<img src="https://user-images.githubusercontent.com/16883585/75211541-da01c680-5749-11ea-9f6c-096dc2ec4dbc.png" width="30"/> MetaMorpheus: Free, Open-Source PTM Discovery

Download the current version here. For first-time Windows users, choose "MetaMorpheusInstaller.msi" and install MetaMorpheus. Check out our <img src ="https://user-images.githubusercontent.com/16841846/40379523-eb130166-5dbb-11e8-8a03-559599cdd560.png">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 <img src ="https://user-images.githubusercontent.com/16841846/40379523-eb130166-5dbb-11e8-8a03-559599cdd560.png">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 <img src ="https://user-images.githubusercontent.com/16841846/40379523-eb130166-5dbb-11e8-8a03-559599cdd560.png">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 <img src ="https://user-images.githubusercontent.com/16841846/40379523-eb130166-5dbb-11e8-8a03-559599cdd560.png">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 <img src ="https://user-images.githubusercontent.com/16841846/40379523-eb130166-5dbb-11e8-8a03-559599cdd560.png">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

Environment:
- 64-bit operating system
- .NET Core 8.0:
  - Windows: https://dotnet.microsoft.com/en-us/download/dotnet/thank-you/sdk-8.0.401-windows-x64-installer
  - macOS, x64 Intel processor: https://dotnet.microsoft.com/en-us/download/dotnet/thank-you/sdk-8.0.401-macos-x64-installer
  - macOS, ARM Apple Silicon processor: https://dotnet.microsoft.com/en-us/download/dotnet/thank-you/sdk-8.0.401-macos-arm64-installer
  - Linux: https://learn.microsoft.com/dotnet/core/install/linux?WT.mc_id=dotnet-35129-website
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 <img src ="https://user-images.githubusercontent.com/16841846/40379523-eb130166-5dbb-11e8-8a03-559599cdd560.png">How to convert files to .mzML 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 <img src ="https://user-images.githubusercontent.com/16841846/40379523-eb130166-5dbb-11e8-8a03-559599cdd560.png">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 <img src ="https://user-images.githubusercontent.com/16841846/40379523-eb130166-5dbb-11e8-8a03-559599cdd560.png">Protein Databases Video on YouTube.