matrix_science - Network

Mascot Server ships with MS2Rescore, which is one of many predictive ML tools for proteomics. Follow this new tutorial if you want to add an...

Mascot Server ships with MS2Rescore, which is one of many predictive ML tools for proteomics. Follow this new tutorial if you want to add an integration to a different AI/ML system.

https://www.matrixscience.com/blog/adding-a-custom-aiml-adapter-to-mascot.html

#proteomics #MassSpec

Agilent have published an application note for recommended MassHunter Qualitative Analysis settings when searching DDA peak lists with...

Agilent have published an application note for recommended MassHunter Qualitative Analysis settings when searching DDA peak lists with Mascot Server. We've added it to a new help page for Agilent instruments.

https://www.matrixscience.com/help/instruments_agilent.html

#proteomics #MassSpec

Mascot newsletter, April 2025:ASMS User Meeting registration is now open.Competitive displacement of lipoprotein lipase by GPIHBP1.MS2PIP...

Mascot newsletter, April 2025:

ASMS User Meeting registration is now open.

Competitive displacement of lipoprotein lipase by GPIHBP1.

MS2PIP models for Thermo instruments.

#proteomics #massspec

https://www.matrixscience.com/nl/202504/newsletter.html

Sometimes you need a very large sequence database, e.g. search all proteobacteria proteins. Mascot Server has no size limit. Search a...

Sometimes you need a very large sequence database, e.g. search all proteobacteria proteins. Mascot Server has no size limit. Search a database of hundreds of millions of protein sequences without running out of resources.

https://www.matrixscience.com/blog/big-databases-and-large-peak-lists.html

#proteomics #MassSpec

If your computer breaks down, do you know how to restore Mascot? As long as you regularly back up the right directories and files, it's...

If your computer breaks down, do you know how to restore Mascot? As long as you regularly back up the right directories and files, it's straightfoward and fully described in the online help:

https://www.matrixscience.com/help/disaster_recovery.html

#proteomics #MassSpec

Mascot Newsletter, March 2025:50% more identifications in Thermo Proteome Discoverer.Maternal immune activation imprints translational...

Mascot Newsletter, March 2025:

50% more identifications in Thermo Proteome Discoverer.

Maternal immune activation imprints translational dysregulation.

Mascot's ML adapter framework (US HUPO 2025 poster).

#proteomics #MassSpec

https://www.matrixscience.com/nl/202503/newsletter.html

Mascot Distiller provides DDA LFQ for Bruker, Sciex, Thermo and Waters instruments. Retention time alignment ("match between...

Mascot Distiller provides DDA LFQ for Bruker, Sciex, Thermo and Waters instruments. Retention time alignment ("match between runs"); ion mobility (Bruker TIMS); fractionation; optimised peak detection; visualisation; and more.

#proteomics #MassSpec

https://www.matrixscience.com/distiller.html

Mascot Newsletter, February 2025:Mascot vs FragPipe: semi-tryptic TMTpro.Characterization of the noncanonical proteome.Mascot Server 3.1 is...

Mascot Newsletter, February 2025:

Mascot vs FragPipe: semi-tryptic TMTpro.

Characterization of the noncanonical proteome.

Mascot Server 3.1 is now available.

#proteomics #MassSpec

https://www.matrixscience.com/nl/202502/newsletter.html

Mascot Distiller can now use machine learning to boost sensitivity of protein quantitation. We processed a Thermo Orbitrap DDA LFQ benchmark...

Mascot Distiller can now use machine learning to boost sensitivity of protein quantitation. We processed a Thermo Orbitrap DDA LFQ benchmark data set, where Distiller now quantitates 14% more proteins at 1% FDR.

#proteomics #MassSpec

https://www.matrixscience.com/blog/mascot-distiller-quantitates-more-proteins-with-machine-learning.html

Do you use Thermo Proteome Discoverer with Mascot Server? Mascot Server 3.1 can now send results refined with machine learning directly to...

Do you use Thermo Proteome Discoverer with Mascot Server? Mascot Server 3.1 can now send results refined with machine learning directly to PD.

PD 3.1: Identify over 20% more proteins.
PD 2.4: Identify over 40% more proteins.

