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Getting Started

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Anthony edited this page Mar 23, 2022 · 3 revisions

Getting Started

Test Installation (Windows GUI)

  1. Download the latest MetaMorpheusInstaller.msi release, and install MetaMorpheus.
  2. Download the example spectra and database files.
  3. Open MetaMorpheus from the start menu, and drag and drop the .raw spectra files and the UniProt .xml database into MetaMorpheus.
  4. Add a series of Tasks to make a workflow for MetaMorpheus to follow. Drag the .toml files (these files store MetaMorpheus's search parameters) (Task1 - Task5) into the application.
  • Task1-SearchTaskconfig.toml - the standard search functionality.
  • Task2-CalibrateTaskconfig.toml - will mass-calibrate the spectra file based on high scoring search results and write a new calibrated .mzML file.
  • Task3-SearchTaskconfig.toml - searches the newly calibrated data file, which demonstrates improved performance (more PSMs, lower mass errors) and allows for tighter search tolerances.
  • Task4-GPTMDTaskconfig.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.
  • Task5-SearchTaskconfig.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.
  1. Click "Run All Tasks!"
  2. 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.
  3. 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.

Typical Usage (Windows GUI)

  1. Open MetaMorpheus from the start menu, and drag and drop your .raw spectra files and protein database into the GUI.
  2. Select "New Calibrate Task" tab and enter appropriate search parameters, using slightly liberal mass tolerances. Then "Add the Calibration Task". Subsequent tasks (searches) will use suggested ppm tolerances automatically generated by the calibration task.
  3. Select "New GPTMD Task" tab. Specify the G-PTM-D modifications that you think may be present in your sample. Many typical modifications are pre-selected. Then "Add the GPTMD Task".
  4. Select "New Search Task" tab. Specify the Post-Search Parameters (e.g. protein parsimony, quantification). Then "Add the Search Task".
  5. Select "Run all tasks!". This search automatically looks for PTMs uncovered in the G-PTM-D step.

Test Installation (Windows Command Line Executable)

Please watch our "How to run MetaMorpheus command line video on YouTube

  1. Download the latest release. Extract "MetaMorpheus_CommandLine.zip" using, for example, 7-Zip.
  2. Download the example spectra and database files to the folder with the CMD.exe executable.
  3. Run the command:
CMD.exe -t Task1-SearchTaskconfig.toml Task2-CalibrateTaskconfig.toml Task3-SearchTaskconfig.toml Task4-GPTMDTaskconfig.toml Task5-SearchTaskconfig.toml -s 04-30-13_CAST_Frac4_6uL.raw 04-30-13_CAST_Frac5_4uL.raw -d uniprot-mouse-reviewed-1-24-2018.xml.gz uniprot-cRAP-1-24-2018.xml.gz
  1. As the third task completes, open the results.txt files for the first and third tasks (before and after calibration). Observe the increase in the number of confident PSMs identified due to calibration.
  2. 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 an addition of new plausible PTMs.

Test Installation (via .NET Core .dll - Linux, macOS, Windows)

  1. Download the latest release. Extract files from "MetaMorpheus_CommandLine.zip".
  2. Download the example spectra and database files to the folder with the CMD.dll file.
  3. Run the command:
  • Thermo RAW files - Linux and Windows only (Thermo does not support macOS):
dotnet CMD.dll -t Task1-SearchTaskconfig.toml Task2-CalibrateTaskconfig.toml Task3-SearchTaskconfig.toml Task4-GPTMDTaskconfig.toml Task5-SearchTaskconfig.toml -s 04-30-13_CAST_Frac4_6uL.raw 04-30-13_CAST_Frac5_4uL.raw -d uniprot-mouse-reviewed-1-24-2018.xml.gz uniprot-cRAP-1-24-2018.xml.gz
  • mzML files - Linux, macOS:
dotnet CMD.dll -t Task1-SearchTaskconfig.toml Task2-CalibrateTaskconfig.toml Task3-SearchTaskconfig.toml Task4-GPTMDTaskconfig.toml Task5-SearchTaskconfig.toml -s mzML/04-30-13_CAST_Frac4_6uL.mzML mzML/04-30-13_CAST_Frac5_4uL.mzML -d uniprot-mouse-reviewed-1-24-2018.xml.gz uniprot-cRAP-1-24-2018.xml.gz
  • mzML files - Windows
dotnet CMD.dll -t Task1-SearchTaskconfig.toml Task2-CalibrateTaskconfig.toml Task3-SearchTaskconfig.toml Task4-GPTMDTaskconfig.toml Task5-SearchTaskconfig.toml -s mzML\04-30-13_CAST_Frac4_6uL.mzML mzML\04-30-13_CAST_Frac5_4uL.mzML -d uniprot-mouse-reviewed-1-24-2018.xml.gz uniprot-cRAP-1-24-2018.xml.gz

Test Conda Installation (Linux, macOS, Windows)

  1. Install miniconda.
  2. Open the terminal and enter conda install -c conda-forge metamorpheus.
  3. Download the example spectra and database files.
  4. Within that folder, run the command:
  • Thermo RAW files - Linux and Windows only (Thermo does not support macOS):
metamorpheus -t Task1-SearchTaskconfig.toml Task2-CalibrateTaskconfig.toml Task3-SearchTaskconfig.toml Task4-GPTMDTaskconfig.toml Task5-SearchTaskconfig.toml -s 04-30-13_CAST_Frac4_6uL.raw 04-30-13_CAST_Frac5_4uL.raw -d uniprot-mouse-reviewed-1-24-2018.xml.gz uniprot-cRAP-1-24-2018.xml.gz
  • mzML files - Linux, macOS:
metamorpheus -t Task1-SearchTaskconfig.toml Task2-CalibrateTaskconfig.toml Task3-SearchTaskconfig.toml Task4-GPTMDTaskconfig.toml Task5-SearchTaskconfig.toml -s mzML/04-30-13_CAST_Frac4_6uL.mzML mzML/04-30-13_CAST_Frac5_4uL.mzML -d uniprot-mouse-reviewed-1-24-2018.xml.gz uniprot-cRAP-1-24-2018.xml.gz
  • mzML files - Windows
metamorpheus -t Task1-SearchTaskconfig.toml Task2-CalibrateTaskconfig.toml Task3-SearchTaskconfig.toml Task4-GPTMDTaskconfig.toml Task5-SearchTaskconfig.toml -s mzML\04-30-13_CAST_Frac4_6uL.mzML mzML\04-30-13_CAST_Frac5_4uL.mzML -d uniprot-mouse-reviewed-1-24-2018.xml.gz uniprot-cRAP-1-24-2018.xml.gz
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