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Matrix Science @matrixscience.bsky.social · 23/09/2026

Proteomics may not be at the top of the list when thinking about cybersecurity. However, from September 2026, the EU Cyber Resilience Act requires software vendors to actively report exploited vulnerabilities. Matrix Science is prepared. www.matrixscience.com/blog/eu-cybe... #proteomics #massspec

matrixscience.com

EU Cyber Resilience Act (CRA)

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Matrix Science @matrixscience.bsky.social · 01/09/2026

There are 26 uppercase Latin letters but only 20 standard amino acids. Which amino acids are B, J, O, U, X and Z? Mascot treats B, X and Z as ambiguity codes per the IUPAC definition, while J, O and U are configurable. #proteomics #massspec www.matrixscience.com/blog/ambigui...

Screenshot of the Mascot configuration editor showing edit buttons for J, O and U.

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Matrix Science @matrixscience.bsky.social · 26/08/2026

Mascot Newsletter, August 2026: Mascot Parser coding skill for AI assistants. Alternative methods for N-terminal protein derivatization. Replacement product keys for new hardware. www.matrixscience.com/nl/202608/ne... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 30/07/2026

Two-Dimensional Thermal Proteome Profiling (2DTPP) is a technique that profiles the thermal stability of a proteome as a function of ligand concentration. We now provide free Python scripts to analyse Mascot results in ProSAP/TPP2D. www.matrixscience.com/blog/2d-tpp-... #proteomics #massspec

Volcano plot showing a broad spread of dose-responsive proteins, with the published proteins of interest highlighted.

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Matrix Science @matrixscience.bsky.social · 29/07/2026

Mascot Newsletter, July 2026: Mascot and Thunder-DDA-PASEF. L/D-lactylation on histones in mouse tissue. Meet us at IMSC 2026. www.matrixscience.com/nl/202607/ne... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 02/07/2026

Mascot Newsletter, June 2026: Mascot DIA posters from ASMS. Extracellular vesicle production from mesenchymal stem cells. Meet us at BSPR 2026 and IMSC 2026. www.matrixscience.com/nl/202606/ne... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 23/06/2026

We've compiled a new skill for coding assistants that helps you write custom quantitation reports for Mascot Distiller. An example script for exporting results into MSstats is included. www.matrixscience.com/blog/automat... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 18/06/2026

It was a pleasure to meet many of you at ASMS 2026 in San Diego, CA this June. We presented three posters featuring Mascot DIA using real data. PDF copies of the posters: www.matrixscience.com/asms_2026.html #proteomics #massspec

matrixscience.com

Matrix Science at ASMS 2026

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Matrix Science @matrixscience.bsky.social · 04/06/2026

Come and collect freebies from booth #616 while stocks last. #ASMS2026

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Matrix Science @matrixscience.bsky.social · 03/06/2026

Let's chat about spectrum-centric DIA with probabilistic scoring today at #ASMS2026. WP 449: Mascot DIA Introduces probabilistic scoring. WP 464: Mascot DIA enables direct comparison of DDA and DIA. WP 622: Overcoming Peptide-Centric DIA Limitations: Discovering Unsuspected Modifications.

WP 449: Mascot DIA Introduces probabilistic scoring.

WP 464: Mascot DIA enables direct comparison of DDA and DIA.

WP 622: Overcoming Peptide-Centric DIA Limitations: Discovering Unsuspected Modifications.

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Matrix Science @matrixscience.bsky.social · 01/06/2026

After tonight's opening plenary at #asms2026, drop by booth #616 and say hi to Mascot developers. Also, we're presenting three posters on Wednesday, WP 449, WP 464 and WP 622.

WP 449: Mascot DIA Introduces probabilistic scoring to spectrum-centric analysis of DIA data.

Probabilistic scoring enables direct control of false positive rate, demonstrated in this poster with MS/MS spectra containing very different noise patterns (ion trap, TMT, Orbitrap AIF).

WP 464: Mascot DIA enables direct comparison of DDA and DIA identification and quantitation results.

Mascot uses the same sequence matching and precursor quantitation algorithms for DDA and DIA spectra, allowing results to be directly compared and the same downstream processing to be used between the two techniques.

