Help & tutorials
Getting started
- Mascot workflow for LC-MS/MS data
- Mascot database search overview
- Tutorial: Peptide Mass Fingerprint search
- Tutorial: Searching uninterpreted MS/MS data
- What’s new in Mascot Server 3.0
Preparing raw data for Mascot
- Tutorial: Optimizing peak picking with Mascot Distiller for any instrument
- Chimeric spectra (DDA, WWA, DIA)
- Agilent instruments
- Bruker instruments
- SCIEX instruments
- Thermo Scientific instruments
- Waters instruments
Submitting a database search
- Tutorial: Optimizing your search parameters
- Data file format
- Search parameter reference
- Enzymes
- Sequence databases
- Common mistakes
- Is your database search reproducible? (short answer: yes)
Modifications
- General approach to modifications
- Site analysis and localisation confidence
- Identifying unsuspected modifications with Error Tolerant search
- Non-specific modifications
- Identifying unsuspected modifications: Sequence Query
- Tutorial: O-fucosylated CID spectra
- Tutorial: Reviewing error tolerant results
- Tutorial: Identifying most common trypsin modifications
- Tutorial: Trypsin autolysis products
Results reports
- Result report overview
- Summary reports for PMF
- Protein Family Summary for MS/MS
- Protein View report
- Peptide View report
- Exporting result reports
- Sharing result reports
Interpreting results
- Understanding protein inference
- Human Proteome Project data interpretation guidelines 3.0
- Tutorial: The plus one dilemma
- Tutorial: Exploring protein inference
- Tutorial: Creating a list of confidently identified proteins
Scoring of proteins and peptides
- Mascot probability-based scoring
- Automatic target-decoy search
- Common myths about protein scores
- Matching and scoring internal fragments
Refining results with machine learning
- How does rescoring with machine learning work?
- Requirements and data flow
- Machine learning core features
- Predicting retention time and spectral similarity with MS2Rescore
- Machine learning quality report
Using machine learning with Mascot client software:
Automation with Mascot Daemon
- Introduction to Mascot Daemon
- Using a shared TaskDB with Mascot Daemon
- Tabulate expression data from multiple analyses with Mascot Daemon
- Automated processing with Mascot Daemon real-time monitor
Quantitation of proteins and peptides
General
- Quantitation overview
- Configuration
- Statistical procedures
- Reporting quantitation datasets with Mascot Server
- Reporting quantitation datasets with Mascot Distiller
- Improving precursor quantitation results with ion mobility filtering
iTRAQ and TMT
- Reporter protocol (MS2) (iTRAQ, TMT)
- MS3 reporter ion quantitation with Mascot Distiller
- TMTpro complementary ions
18O, metabolic, SILAC labelling
- Precursor protocol (MS1) (18O, metabolic, SILAC, etc.)
- Multiplex protocol (MS2)
- Diethylation, Dimethylation and the Deuterium effect
- Partially labelled light and heavy cysteines
Label-free methods (LFQ)
- Replicate protocol (MS1) (label-free)
- Average protocol (MS1) (label-free)
- emPAI (label-free)
- Label-free quantitation in Mascot Distiller (Replicate)
- Fractionated label-free Quantitation in Mascot Distiller (Replicate)
- Youtube: Quantitation Summary: exporting protein expression data for complex experiments
Spectral libraries
Crosslinking
- Crosslinking overview
- Crosslink examples
- Peak picking intact crosslink spectra with Mascot Distiller
- Validating intact crosslinked peptide matches
- Youtube: Identifying intact crosslinks with Mascot Server
Top-down analysis
Mascot – General
- About Matrix Science and Mascot
- A History of Mascot and Mowse
- Mascot FAQ
- Privacy FAQ
- Web Browser Compatibility
- Useful links
Reference – Protein chemistry
Reference – Mass spectrometry
Example data sets shipped with Mascot
- Getting started
- Preparing raw data
- Submitting a search
- Modifications
- Results reports
- Interpreting results
- Scoring
- Rescoring with ML
- Automation with Daemon
- Quantitation
- General
- iTRAQ and TMT
- 18O, metabolic, SILAC
- Label-free methods
- Spectral libraries
- Crosslinking
- Top-down analysis
- Mascot – General
- Reference: Protein chemistry
- Reference: Mass spectrometry
- Example data sets shipped with Mascot