Help & tutorials

What’s new	About
Mascot Server 3.2 Mascot Distiller 3.0 Mascot Daemon 3.2 Mascot DIA LFQ tutorial (PDF, 14 pages)	About Matrix Science and Mascot Trial version at matrixscience.com: Mascot FAQ Privacy FAQ Useful links
Data Independent Acquisition	Data Dependent Acquisition
Mascot DIA overview Mascot DIA workflow for LC-MS/MS Distiller precursor detection for DIA	Mascot DDA overview Mascot DDA workflow for LC-MS/MS
Supported instruments	Raw data and peak lists
Agilent instruments Bruker instruments SCIEX instruments Shimadzu instruments Thermo Scientific instruments Waters instruments	Mascot Generic Format and mzML Chimeric spectra (DIA, DDA, WWA) Peak picking Thermo .RAW data with Mascot Distiller Optimizing peak picking with Mascot Distiller for any instrument
Identifying proteins	Database search reference
Mascot database search overview Searching MS/MS data (DIA, DDA) Peptide Mass Fingerprint search (PMF) Optimizing your search parameters Spectral Library searches Common mistakes Reproducibility	Mascot search parameters Amino acid reference data MS/MS fragmentation Accuracy & resolution Enzymes BLAST & FastA
Modifications and sequence variants	Modifications in depth
Error Tolerant search Reviewing error tolerant results Site analysis and localisation confidence Example: Trypsin autolysis products	General approach to modifications The plus one dilemma Non-specific modifications O-fucosylated CID spectra Sequence Query
Viewing results	Report reference
Result report overview Understanding protein inference Creating a list of confidently identified proteins Exploring protein inference Sharing result reports Machine learning quality report	Summary reports for PMF Protein Family Summary for MS/MS Protein View report Peptide View report Exporting result reports Human Proteome Project data interpretation guidelines 3.0 Web Browser Compatibility
Scoring & statistics	Machine learning
Mascot probability-based scoring Automatic target-decoy search and FDR Predicting retention time and spectral similarity with MS2Rescore Matching and scoring internal fragments Common myths about protein scores	How does rescoring with machine learning work? Requirements and data flow Machine learning core features Client software integration: Using machine learning with Mascot Server 3.1 and Thermo Proteome Discoverer™ (4 pages, 253kB) Using machine learning in Mascot Server 3.1 with Mascot Distiller 2.8 (5 pages, 224kB) Troubleshooting ML integration with Mascot client software
Automation with Mascot Daemon
Introduction to Mascot Daemon Tabulate expression data from multiple analyses with Mascot Daemon Youtube: Quantitation Summary: exporting protein expression data for complex experiments	Automated processing with Mascot Daemon real-time monitor Using a shared TaskDB with Mascot Daemon Mascot Daemon Export Extender (MDXE)
Quantitation
Label-free quantitation	Quantitation reference
Quantitation overview Label-free quantitation in Mascot Distiller Fractionated label-free Quantitation in Mascot Distiller Reporting quantitation datasets with Mascot Distiller Improving precursor quantitation results with ion mobility filtering Mascot DIA LFQ tutorial (PDF, 14 pages)	Configuration Statistical procedures Replicate protocol (MS1) [DDA, DIA] Average protocol (MS1) [DDA, DIA] emPAI [DDA, DIA]
iTRAQ and TMT	¹⁸O, metabolic, SILAC
Reporter protocol (MS2) [DDA] Reporting quantitation datasets with Mascot Server TMTpro complementary ions MS³ reporter ion quantitation with Mascot Distiller	Precursor protocol (MS1) [DDA, DIA] Multiplex protocol (MS2) [DDA] Diethylation, Dimethylation and the Deuterium effect Partially labelled light and heavy cysteines
Other search modes
Crosslinking (DDA)	Top-down analysis (DDA)
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 searches
Sequence database administration
Nucleic acid translation Finding sequence databases Sequence database setup	Youtube: Mascot Server: Setting up a custom database Youtube: Mascot Server: Setting up a Uniprot proteome database How to create a spectral library for contaminants
System administration
PC hardware	Virtual infrastructure
PC specification for Mascot Distiller PC specification for Mascot Server	Hardware virtualisation Mascot Server in the Cloud
Installation	Troubleshooting
Youtube: Install Mascot Server on Windows + IIS System services installed by Mascot products	Software failures caused by lack of disk space
Mascot Security	Backup and restore
Mascot Security: password protected administration Single sign-on (SSO) and Mascot Mascot Security: privacy settings Mascot Security: priority settings Mascot Security: sharing search results How to set up remote working	Disaster recovery Migrating to new hardware

Example data sets shipped with Mascot

MS/MS Ion Search	Help topic
Yeast example (CPTAC study 6)
Heat shock protein (human)
ABRF iPRG2008 (mouse)	Tutorial: Exploring protein inference
Trypsin autolysis products	Trypsin autolysis
Error tolerant search of a small human sample	Reviewing error tolerant results
Negative ion example	Peptide fragmentation
Quantitation	Help topic
Phospho-enriched TMTpro 18-plex (PXD024275)	Quantitation: Reporter protocol
SILAC K+6 R+6 multiplex (Zhang and Neubert, MCP 5 401-411 (2006))	Quantitation: Multiplex protocol
Human cell lysate acquired using a Waters QTof	Quantitation: emPAI protocol
Spectral libraries	Help topic
Yeast spectral library search	Spectral library search
Yeast spectral library plus SwissProt
Crosslinking	Help topic
Chicken lysozyme disulfide bridges (PXD009460)	Crosslink examples
HOP2-MND1 heterodimer crosslinked with EDC, Arabidopsis thaliana (PXD001538)
Human serum albumin crosslinked with DSS/BS3, intra and interlinks (PXD006131)
Top-down	Help topic
Top-down, myoglobin, Bruker ECD, NoCleave	Top-down searches
Top-down, iterleukin, Bruker ECD, no-enzyme
Peptide Mass Fingerprint (PMF)	Help topic
Human keratin (K9)	Human contaminants
Protein PML (human)	Summary reports for PMF
PMF mixture of three proteins (yeast)	PMF Mixture Mode
Heat shock protein (yeast)	How the PMF score is calculated
Sequence Query	Help topic
Error tolerant sequence tag example
Top-down, superoxide dismutase, error tolerant	Top-down searches

Matrix Science

Help & tutorials

What’s new

About

Data Independent Acquisition

Data Dependent Acquisition

Supported instruments

Raw data and peak lists

Identifying proteins

Database search reference

Modifications and sequence variants

Modifications in depth

Viewing results

Report reference

Scoring & statistics

Machine learning

Automation with Mascot Daemon

Quantitation

Label-free quantitation

Quantitation reference

iTRAQ and TMT

18O, metabolic, SILAC

Other search modes

Crosslinking (DDA)

Top-down analysis (DDA)

Sequence database administration

System administration

PC hardware

Virtual infrastructure

Installation

Troubleshooting

Mascot Security

Backup and restore

Example data sets shipped with Mascot

¹⁸O, metabolic, SILAC