Course outline

Learn how to get the best out of Mascot directly from the people who develop and support it.

We have created an intensive 2-day course that covers every aspect of protein identification and characterisation using Mascot. The material is available in two formats: a live, two day course and a webcast. The live course is offered at a limited number of locations each year and there is a registration fee. The webcast is on-demand, self-paced, and free. In both cases, there are hands-on exercises. The main advantage of the live course is the opportunity to ask questions of the presenters.

Course Outline

Day 1


  • The three ways to search MS and MS/MS data
  • Practical tips
  • Why searches can fail

Search Parameters

  • A detailed look at each of the search parameters
  • Tips and common mistakes
  • Setting defaults

Sequence Databases

  • Which database to choose
  • Nucleic acid databases
  • Clustering with UniGene
  • Searching whole genomes


  • Types of modifications
  • Unimod
  • Phosphorylation
  • Error tolerant searches

Scoring & Statistics

  • Different ways of finding a match
  • Probability based scoring
  • Result reports
  • Significance thresholds
  • Assigning peptide matches to proteins
  • Validation

Very Large Searches

  • Challenges of very large searches
  • MudPIT protein scoring
  • Exporting search results

Day 2

Mascot Distiller

  • What is Mascot Distiller?
  • Peak picking
  • Automation
  • Importing search results
  • Calling sequence tags
  • De novo sequencing

Sequence Queries

  • Standard sequence tag
  • Error tolerant sequence tag
  • seq(), comp() and other qualifiers

Mascot Daemon

  • Installing and using Mascot Daemon
  • Data import filters
  • Real-time monitor
  • Follow-up tasks


  • Supported protocols
  • Creating and modifying quantitation

Sequence Database Administration

  • Adding a new database
  • Worked examples
  • Automatic updating

General Mascot Server Administration

  • Configuring Mascot Security
  • Mascot configuration files
  • Mascot log files
  • Cluster mode