Site map
Pages
- About Matrix Science
- Access Mascot Server
- Blog
- Contact us
- Distributors
- Evaluate Mascot Distiller
- Help & tutorials (index)
- Help; A history of Mascot and Mowse
- Help; Accuracy & resolution
- Help; Agilent instruments
- Help; Amino acid reference data
- Help; Automated processing with Mascot Daemon real-time monitor
- Help; Automatic target-decoy searching
- Help; BLAST & FastA
- Help; Bruker instruments
- Help; Chimeric spectra (DDA, WWA, DIA)
- Help; Common mistakes
- Help; Common myths about protein scores
- Help; Contaminants
- Help; Creating a list of confidently identified proteins
- Help; Crosslink search
- Help; Crosslink search; Crosslink examples
- Help; CSV export column headers
- Help; Data file format
- Help; Diethylation, Dimethylation and the Deuterium effect
- Help; Disaster recovery
- Help; Enzymes
- Help; Exploring protein inference
- Help; Export search results
- Help; FAQ
- Help; Fractionated label-free quantitation in Mascot Distiller
- Help; General approach to modifications
- Help; Hardware virtualisation
- Help; Hosting Mascot Server on Amazon Web Services
- Help; How does rescoring with machine learning work?
- Help; How to create a spectral library for contaminants
- Help; How to set up remote working
- Help; Human Proteome Project data interpretation guidelines
- Help; Identifying most common trypsin modifications
- Help; Identifying unsuspected modifications with Error Tolerant search
- Help; Improving precursor quantitation results with ion mobility filtering
- Help; Introduction to Mascot Daemon
- Help; Is your database search reproducible?
- Help; Label-free quantitation in Mascot Distiller
- Help; Machine learning core features
- Help; Machine learning quality report
- Help; Mascot probability-based scoring
- Help; Mascot Security: password protected administration
- Help; Mascot Security: priority settings
- Help; Mascot Security: privacy settings
- Help; Mascot Security: sharing search results
- Help; Mascot Server in the cloud
- Help; Mascot workflow for LC-MS/MS data
- Help; Matching and scoring internal fragments
- Help; MS3 reporter ion quantitation with Mascot Distiller
- 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 features in Mascot Server 2.8
- Help; New features in Mascot Server 3.0
- Help; New features in Mascot Server 3.1
- Help; New web site features, September 2001
- Help; Non-specific modifications
- Help; Nucleic acid translation
- Help; O-fucosylated CID spectra
- Help; Obsolete data file formats
- Help; Obsolete export formats
- Help; Obsolete MS/MS summary reports
- Help; Optimizing your search parameters
- Help; Partially labelled light and heavy cysteines
- Help; PC specification for Mascot Server
- Help; Peak picking intact crosslink spectra with Mascot Distiller
- Help; Peak picking Thermo .RAW data with Mascot Distiller
- Help; Peptide fragmentation
- Help; Peptide Mass Fingerprint search
- Help; Peptide View report
- Help; Predicting retention time and spectral similarity with MS2Rescore
- Help; Privacy FAQ
- Help; Protein Family Summary report (MS/MS)
- Help; Protein View report
- 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; Reporting quantitation datasets with Mascot Distiller
- Help; Requirements and data flow for rescoring
- Help; Result report overview
- Help; Reviewing error tolerant results
- Help; SCIEX Data Explorer
- Help; SCIEX instruments
- Help; Search parameter reference
- Help; Searching uninterpreted MS/MS data
- 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; Single sign-on (SSO) and Mascot
- Help; Site analysis and localisation confidence
- Help; Spectral library search
- Help; Summary reports for PMF
- Help; Tabulate expression data from multiple analyses with Mascot Daemon
- Help; The plus one dilemma
- Help; Thermo instruments
- Help; TMTpro complementary ions
- Help; Top-down searches
- Help; Troubleshooting ML integration with client software
- Help; Trypsin autolysis
- Help; Understanding protein inference
- 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 or migrating Mascot Server
- Help; Updating to Mascot Server 2.7
- Help; Updating to Mascot Server 2.8
- Help; Using a shared TaskDB with Mascot Daemon
- Help; Validating intact crosslinked peptide matches
- Help; Waters instruments
- Help; Web browser compatibility
- Support; Mascot Server; IIS 7 configuration
- Support; Mascot Server; Mascot 2.2.01 for Windows Installation Troubleshooter
- Support; Mascot Server; Mascot 2.2.03 known issues
- 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 Breakfast Meeting Presentations 2020
- Help; ASMS Breakfast Meeting Presentations 2021
- Help; ASMS Breakfast Meeting Presentations 2022
- Help; ASMS Breakfast Meeting Presentations 2023
- Help; ASMS Breakfast Meeting Presentations 2024
- Help; ASMS Breakfast Meeting Presentations 2025
