After a fair bit of frustration, our new excimer laser is installed! We have it coupled to an Element 2, and new laser plus sector magnet (rather than quadupole) mass spectrometry is a steep learning curve for me. Nice to spend the afternoon tinkering in the lab though.
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The NCBI nr FASTA file of protein sequences is no longer updated.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).
Der Mann hat was neues für #Lupus gefunden - oder wie @kabalak selbst sagen würde:
In conclusion, this study uncovers a new dimension of immune crosstalk: a proteolytic plasma network that generates immunoactive fragments with intrinsic self-regulatory capabilities to modulate #inflammation and tissue injury in complex disease contexts. Deciphering these immunoactivities may pave the way for innovative diagnostic and therapeutic strategies in complement-driven pathologies, potentially benefiting a wide range of inflammatory and autoimmune diseases.
#AutoimmuneDiseases #InflammatoryDisease #Science #SLE #proteomics #MassSpec #TeamMassSpec #LupusResearch
https://www.embopress.org/doi/full/10.1038/s44318-025-00598-8
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.
Dr Micha Campbell
Matrix Science Ltd
Tired Cohnina MacGuffin
de.NBI & ELIXIR Germany
Dave Tabb