Help Topic Index

Mascot - General

• Mascot search overview
• A History of Mascot and Mowse
• ASMS 2001 User Meeting presentations
• ASMS 2002 User Meeting presentations
• ASMS 2003 User Meeting presentations
• ASMS 2004 User Meeting presentations
• ASMS 2005 User Meeting presentations
• ASMS 2006 User Meeting presentations
• ASMS 2007 User Meeting presentations
• ASMS 2008 User Meeting presentations
• ASMS 2009 User Meeting presentations
• Mascot FAQ's

Using Mascot

• Search parameter reference
• Data file format
• Scoring algorithm
• Result Report Overview
• Summary Reports for PMF
• Summary Reports for MS/MS
• MS/MS Results Interpretation
• Sharing result reports
• Error tolerant search
• Exporting result reports
• Decoy Databases
• Top-down Searches
• Percolator
• Quantitation

Mascot System Administration

• Sequence database setup
• PC Hardware for Mascot Server

Instrument Specific Tips

• Applied Biosystems | MDS Sciex Analyst
• Applied Biosystems Data Explorer
• Applied Biosystems 4000 Series (TOF/TOF)
• Micromass Masslynx
• Thermo Finnigan Xcalibur

Protein Identification

• Peptide Mass Fingerprint
• Sequence Query
• MS/MS Ion Search

Protein chemistry

• Post translational modifications
• Enzymes
• Autolysis
• Sequence databases
• Nucleic acid translation
• Amino acid reference
• Contaminants
• BLAST & FastA

Mass spectrometry

• MS/MS fragmentation
• Accuracy & resolution
• Quadrupole Ion Trap MS

Miscellaneous

• Mascot brochure (PDF 2.7 Mb)
• Privacy FAQ
• Web Browser Compatibility
• Useful links