SpectrumFinder is a simple command line tool to compare a collection of reference spectrum to other spectrum from one or more mzXML files.

The goal of the SpectrumFinder software is to find similarity between an MS/MS spectrum of reference and other MS/MS spectrums from the same instrument and the same biological sample, with no “a priori” on the peptide precursor mass, in order to find the same peptide sequence carrying different side residues, like glycoforms, that are lost during fragmentation. This kind of modification results in similar MS/MS fragmentation profiles (no m/z shift), but different precursor masses. Other softwares comparing MS/MS spectrums using spectrum libraries such as SpectraSt (Peptide Atlas) or X!Hunter ( are made to look for already identified peptides possibly found using different MS technology. To be efficient, they have to take into account the expected precursor mass (unknown in our case). In order to detect similarities between spectrums obtained using different MS technology, they focuses on shared peaks and the overall common peak intensity (dot products of normalized intensities), which is less sensible to differences of intensities between MS/MS profiles.

The spectrum Finder software uses the “cosine similarity” to find MS/MS spectrums similar to a given reference. This method is not sensible to scale effects and takes into account similar peak intensities distributions.

help and support

Spectrum Finder is developped by the PAPPSO team. We are providing support through our mailing list. Don’t hesitate to register if you want to be informed of new releases or upgrades. The development is open and free, you are welcome to contribute, copy, modify, fork if you need it, respecting the terms of the licence

download and install

SpectrumFinder 1.0 Unix source files are available as a tar.gz file in this directory download this tar.gz file, untar it, compile and install with:

cd spectrum-finder-1.0.0
cmake .
make install

A Windows version is available in this zip file


SpectrumFinder is launched in a command line :

spectrum-finder parameters.xml

parameters.xml files used in this example are available here


SpectrumFinder is a free software distributed under the terms of the GNU GENERAL PUBLIC licence v3.


The source code of SpectrumFinder is hosted by SourceSup. Contributors are welcome to send bug reports or directly access to the subversion repository via SourceSup registration.