greylag: software for tandem mass spectrum peptide identification

Greylag is a suite of programs for MS/MS peptide identification by sequence database search. It solves the same basic problem that programs such as SEQUEST, Mascot, X!Tandem, OMMSA, and MyriMatch do.

Greylag is Free Software, distributed under the GNU General Public License.


Note that greylag is currently in a "beta" state. You're welcome to try it out, but be aware that there may still be some bugs and sharp edges.


More information about greylag's design and implementation, as well as background information on tandem mass spectrum search, is available in the theory of operation (pdf) document.

Getting greylag

You can download the latest release from the greylag project page ( at SourceForge--see the Release Notes (pdf). This site also hosts the mailing lists and bug tracker.

Greylag uses git for distributed source code management. You can browse the project repository from the public mirror at You can also pull your own copy with

$ git clone git://

Installing greylag

See the Installation Guide (pdf) for information about the compiling and installing the various greylag programs.

Using greylag

See the User Guide (pdf) for information about the configuration and usage of the various greylag programs.


Comments, suggestions, and bug reports are welcome! If you try it out, please drop us a line and tell us how it worked (or didn't work) for you.

Credits and Acknowledgements

Greylag would probably not have been possible without access to the source code of MyriMatch, X!Tandem, and OMSSA, which their authors have made available under various Open Source licenses.

Greylag's main spectrum filtering and scoring algorithms are currently based closely on those of MyriMatch. The PCA modification method is based on that of X!Tandem.

The idea for the greylag-validate --bootstrap flag is from Roger Moore (City of Hope).

The initial greylag implementation was written by Mike Coleman, supported by the Stowers Institute for Medical Research.

(this page as pdf)
Thanks to for project hosting.