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Matrix Science
@matrixscience.bsky.social
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Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

https://www.matrixscience.com
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Mascot Newsletter, October 2025:

Spectrum-centric DIA scoring.

Molecular mechanisms of SBK2 kinase on the heart.

Windows update issue with IIS (resolved).

www.matrixscience.com/nl/202510/ne...

#proteomics #massspec
Mascot Newsletter logo
October 29, 2025 at 3:46 PM
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Probabilistic scoring of DIA matches without spectral deconvolution? Not only is it possible, we're working on implementing it in Mascot DIA.

www.matrixscience.com/blog/probabi...

#proteomics #massspec
Illustration of a DIA MS/MS spectrum with unidentified peaks (top) and labelled peaks for two identified peptides (middle and bottom).
September 8, 2025 at 9:03 AM
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Mascot Newsletter, August 2025:

Precursor detection for spectrum-centric DIA.

Reconstructing mediaeval monastic diets.

Microsoft has announced the end of Windows 10 support; your Mascot Server may be affected.

www.matrixscience.com/nl/202508/ne...

#proteomics #massspec
Mascot Newsletter logo
August 19, 2025 at 8:12 AM
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Peptide identification in spectrum-centric DIA depends on accurate precursor mass. The upcoming version of Mascot Distiller includes a novel algorithm that deduces precursor masses from MS/MS scans.

#proteomics #massspec

www.matrixscience.com/blog/youve-g...
MS/MS spectrum of RPQYSNPPVQGEVMEGADNQGAGEQGR zoomed in to the region 1150-1750Da. Several complementary b and y ion pairs are labelled.
July 29, 2025 at 10:03 AM
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Mascot Newsletter, July 2025:

Overview of spectrum-centric DIA and Mascot DIA.

Metaproteomics of bacterioplankton communities.

New pricing tiers for Mascot Server, and price reduction when updating from an old version.

www.matrixscience.com/nl/202507/ne...

#proteomics #massspec
Mascot Newsletter logo
July 25, 2025 at 9:24 AM
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We are working on Mascot DIA, which is a universal spectrum-centric solution for DIA analysis. What is spectrum-centric searching meant to solve? Find out in our blog:

www.matrixscience.com/blog/the-pro...

#proteomics #massspec
Diagram of Mascot DIA: Mascot Distiller processes DIA runs into peak lists and detects precursor masses in MS1 and MS2 scans; these are sent to Mascot Server for database searching; finally, Distiller downloads the PSMs and performs MS1 quantitation.
July 1, 2025 at 3:47 PM
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Mascot Newsletter, June 2025:

Annual user meeting summary and preview of Mascot DIA.

ASMS posters using Mascot: forensics, cancer research, food science, fish, ...

Matrix Science posters on LFQ and machine learning.

www.matrixscience.com/nl/202506/ne...

#proteomics #massspec
Mascot Newsletter
June 19, 2025 at 8:00 AM
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Pick up a free Matrix Science pen, bag or notebook from #ASMS2025 booth #334 -- while stocks last!
Photo of pens, notebooks and promotional bags.
June 4, 2025 at 4:12 PM
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Register now for the Matrix Science Breakfast Meeting at #ASMS2025 on 2nd June: matrixscience.com/workshop.html

There is no charge for attending the meeting, but advance registration is required. #proteomics #MassSpec
Matrix Science Breakfast Meeting, Monday 2nd June: Using MS2Rescore to boost identification rates in complex samples, Tim Van Den Bossche, Computational Omics and Systems Biology Group (CompOmics), Ghent University/VIB-UGent Center for Medical Biotechnology Mascot DIA: Universal spectrum-centric approach, Ville Koskinen, Matrix Science Mascot DIA: Thermo LFQ example, Patrick Emery, Matrix Science
May 30, 2025 at 2:18 PM
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When you refine results with Mascot Server and import into Thermo Proteome Discoverer, you should disable MudPIT scoring. This makes the Protein FDR Validator node much happier.

www.matrixscience.com/blog/identif...

#proteomics #MassSpec
Count of protein hits and peptide matches, comparing Percolator node (6785 proteins) to Mascot ML (6899 proteins).
May 29, 2025 at 2:53 PM
matrixscience.bsky.social
Register now for the Matrix Science Breakfast Meeting at #ASMS2025 on 2nd June: matrixscience.com/workshop.html

There is no charge for attending the meeting, but advance registration is required. #proteomics #MassSpec
Matrix Science Breakfast Meeting, Monday 2nd June: Using MS2Rescore to boost identification rates in complex samples, Tim Van Den Bossche, Computational Omics and Systems Biology Group (CompOmics), Ghent University/VIB-UGent Center for Medical Biotechnology Mascot DIA: Universal spectrum-centric approach, Ville Koskinen, Matrix Science Mascot DIA: Thermo LFQ example, Patrick Emery, Matrix Science
May 22, 2025 at 2:56 PM
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Mascot newsletter, May 2025:

ASMS User Meeting registration is open.

