Matrix Science

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

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...

Illustration of a DIA MS/MS spectrum with unidentified peaks (top) and labelled peaks for two identified peptides (middle and bottom).

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

Mascot Newsletter logo

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

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.

MS/MS spectrum of RPQYSNPPVQGEVMEGADNQGAGEQGR zoomed in to the region 1150-1750Da. Several complementary b and y ion pairs are labelled.

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...

Mascot Newsletter logo

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

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.

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

Mascot Newsletter

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

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

Photo of pens, notebooks and promotional bags.

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

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

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

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

Count of protein hits and peptide matches, comparing Percolator node (6785 proteins) to Mascot ML (6899 proteins).

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

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

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

Mascot Newsletter

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

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

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

Screenshot of the format controls in Protein Family Summary, showing a dropdown item for example_ML_adapter.py

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

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 Newsletter logo

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...

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

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 Newsletter logo

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...

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.

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

Mascot Newsletter

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...

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).

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-...

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).

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...

Table illustrating protein and peptide match counts in Proteome Discoverer 3.1 when using Mascot Server 3.0 and 3.1.

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_...

Mascot Newsletter logo

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

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.

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