# 
MetaMorpheus: Free, Open-Source PTM Discovery [](https://twitter.com/smith_chem_wisc)
[](https://github.com/smith-chem-wisc/MetaMorpheus/releases/latest)
[](https://ci.appveyor.com/project/smith-chem-wisc/metamorpheus/branch/master)
[](https://codecov.io/gh/smith-chem-wisc/MetaMorpheus)
[](https://github.com/smith-chem-wisc/MetaMorpheus/releases)
[](https://hub.docker.com/r/smithchemwisc/metamorpheus/tags?page=1&ordering=last_updated)
[](https://anaconda.org/conda-forge/metamorpheus)
[](https://anaconda.org/conda-forge/metamorpheus)
[](https://anaconda.org/conda-forge/metamorpheus)
Download the current version [here](https://github.com/smith-chem-wisc/MetaMorpheus/releases/latest). For first-time Windows users, choose "MetaMorpheusInstaller.msi" and install MetaMorpheus. Check out our 
[getting started playlist](https://www.youtube.com/playlist?list=PLVk5tTSZ1aWlYiTvJbRj6hjVDq4qH3w__) 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](https://github.com/cwenger/Morpheus) and [G-PTM-D](https://github.com/smith-chem-wisc/gptmd) in a single tool.
Check out the [wiki page](https://github.com/smith-chem-wisc/MetaMorpheus/wiki) for software details!
## Major Features
* Database Search: A robust search algorithm that identifies peptides by their fragmentation spectra. Watch our [Search task YouTube video](https://www.youtube.com/watch?v=sUM12UBJNuA)
* 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](https://www.youtube.com/watch?v=_LfiOqqqj8Q).
* 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](https://www.youtube.com/watch?v=fXGT4XExLBo).
* [Quantification](https://github.com/smith-chem-wisc/MetaMorpheus/wiki/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](https://www.youtube.com/watch?v=jgXRuExtuRI) video on YouTube.
* [O-glycopeptide Characterization](https://github.com/smith-chem-wisc/MetaMorpheus/wiki/O-Glyco-Search-Task): 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
* Environment:
* 64-bit operating system
* .NET Core 6.0:
* Windows: https://dotnet.microsoft.com/download/dotnet/thank-you/runtime-desktop-6.0.4-windows-x64-installer
* macOS, x64 Intel processor: https://dotnet.microsoft.com/en-us/download/dotnet/thank-you/runtime-6.0.4-macos-x64-installer
* macOS, ARM Apple Silicon processor: https://dotnet.microsoft.com/en-us/download/dotnet/thank-you/runtime-6.0.4-macos-arm64-installer
* Linux: https://docs.microsoft.com/dotnet/core/install/linux-package-managers
* Note that the installer (MetaMorpheusInstaller.msi) only works on Windows. The command-line version of MetaMorpheus supports any operating system that supports .NET Core (Windows, MacOS, Linux)
* 8 GB RAM recommended
## Spectra Requirements
* One of the following formats:
* Thermo .raw (Windows and Linux only)
* .mzML file in centroid mode. Please watch our [How to convert files to .mzML](https://www.youtube.com/watch?v=hOJ6ibCA5Pk) video on YouTube.
* .mgf
* 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](https://www.youtube.com/watch?v=SN6_T2JyxhA&list=PLVk5tTSZ1aWlhNPh7jxPQ8pc0ElyzSUQb&index=3) 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](https://www.youtube.com/watch?v=LFvCj04r5kU&index=2&list=PLVk5tTSZ1aWlhNPh7jxPQ8pc0ElyzSUQb) on YouTube.
## Getting Started
Please check out our [wiki](https://github.com/smith-chem-wisc/MetaMorpheus/wiki) for useful information and guides.
Installation and typical usage is described for the on the [Getting Started](https://github.com/smith-chem-wisc/MetaMorpheus/wiki/Getting-Started) page:
* [Test Installation (Windows GUI)](https://github.com/smith-chem-wisc/MetaMorpheus/wiki/Getting-Started#test-installation-windows-gui)
* [Typical Usage (Windows GUI)](https://github.com/smith-chem-wisc/MetaMorpheus/wiki/Getting-Started#typical-usage-windows-gui)
* [Test Installation (Windows Command Line Executable)](https://github.com/smith-chem-wisc/MetaMorpheus/wiki/Getting-Started#test-installation-windows-command-line-executable)
* [Test Installation (via .NET Core .dll - Linux, macOS, Windows)](https://github.com/smith-chem-wisc/MetaMorpheus/wiki/Getting-Started#test-installation-via-net-core-dll---linux-macos-windows)
* [Test Conda Installation (Linux, macOS, Windows)](https://github.com/smith-chem-wisc/MetaMorpheus/wiki/Getting-Started#test-conda-installation-linux-macos-windows)
## References & Citation Guide for MetaMorpheus
MetaMorpheus:
* MetaMorpheus: [Enhanced Global Post-translational Modification Discovery with MetaMorpheus, J Proteome Res **2018**, _17_, 1844-1851.](https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00873)
* Morpheus: [A Proteomics Search Algorithm Specifically Designed for High-Resolution Tandem Mass Spectra, J Proteome Res **2013**, _12_, 13771386](http://pubs.acs.org/doi/abs/10.1021/pr301024c)
GPTMD searches:
* [Global Post-Translational Modification Discovery, J Proteome Res **2017**, _16_, 13831390](https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.6b00034)
* [Global Identification of Protein Post-translational Modifications in a Single-Pass Database Search, J Proteome Res, **2015**, _14_, 47144720](http://pubs.acs.org/doi/abs/10.1021/acs.jproteome.5b00599)
Quantification:
* [Ultrafast Peptide Label-Free Quantification with FlashLFQ, J Proteome Res **2018**, _17_, 386391.](https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00608)
* If you use SILAC quantification: [An atlas of protein turnover rates in mouse tissues, Nat Communications **2021**, _12_, 6778.](https://www.nature.com/articles/s41467-021-26842-3)
Multiple protease parsimony: [Improved Protein Inference from Multiple Protease Bottom-Up Mass Spectrometry Data, J Proteome Res **2019**, _18_, 9, 34293438.](https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00330)
Glycoproteomic searches: [O-Pair Search with MetaMorpheus for O-glycopeptide characterization, Nat Methods **2020**, _17_, 11331138.](https://www.nature.com/articles/s41592-020-00985-5)
Proteogenomic database searches with Spritz: [Spritz: A Proteogenomic Database Engine, J Proteome Res **2021**, _20_, 18261834.](https://pubs.acs.org/doi/10.1021/acs.jproteome.0c00407)
Long-read proteogenomic characterization: [Enhanced protein isoform characterization through long-read proteogenomics, Genome Biology **2022**, _23_, 69.](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02624-y)
## mzLib, an all-purpose mass spectrometry toolchest implemented by MetaMorpheus
[mzLib](https://github.com/smith-chem-wisc/mzLib) is a [nuget](https://www.nuget.org/packages/mzLib/) 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.