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Morpheus search algorithm

a mass spectrometry–based proteomics database search algorithm

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Morpheus is a mass spectrometry–based proteomics database search algorithm designed from the ground up for high-resolution tandem mass spectra. We have discovered that for high-resolution MS/MS, simple spectrum preprocessing and scoring performs superior to more complex algorithms originally developed for low-resolution MS/MS, such as Sequest, Mascot, and OMSSA. Morpheus is also very fast—up to nearly 5 times faster than OMSSA for large human datasets. It is written in C# and is available open source under the permissive MIT License.

Morpheus search algorithm Web Site


Bio-Informatics, Chemistry


MIT License


  • Support for mzML, Thermo .raw, or Agilent .d data
  • Multi-threaded
  • Automatic spectrum-, peptide-, and protein-level FDR
  • Tab-delimited and pepXML outputs


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.NET/Mono, Command-line, Win32 (MS Windows)

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