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We enjoyed seeing many of you at the recent ASMS Conference in Anaheim, CA, and want to share some of the new developments and information that we presented at our Matrix Science User Meeting.

The conference had numerous outstanding presentations showcasing the use of Mascot in a range of applications such as cancer proteomics, biomarker discovery, quantitative proteomics, and biopharmaceuticals. We have summarised a small selection below.


June 2024, #115

ASMS User Meeting
Mascot at ASMS
About Matrix Science


Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

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Matrix Science at ASMS 2024


We held a breakfast meeting, where we presented a number of new Mascot developments. The beta release of the next version of Mascot Server is coming soon. Here are some of the exciting new features you can look forward to.

Machine Learning. The next version of Mascot will integrate MS2Rescore, a modular and user-friendly platform for AI-assisted rescoring of peptide identifications, developed by the Lennart Martens group at the University of Ghent. Our goal in Mascot is that you should be able to click a button to make your results better. To do that, we have integrated DeepLC and MS2PIP model selection directly in the menu controls of the Protein Family Summary report.

Faster Error Tolerant Search. Currently, the Mascot error tolerant search tries every entry in Unimod, which is over 2000 modifications. However, most of the time, you have a rough idea what is definitely not in the sample. In the next version, you can exclude specific modification categories from the error tolerant search, for example, AA substitutions, isotopic labels and artefacts. This makes the search faster as well as more precise.

Custom Distiller Reports. Mascot Distiller 2.8 ships with 14 different reports for analyzing and exporting your quantitation results such as ANOVA, Hierarchical and K-means clustering, PCA, Volcano plots, Table exports, etc. With a bit of knowledge of Python and the Mascot Parser library, you can create your own, custom reports in Distiller for new use cases and workflows.

Automate with Mascot Daemon Actions. Mascot Daemon can run actions automatically before or after a task. These are set up in the External Processes dialog, but because the mechanism is very flexible, it comes with some complexity. We have written a wrapper called Mascot Daemon Export Extender that makes it very easy to automatically run Distiller reports at the end of a task.

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Featured ASMS presentations using Mascot


Here are a few of the interesting ASMS presentations that utilized Mascot for protein identification, quantitation, or characterization. The conference had hundreds of posters each day so unfortunately we cannot include every Mascot poster here.

Chemical Proteomic Strategy Utilizing a Photoreactive Chloroalkane Capture Tag for Target Discovery (TP680)

Alba Katiria González Rivera, Robin Hurst, Sergiy Levin, Michael M. Rosenblatt, Rachel Friedman Ohana

Streamlined target deconvolution strategy utilizing a multipronged chloroalkane capture tag with built-in capabilities for adequate photo-crosslinking and highly selective enrichment.


Identification of 15-keto-PGE 2 post-translational protein modifications by LC/MS/MS to study an anti-inflammatory therapy (TP720)

Fu-An Li, Ling-Hui Wang

Our results suggest a novel anti-inflammatory therapy for diet-induced NASH through administering 15-keto-PGE 2.

Academia Sinica

Peptide Biomarkers in Human Breast Milk: Mass Spectrometry-Based In-Solution Proteomics Analysis for Early Detection and Treatment of Breast Cancer Development (WP066)

Victor Tochukwu Njoku, Danielle Whitham, Lilian Corrice, Brian T. Pentecost, Kathleen F. Arcaro, Costel C. Darie

Validation of specific potential peptide biomarkers in human breast milk for early detection and treatment of Breast Cancer.

University of Massachusetts Amherst

Acetylome analysis of aspirin treated AML cell lines using label-free LC-MS/MS reveals potentially cytostatic modifications in cytosolic and mitochondrial proteins (ThP139)

Luke Higgins, Tommy Shields, Vinothini Rajeeve, Pedro Rodriguez Cutillas

The first analysis of aspirin induced acetylome on AML has revealed new actions of aspirin on protein acetylation.

Barts Cancer Institute

Proteomic evaluation of tardigrades following ionizing radiation reveals increase in DNA repair pathways (ThP791)

Evan R Stair, Courtney Clark-Hatchel, Bob Goldstein, Leslie M. Hicks

Revealing the mechanisms for tardigrade tolerance to ionizing radiation.

The University of Northern Carolina at Chapel Hill
University of North Carolina Asheville



About Matrix Science

Matrix Science is a provider of bioinformatics tools to proteomics researchers and scientists, enabling the rapid, confident identification and quantitation of proteins. Mascot continues to be cited by over 2000 publications every year. Our software products fully support data from mass spectrometry instruments made by Agilent, Bruker, Sciex, Shimadzu, Thermo Scientific, and Waters.

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You can also contact us or one of our marketing partners for more information on how you can power your proteomics with Mascot.

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