The Proteome Discoverer application consists of the following main components.

Component

Description

Proteome Discoverer client

When using Proteome Discoverer, you typically interact with the main window of the Proteome Discoverer client. Use this client to:

  • Create and submit workflows for processing
  • Monitor job progress
  • Configure the server
  • Administer repository data, such as FASTA files, spectral libraries, and modifications
  • Display results

You create workflows in the application’s Workflow Editor and then submit them for execution to the Magellan server, which processes the workflows locally or remotely.

Magellan Server

A server process that waits for submissions of workflows from the Proteome Discoverer client or the Proteome Discoverer Daemon client. The Magellan server can run on the same computer or on a remote machine.

This server registers and manages processing nodes that you use within the data processing workflows, processing workflow jobs, storing data, and general data maintenance. The server is extensible with new processing nodes. The Magellan server publishes client gateways by .NET remoting, and multiple clients can connect to these gateways to communicate with the server. The Magellan server maintains a repository of the registered processing nodes, their configurations, and metadata about the available nodes. The Magellan server also maintains repositories of registered data such as FASTA files, spectral libraries, chemical modifications, and so on.

Proteome Discoverer Daemon Utility

A utility that you can use to automatically start workflow jobs from a remote system. For more information on the Proteome Discoverer Daemon utility, see Using the Proteome Discoverer Daemon utility.

Use this application to:

  • Start batches of files to process
  • Perform multiple searches on multiple raw data files taken from multiple samples or replicates from the same sample
  • Use the command line to automate the submission of workflow jobs to the Magellan server
  • Submit jobs manually