Site map
Pages
- Blog
- Contact us
- Help; ASMS Breakfast Meeting Presentations 2016
- Help; ASMS Breakfast Meeting Presentations 2017
- Help; ASMS Breakfast Meeting Presentations 2018
- Help; ASMS Breakfast Meeting Presentations 2019
- Help; ASMS Workshop and User Meeting 2001
- Help; ASMS Workshop and User Meeting 2002
- Help; ASMS Workshop and User Meeting 2003
- Help; ASMS Workshop and User Meeting 2004
- Help; ASMS Workshop and User Meeting 2005
- Help; ASMS Workshop and User Meeting 2006
- Help; ASMS Workshop and User Meeting 2007
- Help; ASMS Workshop and User Meeting 2008
- Help; ASMS Workshop and User Meeting 2009
- Help; ASMS Workshop and User Meeting 2010
- Help; ASMS Workshop and User Meeting 2011
- Help; ASMS Workshop and User Meeting 2012
- Help; ASMS Workshop and User Meeting 2013
- Help; ASMS Workshop and User Meeting 2014
- Help; ASMS Workshop and User Meeting 2015
- Mascot database search; Access Mascot Server
- Mascot database search; Database search help
- Help; A history of Mascot and Mowse
- Help; AB Sciex Analyst
- Help; AB Sciex Data Explorer
- Help; AB Sciex TOF/TOF
- Help; Accuracy & resolution
- Help; Amino acid reference data
- Help; BLAST & FastA
- Help; Contaminants
- Help; Crosslink search
- Help; Crosslink search; Crosslink examples
- Help; CSV export column headers
- Help; Data file format
- Help; Decoy databases
- Help; Enzymes
- Help; Error tolerant search
- Help; Export search results
- Help; FAQ
- Help; IIS 7 configuration
- Help; Mascot search parameters
- Help; Modifications
- Help; MS/MS Ions Search
- Help; MS/MS Results Interpretation
- Help; New features in Mascot 1.5
- Help; New features in Mascot 1.9
- Help; New features in Mascot 2.0
- Help; New features in Mascot 2.1
- Help; New features in Mascot 2.2
- Help; New features in Mascot 2.3
- Help; New features in Mascot 2.4
- Help; New features in Mascot 2.5
- Help; New features in Mascot Server 2.6
- Help; New features in Mascot Server 2.7
- Help; New web site features, September 2001
- Help; Nucleic acid translation
- Help; PC specification for Mascot Server
- Help; Peptide fragmentation
- Help; Peptide Mass Fingerprint
- Help; Percolator
- Help; Privacy FAQ
- Help; Quantitation; Average protocol
- Help; Quantitation; Configuration
- Help; Quantitation; emPAI protocol
- Help; Quantitation; Multiplex protocol
- Help; Quantitation; Overview
- Help; Quantitation; Precursor protocol
- Help; Quantitation; Replicate protocol
- Help; Quantitation; Report format
- Help; Quantitation; Reporter protocol
- Help; Quantitation; Statistical procedures
- Help; Result report overview
- Help; Scoring
- Help; Sequence database migration
- Help; Sequence database setup
- Help; Sequence database setup; Contaminants
- Help; Sequence database setup; Database Manager
- Help; Sequence database setup; EMBL EST
- Help; Sequence database setup; Generic database
- Help; Sequence database setup; IPI
- Help; Sequence database setup; Manual configuration and updating
- Help; Sequence database setup; NCBI EST (OBSOLETE)
- Help; Sequence database setup; NCBI nr
- Help; Sequence database setup; NCBI nr with gi numbers (OBSOLETE)
- Help; Sequence database setup; Spectral library
- Help; Sequence database setup; SwissProt
- Help; Sequence database setup; TrEMBL
- Help; Sequence database setup; UniProt proteomes
- Help; Sequence database setup; UniRef
- Help; Sequence databases
- Help; Sequence Query
- Help; Sharing result reports
- Help; Spectral library search
- Help; Summary Reports for MS/MS
- Help; Summary reports for PMF
- Help; Thermo Xcalibur
- Help; Top-down searches
- Help; Trypsin autolysis
- Help; Updating and upgrading to Mascot Server 2.4
- Help; Updating and upgrading to Mascot Server 2.5
- Help; Updating and upgrading to Mascot Server 2.6
- Help; Updating to Mascot Server 2.7
- Help; Waters Masslynx
- Help; Web browser compatibility
- Technical support; Mascot Server; Mascot 2.2.01 for Windows Installation Troubleshooter
- Technical support; Mascot Server; Mascot 2.2.03 known issues
