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Matrix Science @matrixscience.bsky.social · 21d

We are pleased to announce a new distributor for Matrix Science products! Customers in India can now buy Mascot Server through BioInnovations, who provide products and services for life sciences and analytical and clinical labs. #proteomics #massspec

www.matrixscience.com/whats_new/ne...

New Mascot distributor in India: BioInnovations

www.matrixscience.com

Matrix Science @matrixscience.bsky.social · Sep 8

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).

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Matrix Science @matrixscience.bsky.social · Aug 19

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

Matrix Science @matrixscience.bsky.social · Aug 19

1. Precursor detection is performed before the database search.
2. The algorithm tries pairing up ions with no prior knowledge of which ones are the complementary pairs. It's a "brute force" approach with a few shortcuts to speed up the computation.

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Matrix Science @matrixscience.bsky.social · Jul 29

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.

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Matrix Science @matrixscience.bsky.social · Jul 25

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

Matrix Science @matrixscience.bsky.social · Jul 1

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.

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Matrix Science @matrixscience.bsky.social · Jun 19

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

Matrix Science @matrixscience.bsky.social · Jun 5

Come see our poster ThP 265 today at #ASMS2025: Machine learning-enabled Mascot Server API improves
LFQ in client software like Thermo Proteome Discoverer

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Matrix Science @matrixscience.bsky.social · Jun 4

Pick up a free Matrix Science pen, bag or notebook from #ASMS2025 booth #334 -- while stocks last!

Photo of pens, notebooks and promotional bags.

Matrix Science @matrixscience.bsky.social · Jun 3

Come see our poster TP 505 today at #ASMS2025 : Customizable machine learning adapter improves LFQ in Mascot Distiller

Matrix Science @matrixscience.bsky.social · May 30

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

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Matrix Science @matrixscience.bsky.social · May 29

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).

Matrix Science @matrixscience.bsky.social · May 22

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

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Matrix Science @matrixscience.bsky.social · May 20

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

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Matrix Science @matrixscience.bsky.social · May 15

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

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Matrix Science @matrixscience.bsky.social · May 1

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

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Matrix Science @matrixscience.bsky.social · Apr 24

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.

www.matrixscience.com/help/instrum...

#proteomics #MassSpec

Mascot help: Agilent instruments

www.matrixscience.com

Matrix Science @matrixscience.bsky.social · Apr 17

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...

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Matrix Science @matrixscience.bsky.social · Apr 2

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.

www.matrixscience.com/blog/big-dat...

#proteomics #MassSpec

Big databases and large peak lists

www.matrixscience.com

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Matrix Science @matrixscience.bsky.social · Mar 20

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:

www.matrixscience.com/help/disaste...

#proteomics #MassSpec

Mascot database search protein identification software | Disaster recovery

Disaster recovery strategy, what to back up and how to restore configuration files, search results and sequence databases for Mascot Server, Distiller and Daemon

www.matrixscience.com

Matrix Science @matrixscience.bsky.social · Mar 11

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...

Matrix Science @matrixscience.bsky.social · Feb 24

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.

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Matrix Science @matrixscience.bsky.social · Feb 18

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...

Matrix Science @matrixscience.bsky.social · Feb 14

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).