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- Help; ASMS Breakfast Meeting Presentations 2016
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- Help; ASMS Meeting Presentations 2021
- Help; ASMS Workshop and User Meeting 2001
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- 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; Chimeric spectra (DDA, WWA, DIA)
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- Help; Crosslink search; Crosslink examples
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- Help; Data file format
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- 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
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- Help; New features in Mascot 2.3
- Help; New features in Mascot 2.4
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- Help; New features in Mascot Server 2.6
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- Help; New features in Mascot Server 2.8
- Help; New web site features, September 2001
- Help; Nucleic acid translation
- Help; PC specification for Mascot Server
- Help; Peptide fragmentation
- Help; Peptide Mass Fingerprint
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- Help; Quantitation; Average protocol
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- Help; Quantitation; emPAI protocol
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- Help; Sequence database setup; EMBL EST
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- 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
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- Help; Updating and upgrading to Mascot Server 2.4
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- Technical support; Mascot Distiller
- Technical support; Mascot Distiller; Change history
- Technical support; Mascot Distiller; Version 1.0
- Technical support; Mascot Distiller; Version 1.1
- Technical support; Mascot Distiller; Version 2.0
- Technical support; Mascot Distiller; Version 2.1
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- Technical support; Mascot Distiller; Version 2.3
- Technical support; Mascot Distiller; Version 2.4
- Technical support; Mascot Distiller; Version 2.5
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- Technical support; Mascot Distiller; Version 2.7
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- Technical support; Mascot Parser
- Technical support; Mascot Parser; Change history
- Technical support; Mascot Server
- Technical support; Mascot Server; Version 1.7
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- 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 Server; Version 2.8
- Technical support; Mascot Wizard
- Terms of use
- Useful links
Posts
- Blog
- 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?
- Single sign-on (SSO) and Mascot
- Solving a puzzle with Mascot Distiller de novo
- The minutiae of database management
- Validating intact crosslinked peptide matches
- Variable Modifications in Mascot 2.7
- Using the Quantitation Summary to create reports and charts
- Tabulate expression data from multiple analyses with Mascot Daemon
- Human Proteome Project data interpretation guidelines
- 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