Matrix Science is a provider of bioinformatics tools to proteomics researchers and scientists. Follow us for regular news and updates about Mascot products.
Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years
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.
https://www.matrixscience.com/blog/strange-software-failures-check-your-disk-space.html
Mascot Newsletter, December 2025:
NCBI nr FASTA replacement.
Immunoregulation during pregnancy.
Mascot Server as system service on Linux.
@pwilmart Our example and blog article were written in response to Hijazi et al.'s paper "Mind Your Spectra: Points to be Aware of When Validating the Identification of Isobaric Histone Peptidoforms", where they point out that some other software packages default to S/N and don't give a choice. Mascot Distiller defaults to using the peak area.
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.
https://www.matrixscience.com/blog/peak-list-arcana-area-vs-signal-to-noise.html
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.
The NCBI nr FASTA file of protein sequences is no longer updated.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.
https://www.matrixscience.com/blog/replacements-for-ncbi-nr.html
Mascot Newsletter, October 2025:
Spectrum-centric DIA scoring.
Molecular mechanisms of SBK2 kinase on the heart.
Windows update issue with IIS (resolved).
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.
We are pleased to announce a new distributor for Matrix Science products! Customers in India can now buy Mascot Server through BioInnovations, who provide instruments, software, services and consumables for life sciences and analytical and clinical labs. #proteomics #massspec
https://www.matrixscience.com/whats_new/new-mascot-distributor-in-india-bioinnovations.html
Probabilistic scoring of DIA matches without spectral deconvolution? Not only is it possible, we're working on implementing it in Mascot DIA.
https://www.matrixscience.com/blog/probabilistic-spectrum-centric-scoring-for-dia.html
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.
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.
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.
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:
https://www.matrixscience.com/blog/the-promise-of-spectrum-centric-dia.html
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.
Register now for the Matrix Science Breakfast Meeting at #ASMS2025 on 2nd June: https://matrixscience.com/workshop.html
There is no charge for attending the meeting, but advance registration is required. #proteomics #MassSpec
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.
Register now for the Matrix Science Breakfast Meeting at #ASMS2025 on 2nd June: https://matrixscience.com/workshop.html
There is no charge for attending the meeting, but advance registration is required. #proteomics #MassSpec
Mascot newsletter, May 2025:
ASMS User Meeting registration is open.
Oxygen metabolism in horses.
Big databases and large peak lists.
Register now for the Matrix Science Breakfast Meeting at #ASMS2025 on 2nd June: https://matrixscience.com/workshop.html
There is no charge for attending the meeting, but advance registration is required. #proteomics #MassSpec