WP 622: Overcoming Peptide-Centric DIA Limitations: Discovering Unsuspected Modifications in Narrow-Window DIA Using Mascot Error Tolerant Search.

The Mascot Error Tolerant search is a two-pass search: a standard first-pass search identifies proteins, then a comprehensive second pass iterates through the entire Unimod modification list, plus sequence variants.

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Matrix Science @matrixscience.bsky.social · 26/05/2026

Mascot Newsletter, May 2026: We're presenting three DIA posters at ASMS 2026. Oleuropein-based olive leaf extract with cardiovascular exercise. Upcoming conferences: BSPR 2026 and IMSC 2026. www.matrixscience.com/nl/202605/ne... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 05/05/2026

Matrix Science will be attending BSPR2026 in Cambridge, UK, on 13-15 July. Come chat with us about the latest developments with Mascot. Abstract and early bird registration deadline is 15 May, so it's best to book your place soon! #proteomics #massspec #BSPR2026

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Matrix Science @matrixscience.bsky.social · 29/04/2026

You can now use large language model (LLM) coding assistants to interact with Mascot Server. This includes anything that can be programmed with the LLM, from simple automation tasks to complex mining and merging of results. www.matrixscience.com/blog/automat... #proteomics #MassSpec

Example QC report for a DDA data set generated using Claude.

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Matrix Science @matrixscience.bsky.social · 28/04/2026

Mascot Newsletter, April 2026: Mycobacteria spectral libraries. Orthogonal translation systems for lysine aminoacylation. Matrix Science at ASMS 2026. www.matrixscience.com/nl/202604/ne... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 30/03/2026

Mascot Newsletter, March 2026: Search BLIB spectral libraries with Mascot. PET hydrolase expressed in fruit flies. UK office has moved. www.matrixscience.com/nl/202603/ne... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 27/03/2026

matrixscience.com is being overwhelmed by millions of HTTP requests from distributed botnets, essentially a distributed denial of service (DDoS) attack. We are forced to mitigate it by restrict access to certain pages of dynamic content. www.matrixscience.com/whats_new/mi... #proteomics #massspec

matrixscience.com

Mascot search engine | Protein identification software for mass spec data

Mascot software from Matrix Science - identification, characterisation and quantitation of proteins using mass spectrometry data

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Matrix Science @matrixscience.bsky.social · 24/03/2026

Thunder-DDA-PASEF is an acquisition strategy for capturing more human leukocyte antigen (HLA) class I peptide ligands on Bruker timsTOF instruments. This month's blog shows how you can process Thunder-DDA-PASEF data with Mascot Distiller. www.matrixscience.com/blog/process... #proteomics #massspec

Bar chart comparison of standard acqusition method compared to Thunder-DDA-PASEF.

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Matrix Science @matrixscience.bsky.social · 04/03/2026

Using the blib2msp converter, Mascot Server can now search DDA spectral libraries in BLIB format. Here's an example for identifying mycobacteria. www.matrixscience.com/blog/identif... #proteomics #massspec

Pie chart illustration of the top species detected: Mycobacteroides abscessus (61%); Sus scrofa (22%); Homo sapiens (11%); Mycolicibacterium goodii (5.6%).

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Matrix Science @matrixscience.bsky.social · 03/03/2026

The UK office of Matrix Science Ltd has moved one block up the road. New address: 83 Baker Street, London W1U 6AG, UK. There is no other change to bank details or email addresses. www.matrixscience.com/whats_new/ch...

matrixscience.com

Change of address for UK office

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Matrix Science @matrixscience.bsky.social · 26/02/2026

Mascot Newsletter, February 2026: Strange software errors? Check your disk space. Proteomic signatures in human fingertip regeneration. Customise columns in the search log. www.matrixscience.com/nl/202602/ne... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 11/02/2026

Mascot Server can create and search NIST MSP formatted spectral libraries but not BLIB -- until now! We have developed an MSP to BLIB to MSP converter that allows Mascot Server to use BLIB libraries. www.matrixscience.com/blog/convert... #proteomics #massspec

Screenshot of blib2msp.pl output, displaying conversion results, time spent and a table of peptide modifications in the spectral library.