Oxygen metabolism in horses (@castiglionelab.bsky.social).

Big databases and large peak lists.

www.matrixscience.com/nl/202505/ne...

#proteomics #massspec
Mascot Newsletter
May 20, 2025 at 8:35 AM
matrixscience.bsky.social
Register now for the Matrix Science Breakfast Meeting at #ASMS2025 on 2nd June: matrixscience.com/workshop.html

There is no charge for attending the meeting, but advance registration is required. #proteomics #MassSpec
Matrix Science Breakfast Meeting, Monday 2nd June: Using MS2Rescore to boost identification rates in complex samples, Tim Van Den Bossche, Computational Omics and Systems Biology Group (CompOmics), Ghent University/VIB-UGent Center for Medical Biotechnology Mascot DIA: Universal spectrum-centric approach, Ville Koskinen, Matrix Science Mascot DIA: Thermo LFQ example, Patrick Emery, Matrix Science
May 15, 2025 at 3:04 PM
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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.

www.matrixscience.com/blog/adding-...

#proteomics #MassSpec
Screenshot of the format controls in Protein Family Summary, showing a dropdown item for example_ML_adapter.py
May 1, 2025 at 2:12 PM
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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

www.matrixscience.com/nl/202504/ne...
Mascot Newsletter logo
April 17, 2025 at 9:13 AM
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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

www.matrixscience.com/nl/202503/ne...
Mascot Newsletter logo
March 11, 2025 at 4:34 PM
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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

www.matrixscience.com/distiller.html
Screenshot of an LFQ project in Mascot Distiller. Left window: XICs of a peptide match with retention time alignment enabled. Right window: isotopic distribution of the precursor peaks in the survey (MS) scan.
February 24, 2025 at 2:56 PM
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Mascot Newsletter, February 2025:

Mascot vs FragPipe: semi-tryptic TMTpro.

Characterization of the noncanonical proteome.

Mascot Server 3.1 is now available.

#proteomics #MassSpec

www.matrixscience.com/nl/202502/ne...
Mascot Newsletter
February 18, 2025 at 2:54 PM
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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

www.matrixscience.com/blog/mascot-...
Table comparing counts of protein hits and proteins quantified by Mascot Distiller between Mascot Server 3.0 (no refining) and Mascot Server 3.1 (with MS2PIP HCD2021).
February 14, 2025 at 2:15 PM
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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

www.matrixscience.com/blog/using-m...
Number of protein groups and peptide groups in PD 3.1 and PD 2.4, comparing Mascot 3.0 (no ML) with Mascot 3.1 (with ML).
February 6, 2025 at 4:04 PM
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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

www.matrixscience.com/help/mascot_...
Table illustrating protein and peptide match counts in Proteome Discoverer 3.1 when using Mascot Server 3.0 and 3.1.
February 3, 2025 at 9:56 AM
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Mascot Newsletter, January 2025:

Learn how Mascot uses machine learning.

Characterising a bacterial microcompartment.

Mascot protein inference.

www.matrixscience.com/nl/202501/ne...

#proteomics #MassSpec
Mascot Newsletter logo
January 24, 2025 at 12:04 PM
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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.

www.matrixscience.com/help.html#EX...

#proteomics #MassSpec
Table of example data sets shipped with Mascot. Sections visible in the screenshot are MS/MS Ion Search, Quantitation, Spectral Libraries, Crosslinking and Top-down.
January 20, 2025 at 9:35 AM
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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.

www.matrixscience.com/help/site_an...

#proteomics #MassSpec
Illustration of site analysis confidence. The top three matches to the spectrum have the same sequence (DIGSESTEDQAMEDIK) with two serines and one threonine, one of which is phosphorylated. Mascot reports site localisation confidence S4 85%, S6 15% and T7 0.7%.
January 9, 2025 at 9:57 AM
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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.

www.matrixscience.com/blog/mascot-...
#proteomics #massspec
Illustration of the score distribution, estimated FDR, count of significant sequences and two peptide matches with TMTpro ratios visible.
December 19, 2024 at 1:02 PM