Welcome to the MacCoss Lab Proteomics Analysis Documentation!

These pages provide instructions for processing different kinds of proteomics data using fully-automated workflows on the Genome Sciences (GS) cluster. These workflows, written in Nextflow, automate the entire process–starting with the raw mass spectrometer data and ending with data visualization in tools like Limelight or Skyline.

Analysis Workflows

• DDA using Comet
  • Prerequisites
  • Workflow Steps
  • Running with tmux
  • Specifying a Cluster Queue
• Open Modification DDA using Magnum
  • Prerequisites
  • Workflow Steps
  • Running with tmux
  • Specifying a Cluster Queue
• De novo DDA using Casanovo
  • Prerequisites
  • Workflow Steps
  • Running with tmux
  • Specifying a Cluster Queue
• DIA Analysis
  • Prerequisites
  • Workflow Steps
  • Running with tmux
  • Specifying a Cluster Queue
• Carafe
  • Prerequisites
  • Workflow Steps
  • Running with tmux
  • Specifying a Cluster Queue

Helper Guides

• Setting up Limelight Credentials
  • Citing and Getting Help
• Setting up PanoramaWeb Credentials
• Connecting to a GSIT (Nexus) via SSH
  • macOS
  • Windows
  • Preventing SSH Timeouts
• Getting Help

Indices and tables

• Index

• Module Index

• Search Page