Mascot Newsletter logo.
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
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
Bar chart comparison of standard acqusition method compared to Thunder-DDA-PASEF.
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
Pie chart illustration of the top species detected: Mycobacteroides abscessus (61%); Sus scrofa (22%); Homo sapiens (11%); Mycolicibacterium goodii (5.6%).
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
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...
Mascot Newsletter logo.
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
Screenshot of blib2msp.pl output, displaying conversion results, time spent and a table of peptide modifications in the spectral library.
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
Mascot Newsletter logo
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
Screenshot of Mascot Distiller showing the menu item for cleaning up old cache files.
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
Mascot Newsletter logo
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
Example MS/MS spectrum of KQLATKAAR using peak area as peak intensity (top) or signal-to-noise as peak intensity (bottom).
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...
Mascot Newsletter logo
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
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
The DDoS attack on matrixscience.com appears to be over. Functionality has been resumed and we will continue monitoring the system.
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.
Mascot Newsletter logo
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 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
