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Posts
- Blog
- 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
- 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
- Moving old searches to cold storage
- Mascot Distiller 2.8.3 patch release
- Mascot Server 2.8.2 patch release
- New pricing for updating older Mascot Server licences
- Mascot Distiller 2.8.2 patch release
- Mascot Server 2.8.1 patch release
- Mascot Distiller 2.8.1 patch release
- Release of Mascot Server 2.8
- Mascot Server 2.8 preview
- Mascot Distiller 2.8 released
- 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