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Vignette: Bottom up mouse
This page will walk you through using the MetaMorpheus graphical user interface (GUI) with a standard set of files we have provided for you. This tutorial assumes you're running Microsoft Windows; Windows is required to use the GUI. However, the command-line version can be used on Windows, Linux, or OSX.
First, click this link to view the latest release of MetaMorpheus. Download MetaMorpheus by clicking "MetaMorpheusInstaller.msi". Run the installer and install MetaMorpheus.
Then, download the vignette files from here: https://uwmadison.box.com/s/woh246eq30vtckxsfbae5pw0ltoznlca
1. Open MetaMorpheus from the start menu.
2. Add the .raw spectra files and the UniProt .xml.gz protein databases you just downloaded into MetaMorpheus, by drag-and-drop or by clicking the "Add" buttons in MetaMorpheus.
3. Add a series of Tasks to make a workflow for MetaMorpheus to follow. To do this, drag the five .toml files (these files store MetaMorpheus's search parameters) into the application.
Task1SearchExample.toml - the standard search functionality.
Task2CalibrationExample.toml - will mass-calibrate the spectra file based on high-scoring search results and write a new calibrated .mzML file.
Task3SearchExample.toml - searches the newly calibrated data file, which demonstrates improved performance (more PSMs, lower mass errors) and allows for tighter search tolerances.
Task4GptmdExample.toml - searches the calibrated data file to find high-probability PTMs. This search task generates a new .xml protein database with annotated PTM possibilities discovered by G-PTM-D.
Task5SearchExample.toml - searches the calibrated input file against the G-PTM-D .xml database. This search result is the highest confidence in terms of total PSMs and modified peptides.
4. Click "Run All Tasks!"
As the third task completes, open the results.txt files for the first and third tasks (before and after calibration, respectively). Observe the increase in the number of confident PSMs and identified peptides due to calibration.
As the fifth task completes, open the results.txt files for the third and fifth tasks. Observe the increase in the number of confident PSMs identified due to discovered PTM-containing peptides.
To view your results files from all the tasks, click the "Open" button next to the text box which specifies the output folder. The subfolders include the results from each task (for example, the search task writes PSM results, the calibration task writes calibrated .mzML files, and the G-PTM-D task writes the .xml database with PTM annotations). The "Task Settings" folder writes the settings that you performed the search(es) with to .toml files. These .toml files can be dragged-and-dropped into MetaMorpheus to re-use search settings.