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...

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, 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

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, 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

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, 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

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

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

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

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, 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

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 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, 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, 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...

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, 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...

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-...

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...

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, January 2025: Learn how Mascot uses machine learning. Characterising a bacterial microcompartment. Mascot protein inference. www.matrixscience.com/nl/202501/ne... #proteomics #MassSpec

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

If a peptide has two serines and a single phosphate, site assignment may be ambiguous. Mascot helps by calculating a site localisation confidence, where the assignment with more MS/MS evidence gets higher confidence. www.matrixscience.com/help/site_an... #proteomics #MassSpec

Database searches with semi-specific enzyme traditionally have low sensitivity due to the large search space. Except, Mascot Server 3.0 includes MS²PIP, which boosts sensitivity. We've compared the results to a recent FragPipe publication. www.matrixscience.com/blog/mascot-... #proteomics #massspec