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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

System Requirements

Spectra Requirements

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:


Crosslinking MS (XL-MS) search: Identification of MS-Cleavable and Noncleavable Chemically Cross-Linked Peptides with MetaMorpheus , J. Proteome Res. 2018, 17, 7, 2370–2376.

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.

Spectral library GPTMD search: A Hybrid Spectral Library and Protein Sequence Database Search Strategy for Bottom-Up and Top-Down Proteomic Data Analysis, J of Proteome Res 2022, 21, 2609-2618

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.