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Matrix Science @matrixscience.bsky.social · 29/01/2026

Mascot Newsletter, January 2026: Ion intensity: peak area vs signal to noise? Duplexing deuterated water-labeled samples for protein turnover rate estimation. Role-based access with Mascot Security is useful in a variety of cases. www.matrixscience.com/nl/202601/ne... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 09/01/2026

Proteomics software is prone to filling up the disk with data and temp files, which can cause weird issues. This blog article lists the most common errors in Mascot products and how to free up disk space. www.matrixscience.com/blog/strange... #proteomics #massspec

Screenshot of Mascot Distiller showing the menu item for cleaning up old cache files.

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Matrix Science @matrixscience.bsky.social · 18/12/2025

Mascot Newsletter, December 2025: NCBI nr FASTA replacement. Immunoregulation during pregnancy. Mascot Server as system service on Linux. www.matrixscience.com/nl/202512/ne... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 01/12/2025

When raw data is processed into peak lists, there is a choice: how should peak intensity be calculated? Mascot Distiller defaults to peak area. The alternative, signal-to-noise (S/N), can be useful with detecting diagnostic ions. #proteomics #massspec www.matrixscience.com/blog/peak-li...

Example MS/MS spectrum of KQLATKAAR using peak area as peak intensity (top) or signal-to-noise as peak intensity (bottom).

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Matrix Science @matrixscience.bsky.social · 27/11/2025

Mascot Newsletter, November 2025: Top-3 quant with DDA-PASEF. ZooMS peptide markers for South American Xenarthrans. Migrating from Windows 10 to Linux could extend the lifetime of your hardware. www.matrixscience.com/nl/202511/ne... #proteomics #massspec

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Matrix Science @matrixscience.bsky.social · 10/11/2025

The NCBI nr FASTA file of protein sequences is no longer updated. We've summarised instructions for creating it from the BLAST database -- or you may be better off using TrEMBL. www.matrixscience.com/blog/replace... #proteomics #massspec

matrixscience.com

Replacements for NCBI nr

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Matrix Science @matrixscience.bsky.social · 06/11/2025

The free Mascot service at matrixscience.com is currently being hammered by a distributed denial of service (DDoS) attack. The incident started around 11:00 GMT. We have mitigated the attack, which means some Mascot functionality is unavailable for now.

matrixscience.com

Mascot search engine | Protein identification software for mass spec data

Mascot software from Matrix Science - identification, characterisation and quantitation of proteins using mass spectrometry data

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Matrix Science @matrixscience.bsky.social · 29/10/2025

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

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Matrix Science @matrixscience.bsky.social · 17/10/2025

Mascot Daemon can export protein level quant intensities for replicate LFQ, SILAC and iTRAQ/TMT. The latest version can also export intensity values calculated using the "Top-3" method, illustrated here with DDA-PASEF data. www.matrixscience.com/blog/top-3-q... #proteomics #massspec

matrixscience.com

Top-3 Quantitation Summary in Mascot Daemon 3

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Matrix Science @matrixscience.bsky.social · 18/09/2025

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...

matrixscience.com

New Mascot distributor in India: BioInnovations

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Matrix Science @matrixscience.bsky.social · 08/09/2025

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 · 19/08/2025

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

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Matrix Science @matrixscience.bsky.social · 29/07/2025

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 · 25/07/2025

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

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Matrix Science @matrixscience.bsky.social · 01/07/2025

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 · 19/06/2025

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

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Matrix Science @matrixscience.bsky.social · 05/06/2025

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 · 04/06/2025

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

Photo of pens, notebooks and promotional bags.

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Matrix Science @matrixscience.bsky.social · 03/06/2025

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

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Matrix Science @matrixscience.bsky.social · 30/05/2025

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 · 29/05/2025

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).

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Matrix Science @matrixscience.bsky.social · 22/05/2025

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Matrix Science @matrixscience.bsky.social · 20/05/2025

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 · 15/05/2025

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Matrix Science @matrixscience.bsky.social · 01/05/2025

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 · 24/04/2025

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

matrixscience.com

Mascot help: Agilent instruments

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Matrix Science @matrixscience.bsky.social · 17/04/2025

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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