#proteomics #MassSpec

https://www.matrixscience.com/blog/using-machine-learning-with-mascot-and-proteome-discoverer.html

Mascot Server 3.1 is a patch release that enhances integration with Thermo Proteome Discoverer and fixes a few important bugs introduced in...

Mascot Server 3.1 is a patch release that enhances integration with Thermo Proteome Discoverer and fixes a few important bugs introduced in Mascot Server 3.0. You can now import refined results directly from Mascot into PD.

#proteomics #MassSpec

https://www.matrixscience.com/help/mascot_server_3_1_release.html

Mascot Newsletter, January 2025:Learn how Mascot uses machine learning.Characterising a bacterial microcompartment.Mascot protein...

Mascot Newsletter, January 2025:

Learn how Mascot uses machine learning.

Characterising a bacterial microcompartment.

Mascot protein inference.

https://www.matrixscience.com/nl/202501/newsletter.html

#proteomics #MassSpec

Mascot Server has a lot of functionality and it's sometimes hard to know where to start. The online help now has a table of example data...

Mascot Server has a lot of functionality and it's sometimes hard to know where to start. The online help now has a table of example data sets shipped with Mascot, including links to the corresponding help topics.

https://www.matrixscience.com/help.html#EXAMPLES

#proteomics #MassSpec

If a peptide has two serines and a single phosphate, site assignment may be ambiguous. Mascot helps by calculating a site localisation...

If a peptide has two serines and a single phosphate, site assignment may be ambiguous. Mascot helps by calculating a site localisation confidence, where the assignment with more MS/MS evidence gets higher confidence.

https://www.matrixscience.com/help/site_analysis_help.html

#proteomics #MassSpec

Database searches with semi-specific enzyme traditionally have low sensitivity due to the large search space. Except, Mascot Server 3.0...

Database searches with semi-specific enzyme traditionally have low sensitivity due to the large search space. Except, Mascot Server 3.0 includes MS²PIP, which boosts sensitivity. We've compared the results to a recent FragPipe publication.

https://www.matrixscience.com/blog/mascot-vs-fragpipe-uncovering-endogenous-proteolytic-processing.html
#proteomics #massspec

Mascot Newsletter, December 2024:Predicted fragment intensities with Mascot Server 3.0.Self-ligating surface receptor and CD8+...

Mascot Newsletter, December 2024:

Predicted fragment intensities with Mascot Server 3.0.

Self-ligating surface receptor and CD8+ T-cells.

Saving search results as HTML.

https://www.matrixscience.com/nl/202412/newsletter.html
#proteomics #massspec

Mascot Daemon is the automation client bundled with Mascot Server. The Quantitation Summary report is an easy way to export protein...

Mascot Daemon is the automation client bundled with Mascot Server. The Quantitation Summary report is an easy way to export protein expression data for complex experiments.

https://youtu.be/4Ds59gYhL4Q

#proteomics #massspec

Check out how Mascot Server 3.0 and MS²PIP work together to boost protein and peptide identifications.https://youtu.be/O7LSREqiW8o...

Check out how Mascot Server 3.0 and MS²PIP work together to boost protein and peptide identifications.

https://youtu.be/O7LSREqiW8o

#proteomics #MassSpec

Mascot Server 3.0 produces excellent results with Thermo Orbitrap instruments. We processed a DDA LFQ benchmark by Bart van Puyvelde et al....

Mascot Server 3.0 produces excellent results with Thermo Orbitrap instruments. We processed a DDA LFQ benchmark by Bart van Puyvelde et al. using MS2PIP model HCD2021. Old Mascot: 4667 protein hits; Mascot 3.0: 5007 protein hits.

https://www.matrixscience.com/blog/best-ms2pip-model-for-thermo-orbitrap.html
#proteomics #MassSpec

Creating a list of confidently identified proteins is easy.1) Run the database search in Mascot.2) Version 3.0 defaults to 1% sequence FDR....

Creating a list of confidently identified proteins is easy.
1) Run the database search in Mascot.
2) Version 3.0 defaults to 1% sequence FDR. Filter out one-hit wonders in Report Builder, if desired.
4) Export as CSV -- done.

https://www.matrixscience.com/help/creating_a_list_of_confidently_identified_proteins.html
#proteomics #MassSpec