You can now use large language model (LLM) coding assistants to interact with Mascot Server. This includes anything that can be programmed with the LLM, from simple automation tasks to complex mining and merging of results. www.matrixscience.com/blog/automat... #proteomics #MassSpec

Mascot Newsletter, April 2026: Mycobacteria spectral libraries. Orthogonal translation systems for lysine aminoacylation. Matrix Science at ASMS 2026. www.matrixscience.com/nl/202604/ne... #proteomics #massspec

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

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

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, 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

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, 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

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, December 2025: NCBI nr FASTA replacement. Immunoregulation during pregnancy. Mascot Server as system service on Linux. www.matrixscience.com/nl/202512/ne... #proteomics #massspec

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, 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, 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...

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