Matrix Science
@matrixscience.bsky.social
Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years
https://www.matrixscience.com
https://www.matrixscience.com
The NCBI nr FASTA file of protein sequences is no longer updated.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
www.matrixscience.com/blog/replace...
#proteomics #massspec
Replacements for NCBI nr
www.matrixscience.com
November 10, 2025 at 2:46 PM
The NCBI nr FASTA file of protein sequences is no longer updated.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
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.
Mascot search engine | Protein identification software for mass spec data
Mascot software from Matrix Science - identification, characterisation and quantitation of proteins using mass spectrometry data
matrixscience.com
November 6, 2025 at 5:11 PM
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 search engine | Protein identification software for mass spec data
Mascot software from Matrix Science - identification, characterisation and quantitation of proteins using mass spectrometry data
matrixscience.com
November 6, 2025 at 1:55 PM
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
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
October 29, 2025 at 3:46 PM
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
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
www.matrixscience.com/blog/top-3-q...
#proteomics #massspec
Top-3 Quantitation Summary in Mascot Daemon 3
www.matrixscience.com
October 17, 2025 at 2:52 PM
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
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...
www.matrixscience.com/whats_new/ne...
New Mascot distributor in India: BioInnovations
www.matrixscience.com
September 18, 2025 at 9:19 AM
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...
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
www.matrixscience.com/blog/probabi...
#proteomics #massspec
September 8, 2025 at 9:03 AM
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
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
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
August 19, 2025 at 8:12 AM
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
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...
#proteomics #massspec
www.matrixscience.com/blog/youve-g...
July 29, 2025 at 10:03 AM
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...
#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
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
July 25, 2025 at 9:24 AM
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
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
www.matrixscience.com/blog/the-pro...
#proteomics #massspec
July 1, 2025 at 3:47 PM
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
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
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
June 19, 2025 at 8:00 AM
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
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
LFQ in client software like Thermo Proteome Discoverer
June 5, 2025 at 11:43 AM
Come see our poster ThP 265 today at #ASMS2025: Machine learning-enabled Mascot Server API improves
LFQ in client software like Thermo Proteome Discoverer
LFQ in client software like Thermo Proteome Discoverer
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
There is no charge for attending the meeting, but advance registration is required. #proteomics #MassSpec
May 30, 2025 at 2:18 PM
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
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
www.matrixscience.com/blog/identif...
#proteomics #MassSpec
May 29, 2025 at 2:53 PM
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
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
There is no charge for attending the meeting, but advance registration is required. #proteomics #MassSpec
May 22, 2025 at 2:56 PM
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
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
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
May 20, 2025 at 8:35 AM
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
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
There is no charge for attending the meeting, but advance registration is required. #proteomics #MassSpec
May 15, 2025 at 3:04 PM
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
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
www.matrixscience.com/blog/adding-...
#proteomics #MassSpec
May 1, 2025 at 2:12 PM
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
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
www.matrixscience.com/help/instrum...
#proteomics #MassSpec
Mascot help: Agilent instruments
www.matrixscience.com
April 24, 2025 at 3:23 PM
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
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...
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...
April 17, 2025 at 9:13 AM
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...
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
www.matrixscience.com/blog/big-dat...
#proteomics #MassSpec
Big databases and large peak lists
www.matrixscience.com
April 2, 2025 at 2:24 PM
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
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
www.matrixscience.com/help/disaste...
#proteomics #MassSpec
Mascot database search protein identification software | Disaster recovery
Disaster recovery strategy, what to back up and how to restore configuration files, search results and sequence databases for Mascot Server, Distiller and Daemon
www.matrixscience.com
March 20, 2025 at 9:54 AM
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
www.matrixscience.com/help/disaste...
#proteomics #MassSpec