- Mascot database search; Mascot search overview
- Mascot Server technical support; IIS configuration
- Mascot training; Course outline
- Mascot training; Live course
- Mascot training; Webcast course
- News
- News; Press releases
- Newsletter
- Products; Licensing overview
- Products; Mascot Daemon
- Products; Mascot Distiller
- Products; Mascot Distiller; Download
- Products; Mascot Distiller; Toolboxes
- Products; Mascot Parser
- Products; Mascot Parser; Download
- Products; Mascot Server
- Products; Mascot Server; Mascot Cluster
- Products; Mascot Wizard
- Products; Sales enquiries
- Site map
- Technical support; Mascot Daemon
- Technical support; Mascot Daemon; Version 2.0
- Technical support; Mascot Daemon; Version 2.1
- Technical support; Mascot Daemon; Version 2.3
- Technical support; Mascot Daemon; Version 2.4
- Technical support; Mascot Distiller
- Technical support; Mascot Distiller; Change history
- Technical support; Mascot Parser
- Technical support; Mascot Parser; Change history
- Technical support; Mascot Server
- Technical support; Mascot Server; Version 1.7
- Technical support; Mascot Server; Version 1.8
- Technical support; Mascot Server; Version 1.9
- Technical support; Mascot Server; Version 2.0
- Technical support; Mascot Server; Version 2.1
- Technical support; Mascot Server; Version 2.2
- Technical support; Mascot Server; Version 2.3
- Technical support; Mascot Server; Version 2.4
- Technical support; Mascot Server; Version 2.5
- Technical support; Mascot Server; Version 2.6
- Technical support; Mascot Server; Version 2.7
- Technical support; Mascot Wizard
- Terms of use
- Useful links
Posts
- Blog
- How to set up remote working
- Disulfide bond characterisation
- The Third Column: MS/MS fragment ion decharging in Mascot Server 2.7
- Protein FDR in Mascot Server 2.7
- Disaster recovery
- Is your database search reproducible?
- Common myths about protein scores
- The three Ds: Diethylation, Dimethylation and the Deuterium effect
- Identify proteins by more than ‘gut’ feeling
- What are you inferring?
- Back to basics 5: Peptide-spectrum match statistics
- Mascot workflows in Proteome Discoverer
- Back to basics 4: Mascot Daemon
- X!Hunter MGF libraries
- O-fucosylated CID spectra
- Don’t wait: use spectral libraries now
- The plus one dilemma
- Back to basics 3: Quantitation statistics
- Mascot Server cluster mode
- Back to Basics 2: Common mistakes
- Back to Basics: Optimize your search parameters
- Mascot Distiller 2.7: Farewell to re-gridding
- Higher accuracy for oxidation profiles
- Keeping genome databases up to date
- Stepping up security
- MS3 reporter ion quantitation with Mascot Distiller
- Results round-up for the ‘dark matter’ challenge
- A quarter-century in 2018
- Using a shared TaskDB with Mascot Daemon
- Step away from the iodoacetamide
- How to create a spectral library for contaminants
- Exporting spectral library search results
- The most analysed protein is …
- Trying to illuminate proteomics ‘dark matter’
- Ion series for EThcD
- Mascot Security: priority settings
- Mascot Security: privacy settings
- Exporting search results: tips and tricks
- How many of you are there in there? Processing and searching chimeric MS/MS spectra with Mascot Distiller and Mascot Server
- Protein inference for spectral library searches
- Benchmarking your Mascot Server
- Retention time
- Getting the most out of your Mascot Server hardware
- Not Better Together: Processing and searching combined CID+ETD datasets with Mascot Distiller 2.6
- Improved security for Mascot Installations under Linux
- High FDRs for methylated peptides III
- High FDRs for methylated peptides II
- High FDRs for methylated peptides
- Some peaks are more equal than others
- Selenocysteine
- Disruption ahead for NCBI databases
- 64 Baker Street
- Shooting fish in a barrel
- PSI file formats, part 4: mzTab
- Mass-tolerant vs Error tolerant
- PSI file formats, part 3: repositories
- Search only for peptides we care about?
