Eliminate > 95% of noise peaks
Reduction of 60% to 80% of file size
> 90% identifications remained

PeakStrainer is an implementation of the paper Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics.

PeakStrainer is a tool to de-noise high resolution FT MS and FT MS/MS spectra. It does this by removing signals that poorly repeat in successively acquired scans – independently of their intensity.

Peaks in panel B are not repeated with the required rate – within the pre-defined m/z range, they were only detected in 9% or, respectively, 27% of acquired scans – they will be removed. In contrast, peaks in panels C and D were detected in each scan and will be retained. In this way, it is possible to remove > 90% peaks without losing a single bona fide fragment.

The input to the application is a *.raw files and the output at intermediate stages are *.CSV and final results are stored as *.mzXML files.


If you use the software for a publication please use DOI 10.17617/1.47 as a reference. If you would like to reference the paper please use DOI 10.1021/acs.analchem.7b00794

If you would like to share your process and or data, please feel free to provide the data in the Issues page and we will find a place for it in the wiki.

Quick Start

  • Install msFilereader(see wiki)
  • Download
  • Unzip the file
  • run peakStrainerApp.bat
  • select one or more *.raw files
  • click finish to process with default settings

After processing *.mzXML files will be created in the same directory as the *.raw files

Wiki and source code

To find out more and get the python source code please visit


Dr. Jacobo Miranda Ackerman

Contact: mirandaa(at)