- Help; ASMS User Meetings
- 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
- Help; HUPO World Congress 2024
- Help; Mascot search overview
- Help; System administration help
- Mascot training; Classic training course (archive recording, 2014)
- Mascot training; Modules and materials
- 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
- Quote request
- Site map
- Solutions; Mascot DIA
- Solutions; Mascot for core labs
- Solutions; Mascot for educators
- Solutions; Mascot for industry
- Solutions; Mascot for researchers
- Support; Mascot Daemon
- Support; Mascot Daemon; Version 2.0
- Support; Mascot Daemon; Version 2.1
- Support; Mascot Daemon; Version 2.2
- Support; Mascot Daemon; Version 2.3
- Support; Mascot Daemon; Version 2.4
- Support; Mascot Daemon; Version 2.5
- Support; Mascot Daemon; Version 2.6
- Support; Mascot Daemon; Version 2.7
- Support; Mascot Daemon; Version 2.8
- Support; Mascot Daemon; Version 3.0
- Support; Mascot Distiller
- Support; Mascot Distiller; Change history
- Support; Mascot Distiller; Version 1.0
- Support; Mascot Distiller; Version 1.1
- Support; Mascot Distiller; Version 2.0
- Support; Mascot Distiller; Version 2.1
- Support; Mascot Distiller; Version 2.2
- Support; Mascot Distiller; Version 2.3
- Support; Mascot Distiller; Version 2.4
- Support; Mascot Distiller; Version 2.5
- Support; Mascot Distiller; Version 2.6
- Support; Mascot Distiller; Version 2.7
- Support; Mascot Distiller; Version 2.8
- Support; Mascot Parser
- Support; Mascot Parser; Change history
- Support; Mascot Server
- Support; Mascot Server; IIS configuration
- Support; Mascot Server; Version 1.7
- Support; Mascot Server; Version 1.8
- Support; Mascot Server; Version 1.9
- Support; Mascot Server; Version 2.0
- Support; Mascot Server; Version 2.1
- Support; Mascot Server; Version 2.2
- Support; Mascot Server; Version 2.3
- Support; Mascot Server; Version 2.4
- Support; Mascot Server; Version 2.5
- Support; Mascot Server; Version 2.6
- Support; Mascot Server; Version 2.7
- Support; Mascot Server; Version 2.8
- Support; Mascot Server; Version 3.0
- Support; Mascot Server; Version 3.1
- Support; Mascot Wizard
- Terms of use
- Useful links
Posts
- Blog
- The promise of spectrum-centric DIA
- Identify more proteins using Mascot and Proteome Discoverer with this one small trick
- Adding a custom AI/ML adapter to Mascot
- Big databases and large peak lists
- Mascot Distiller quantitates more proteins with machine learning
- Using machine learning with Mascot and Proteome Discoverer
- Mascot vs FragPipe: Uncovering endogenous proteolytic processing
- Best MS2PIP model for Thermo Orbitrap
- Tutorial: Selecting the best MS2PIP model
- Tutorial: Selecting the best DeepLC model
- Predicted RT and fragment intensity in Mascot Server 3.0
- How does rescoring with machine learning work?
- Matrix Science at ASMS 2024
- 30 years of Sequence Tags
- Mascot workflow for LC-MS/MS data
- Tutorial: Creating custom reports in Mascot Distiller
- How to run the public Mascot service
- Mascot security – guest users and administrators
- ABRF iPRG 2023 crosslinking study
- Finding unsuspected modifications in narrow-window DIA data using the Mascot Error Tolerant Search
- Spectrum-centric searching of narrow window DIA data with Mascot Server
- Mascot Distiller 20th anniversary
- Identifying peptides from chimeric spectra (DDA, DIA)
- Get better HCD results by matching internal fragments
- Mascot Daemon Export Extender
- How old is the software in that publication?
- Get more search speed with SplitNumberOfQueries
- Generating high quality spectral libraries for DIA-MS
- 25 years of Matrix Science
- Mascot in the Cloud
- Peak picking intact crosslink spectra with Mascot Distiller
- Paleoproteomics
- Complementary reporter ion clusters in TMT/TMTpro labeling
- Reporting quantitation datasets with Mascot Distiller 2.8
- Downloading UniProt proteomes via new API
- Does your search engine show the evidence?
- Divide and conquer: Fractionated Label Free Quantitation in Mascot Distiller 2.8.2
- mzIdentML 1.2
- NCBI nr in Mascot Server 2.8.1
- Analyzing the disulfide bond structure of the SARS-Cov-2 Spike protein
- Single-cell peptide fragmentation spectra
- Default or prof_prof? Peak picking Thermo .RAW data with Mascot Distiller
- Mascot cluster installation security on Linux
- Retiring the File Transfer Protocol (FTP)
- Choosing hardware for Mascot Distiller
- Identify more HLA peptides
- Addressing disk bottlenecks
- Error tolerant searches now show statistical significance
- NCBI nr tips
- Improving precursor quantitation results with ion mobility filtering
- Global thinking: Label Free Quantitation in Mascot Distiller 2.8
- How much cashmere is in this sweater?
- Unipept and Mascot
- NIST Human HCD Spectral Libraries
- How large a Mascot Server licence do I need?