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MatrixScience
Приєднався 26 лют 2016
Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years
Take the guesswork out of protein identification with Mascot Server, the benchmark for identification, characterisation and quantitation of proteins using mass spectrometry data.
Get closer to your raw data with Mascot Distiller, giving direct access to all popular file formats for peak picking, de novo sequencing, quantitation, and more.
Take the guesswork out of protein identification with Mascot Server, the benchmark for identification, characterisation and quantitation of proteins using mass spectrometry data.
Get closer to your raw data with Mascot Distiller, giving direct access to all popular file formats for peak picking, de novo sequencing, quantitation, and more.
Tutorial for ABRF iPRG 2023 crosslinking study
Analyse the data from the ABRF iPRG 2023 crosslinking study using Mascot. Presented by Richard Jacob, Matrix Science. Prepare and configure Mascot Server for the data set. Process automatically with Mascot Server and Distiller. Evaluate the crosslinking results. Export the results to xiVIEW for further analysis and visualization.
Tutorial materials (peak lists, processing options, example searches):
www.matrixscience.com/blog/abrf-iprg-2023-crosslinking-study.html
ABRF page: www.abrf.org/proteome-informatics-iprg-.
Timestamp
0:00 Intro
1:23 Set up the database
3:43 Test search to determine crossling proteins
8:23 Test search results
10:06 Configure a crosslinking method
12:49 Mascot Server increase MaxVarMods
14:01 Restart Mascot Daemon after adding a new crosslinking method
12:36 Mascot Distiller peak list configuration
15:40 Search the raw data crosslink data using Mascot Daemon and Distiller
18:07 Crosslinking search results
21:24 Validating crosslinking results
22:04 Exporting the results for xiView
23:59 Import the results into xiView
24:55 Viewing the results in xiView
27:26 Searching the data on the public Mascot Server
28:58 Using a demo version of Mascot Distiller to process the raw data
32:02 Summary
Tutorial materials (peak lists, processing options, example searches):
www.matrixscience.com/blog/abrf-iprg-2023-crosslinking-study.html
ABRF page: www.abrf.org/proteome-informatics-iprg-.
Timestamp
0:00 Intro
1:23 Set up the database
3:43 Test search to determine crossling proteins
8:23 Test search results
10:06 Configure a crosslinking method
12:49 Mascot Server increase MaxVarMods
14:01 Restart Mascot Daemon after adding a new crosslinking method
12:36 Mascot Distiller peak list configuration
15:40 Search the raw data crosslink data using Mascot Daemon and Distiller
18:07 Crosslinking search results
21:24 Validating crosslinking results
22:04 Exporting the results for xiView
23:59 Import the results into xiView
24:55 Viewing the results in xiView
27:26 Searching the data on the public Mascot Server
28:58 Using a demo version of Mascot Distiller to process the raw data
32:02 Summary
Переглядів: 110
Відео
Administration and Configuration (archive recording, 2014)
Переглядів 30Рік тому
Presented by Richard Jacob, Matrix Science. A description of Mascot Security and how it can be configured to control access to a Mascot Server. The Mascot Configuration Editor. Log files and trouble-shooting. The searches log and its user interface. Mascot cluster mode. Guide to sources of information. This video is part of the classic Mascot training course recorded in 2014. For up to date tra...
Sequence Database Administration (archive recording, 2014)
Переглядів 31Рік тому
Presented by David Creasy, Matrix Science. Types of database. The Fasta format. Parse rules. Mascot Database Manager: key concepts and first use. Adding a new database: detailed walk-throughs for common examples. Configuring an update schedule. Database Status. Trouble-shooting. This video is part of the classic Mascot training course recorded in 2014. For up to date training material and tutor...
Quantitation (archive recording, 2014)
Переглядів 75Рік тому
Presented by Patrick Emery, Matrix Science. All popular methods for MS-based quantitation can be divided into six 'protocols'. Three protocols are implemented in Mascot Server, three in Distiller. Creating and modifying quantitation methods. emPAI for spectral counting. Multiplex for quantitation using MS/MS sequence ion abundance. Corrections for isotope satellites and underenrichment. Reporte...
Mascot Daemon (archive recording, 2014)
Переглядів 48Рік тому
Presented by John Cottrell, Matrix Science. Installing and using Mascot Daemon. Data import filters for processing raw files into peak lists. Real-time monitor tasks for passive automation. Follow-up tasks for cascaded searching against a series of databases or using different sets of search parameters. External processes, sharing the Daemon task database, and troubleshooting. This video is par...
Sequence Queries (archive recording, 2014)
Переглядів 83Рік тому
Presented by Richard Jacob, Matrix Science. Error tolerant sequence tags are a powerful way of finding unknown modifications. Using Distiller to call tags manually and automatically. Database searching of sequence tags using Mascot. A general strategy for discovery proteomics. This video is part of the classic Mascot training course recorded in 2014. For up to date training material and tutoria...
