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
Introduction
- 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
Modifications
- 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
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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
Quantitation
- Supported protocols
- Creating and modifying quantitation
methods
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
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