; [prefix]feature.tsv is generated.
  • -minC: minimum charge of peaks (default: 2)
  • -maxC: maximum charge of peaks (default: 100)
  • -minM: minimum mass of peaks (default: 1000)
  • -maxM: maximum mass of peaks (default: 100000)
  • -tol: tolerance in PPM (default: 10)


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

  • under construction – the newer version with per-charge-intensity gaussian fitting scoring is to be published soon. The advanced parameters should be finalized before official publication of FLASHDeconv.


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 input mzML file conversion from raw file, we recommend not to use any peak picking method.


You can specify a file or a directory for -in and -out options


1. -in [infile] -out [outfile]

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

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

./FLASHDeconv -in /User/me/data/infile.mzml -out /User/me/out/outfile

In /User/me/out/ directory, outfilefeature.tsv  will be generated.


2. -in [infile] -out [outdir]

./FLASHDeconv -in /User/me/data/infile.mzml -out /User/me/out/

In /User/me/out/ directory, infilefeature.tsv  will be generated (output filename follows input filename).


3. -in [dir] -out [file]

./FLASHDeconv -in /User/me/data/ -out /User/me/out/outfile

FLASHDeconv will find all mzML files in /User/me/data/ (recursively) and process them. In /User/me/out/ directory, outfilefeature.tsv will be generated (all features are written in this file).


4. -in [dir] -out [dir]

./FLASHDeconv -in /User/me/data/ -out /User/me/out/

FLASHDeconv will find all mzML files in /User/me/data/ (recursively) and process them. In /User/me/out/ directory, an output file will be generated for each input file.


Output file:

Under construction.