Mascot Distiller (archive recording, 2014)
Переглядів 92Рік тому
Presented by David Creasy, Matrix Science. An overview of Mascot Distiller, including the user interface, supported raw file formats, and how the peak picking differs from conventional approaches. Batch automation via Mascot Daemon. The Developer Toolbox provides an API that allows code to be independent of file format. Search Toolbox enables Mascot database search results to be imported and im...
Very Large Searches (archive recording, 2014)
Переглядів 45Рік тому
Presented by Patrick Emery, Matrix Science. Merging peak lists. The protein family report, which is paged and cached to handle very large result sets. Clustering of proteins into families. How the Report Builder tab can be used to create a filtered and customised table of proteins for publication. The difference between Standard and Mudpit protein scoring for MS/MS searches. Exporting search re...
Scoring and Statistics (archive recording, 2014)
Переглядів 118Рік тому
Presented by John Cottrell, Matrix Science. What is probability based scoring and why is it important. Significance thresholds and expectation values. Target decoy search to estimate false discovery rate. Sensitivity improvement with Percolator. This video is part of the classic Mascot training course recorded in 2014. For up to date training material and tutorials, please check our UA-cam chan...
Modifications (archive recording, 2014)
Переглядів 67Рік тому
Presented by Richard Jacob, Matrix Science. Distinctions between chemical modifications and post-translational modifications. The Unimod database of modifications. Phosphorylation and site analysis. Using an error tolerant search to discover unexpected modifications, non-specific cleavage products, and SNPs. This video is part of the classic Mascot training course recorded in 2014. For up to da...
Sequence Databases (archive recording, 2014)
Переглядів 112Рік тому
Presented by David Creasy, Matrix Science. The characteristics of different types of database (protein, EST, genomic DNA). Which database to choose for which type of search. Use of Unigene indexes to clean up EST search results by mapping accessions to genes. Searching assembled genomes. This video is part of the classic Mascot training course recorded in 2014. For up to date training material ...
Search Parameters (archive recording, 2014)
Переглядів 262Рік тому
Presented by Patrick Emery, Matrix Science. A detailed look at each of the search parameters. Tips on choosing settings and how to avoid common mistakes. After watching this presentation, please try the hands-on exercises: www.matrixscience.com/training/exercises.html This video is part of the classic Mascot training course recorded in 2014. For up to date training material and tutorials, pleas...
Introduction to Database Searching using Mascot (archive recording, 2014)
Переглядів 1,8 тис.Рік тому
Presented by John Cottrell, Matrix Science. An overview of the three different ways to search MS and MS/MS data against sequence databases highlighting their strengths and weaknesses. This presentation can be skipped if you are already familiar with the basics of database searching. This video is part of the classic Mascot training course recorded in 2014. For up to date training material and t...
Improvements in Error Tolerant Searches (Mascot Server 2.8)
Переглядів 602 роки тому
ASMS 2021 presentation from Matrix Science. Mascot Server 2.8 includes several improvements to error tolerant searching, including false discovery rate estimation using target-decoy searching. Presented by John Cottrell, Matrix Science. Try Mascot Server for free: www.matrixscience.com/search_form_select.html Slides are available in PDF format on our website: www.matrixscience.com/pdf/2021WKSHP...
LFQ for the masses
Переглядів 1392 роки тому
ASMS 2021 presentation from Matrix Science. Mascot Distiller supports label-free quantitation (LFQ) using several different methods. This presentation describes how to do LFQ in Mascot Distiller 2.8 using extracted ion chromatograms (XICs). Presented by Richard Jacob, Matrix Science. Get a free trial of Mascot Distiller: www.matrixscience.com/distiller_download.html Slides are available in PDF ...
Identifying intact crosslinks with Mascot Server
Переглядів 3034 роки тому
Identifying intact crosslinks with Mascot Server
Quantitation Summary: exporting protein expression data for complex experiments
Переглядів 1654 роки тому
Quantitation Summary: exporting protein expression data for complex experiments
Install Mascot Server on Windows + IIS
Переглядів 7828 років тому
Install Mascot Server on Windows IIS
Mascot Server: Setting up a Uniprot proteome database
Переглядів 3,9 тис.8 років тому
Mascot Server: Setting up a Uniprot proteome database
Mascot Server: Setting up a custom database
Переглядів 4,1 тис.8 років тому
Mascot Server: Setting up a custom database
actually we have v2.5, can we upgrade it to 2.8 for free?
Updating from 2.5 to 2.8 is a paid update. Send us an e-mail to support@matrixscience.com citing your product key and we're happy to give you a no-obligation quote.
Thank you!
You're welcome!