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GalaxyP Workflow: Protein Identification (using Search GUI and Peptide Shaker) Inputs Outputs Customizing the Workflow

readme.md

GalaxyP Workflow: Protein Identification (using Search GUI and Peptide Shaker)

This workflow supplements the GalaxyP tutorial on Protein ID (Link). You can find two versions of the same workflow: one is designed for a single MS run as an input. It can also be used for parallel analysis of multiple MS runs. Each MS run will result in a separate output file. The second workflow is designed for multiple MS runs to be combined into a single output file.

An overview of the workflow is given below:

Protein ID Workflow

Inputs

Two inputs are needed:

  1. A protein FASTA database to be searched against. Using the current settings, a database without decoys is needed. The decoys will be automatically added by Search GUI 🔧 . To learn more about databases, please consider the tutorial on database handling. For creating a database, you can also use a ready-made workflow.

  2. At least one mass spectrometry data file in the mzML format. With the current settings, you will need a non-centroided mzML (raw data, no prior peak-picking). If you have data in another format or already centroided data, please consider the section below.

Outputs

The workflow provides the identified proteins, peptides and PSMs as an output. For details on the Peptide Shaker 🔧 outputs, please consider the tutorial on database handling.

Customizing the Workflow

You can customize the workflow after importing it to your Galaxy instance. Click on Workflows, choose this workflow and click on Edit.

  • Using a centroided mzML file: Delete the tool PeakPickerHiRes 🔧 , use the mzML directly as an input for FileConverter 🔧 .

  • Using another MS file format than mzML:

    • For *.mgf: Delete the tool PeakPickerHiRes 🔧 and FileConverter 🔧 , use the mzML directly as an input for Search GUI 🔧 .
    • For *.raw: Convert to mzML before running the workflow. For details, please consider the tutorial on database handling.
    • For other formats: Use the FileConverter 🔧 to convert to mzML (profile data) or directly to mgf (centroided data).