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MetaMorpheus: Free, Open-Source PTM Discovery Follow us on Twitter

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Download the current version here. For first-time Windows users, choose "MetaMorpheusInstaller.msi" and install MetaMorpheus. Check out our getting started playlist on YouTube

MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability. This program combines features of Morpheus and G-PTM-D in a single tool.

Check out the wiki page for software details!

Major Features

  • Database Search: A robust search algorithm that identifies peptides by their fragmentation spectra. Watch our Search task YouTube video
  • Calibration: A calibration tool that uses peptides identified by a database search to calibrate the m/z values of all peaks in the spectra. This improves the quality of any subsequent search or analysis of the data. Watch our calibration task YouTube video.
  • G-PTM-D: Post-translational modification (PTM) discovery, which expands the scope of peptide identifications to include both known and unknown PTMs. Watch our GPTMD task YouTube video.
  • Quantification: Ultrafast label-free peptide quantification with FlashLFQ. MS2-identified peptides are used as "seeds" for peakfinding, including PTM-containing peptides. Watch our Label-free quantification with MetaMorpheus video on YouTube.
  • O-glycopeptide Characterization: O-Pair Search identifies O-glycopeptides using an ion-indexed open modification search and localizes O-glycosites using graph theory and probability-based localization.

System Requirements

Spectra Requirements

  • One of the following formats:
  • MS1 and MS2 scans
  • If you would like to know more about the types of files that can be searched with MetaMorpheus, please watch our Mass Spectra Files Video on YouTube.

Database Requirements

UniProt .XML or .fasta format; may be used in compressed (.gz) format. If you would like to know how to obtain a UniProt .XML databases, please watch our Protein Databases Video on YouTube.

Getting Started

Please check out our wiki for useful information and guides.

Installation and typical usage is described for the on the Getting Started page:

References & Citation Guide for MetaMorpheus


GPTMD searches:


Multiple protease parsimony: Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data, J Proteome Res 2019, 18, 9, 3429–3438.

Glycoproteomic searches: O-Pair Search with MetaMorpheus for O-glycopeptide characterization, Nat Methods 2020, 17, 1133–1138.

Proteogenomic database searches with Spritz: Spritz: A Proteogenomic Database Engine, J Proteome Res 2021, 20, 1826–1834.

Long-read proteogenomic characterization: Enhanced protein isoform characterization through long-read proteogenomics, Genome Biology 2022, 23, 69.

mzLib, an all-purpose mass spectrometry toolchest implemented by MetaMorpheus

mzLib is a nuget package that we created as an all-purpose toolchest for mass-spec data analysis and many of its functions provide the tools for MetaMorpheus. mzLib is freely available for use in mass-spec applications. You do not need to download mzLib separately to run MetaMorpheus; it is already included.