- PSI file formats, part 2: validation
- PSI file formats, part 1: mzIdentML
- Integrating Mascot into a proteomics pipeline (Part 2)
- Expressed Sequence Tags
- Searching DIA data, especially Swath
- Creating a list of confidently identified proteins
- Running Mascot Server on a supercomputer
- Using Mascot security to share search results
- How Mascot Insight uses gene ontology and molecular interaction data
- Integrating Mascot into a proteomics pipeline
- Spring clean your mascot.dat
- Peak list arcana*
- How long should a search take? – Data and search parameters
- How long should a search take? – Hardware and configuration
- Does protein FDR have any meaning?
- Modifications round-up, part 2
- Modifications round-up, part 1
- Current challenges in quantitative proteomics
- Running Mascot in a virtual machine
- Backing up your Mascot Server
- Site analysis
- Non-standard amino acid residues
- When to use Combination searches
- Don’t get stuck in a queue
- Quantify then identify or identify then quantify?
- High mass accuracy: fragments
- High mass accuracy: precursors
- News
- New databases and greater maximum search size
- Release of Mascot Server 2.7
- Mascot Server 2.7 preview
- 2019 ASMS user meeting presentations now online
- 2018 ASMS user meeting presentations now online
- 20% off Mascot Server updates for 20th anniversary
- Mascot 2.6.2 patch release
- Mascot Distiller 2.7 released
- 2017 ASMS user meeting presentations now online
- Mascot 2.6.1 patch release
- Release of Mascot Server 2.6
- Mascot Server 2.6 preview
- NCBInr is dead, long live NCBIprot
- 2016 ASMS user meeting presentations now online
- Mascot Distiller 2.6 released
- New YouTube video
- Peak picking tutorial
- 2015 ASMS user meeting presentations now online
- Training presentations updated
- Mascot 2.5.1 patch release
- 2014 ASMS user meeting presentations now online
- Mascot 2.5 stress test
- ASMS 2014
- Press release announcing launch of Mascot Insight
- 2013 ASMS user meeting presentations now online
- Matrix Science receives DGMS Award
- New look for the Matrix Science website
- Training courses in 2013
- Free webcast version of Mascot training now available
- Matrix Science wins 2012 HUPO Science and Technology Award
- Mascot Distiller now supports a variable modification on the same residue as the label
- 2012 ASMS user meeting presentations now online
- Mascot Server 2.4 released
- Mascot Distiller 2.4 released
- 2011 ASMS user meeting presentations now online
- Training course dates for 2011
- 2010 ASMS user meeting presentations now online
- EST databases on this site switched from GenBank to EMBL
- Mascot Server 2.3 released
- Mascot 2.3 beta test
- Mascot Distiller 2.3 released
- 2009 ASMS user meeting presentations now online
- Larger searches permitted on free public Mascot Server
- Mascot Distiller Quantitation Toolbox released
- 2008 ASMS user meeting presentations now online
- EST_others database split into three parts based on taxonomy
- Press release describing integration between Mascot and Thermo Fisher Scientific BioWorks
- Mascot Parser is now free of charge!
- New help page describes how to configure MSIPI
- New training course dates for 2008
- New patch available for Mascot Server 2.2
- New release of Mascot Wizard
- Press release announcing collaboration between Proxeon and Matrix Science
- 2007 ASMS user meeting presentations now online
- New maintenance release of Mascot Distiller (2.1.1)
- Mascot version 2.2 is now running on this server
- Mascot Distiller 2.1 released
- New help page for Applied Biosystems Data Explorer
- 2006 ASMS user meeting presentations now online
- New patches available for Mascot Server and Mascot Daemon
- New help page for target-decoy searching
- New help page describing PC hardware for Mascot Server
- Mascot Distiller 2.0 released
- New patches available for Mascot Server and Mascot Daemon
- New Flash movies to illustrate the look and feel of Mascot Integra