Data analysis in mass spectrometry proteomics is complex and, nowadays, almost entirely software driven. Processing a raw file, peptide identification by database searching, protein inference and protein quantitation all have many steps and built-in assumptions, not to mention a huge number of parameters. Software continues to evolve as does best practice. Whether you are new ..read more

We are pleased to announce a new distributor for Matrix Science products! Customers in Europe can now buy Mascot through MS Wil B.V., a one-stop-shop for fine mass spectrometry tools. MS Wil is selling new licences for Mascot Server and Mascot Distiller as well as updates and upgrades to existing licences. The new distribution agreement ..read more

Mascot Distiller 2.8 reports are written in Python, a commonly used programming language, and use Mascot Parser to access the search and quantitation results. We supply a range of standard reports, including reports for quality, clustering and statistical analysis, which we took a look at in an earlier blog article. In addition to these, you ..read more

The public Mascot service running on this website recently had its 25th birthday: the service was launched in November 1998. The purpose is to let you evaluate the product before buying, but it’s also useful for small data sets and proteomics training courses. We’re a small company and our main activity is software development. The ..read more

Mascot Server ships with predefined configuration for several sequence databases, stored in databases_1.xml. The following definitions have become obsolete and have now been removed from databases_1.xml: IPI_arabidopsis IPI_bovine IPI_chicken IPI_human IPI_mouse IPI_rat IPI_zebrafish SARS-CoV-2 The International Protein Index (IPI) databases were superceded by Uniprot proteomes as long ago as September 2011. We kept the predefined ..read more

We have upgraded the server hardware and operating system, as well as migrated to a new hosting provider. The website and the free Mascot service should now operate normally. If you discover any issues, please contact us at support@matrixscience.com. We have additionally moved searches older than 1 Jan 2020 to cold storage. If you submitted ..read more

Mascot Security is a role-based access system that allows administrators to control different aspects of privacy and priority access. It integrates with authentication systems like Microsoft Active Directory (AD) and various single sign-on systems. It can also be configured for a core lab, where search results can be shared with collaborators without them having access to ..read more

One of the great things about the Association of Biomolecular Resource Facilities (ABRF) is their technical studies involving real samples and data. The three proteomics research groups, Proteomics (PRG), Proteome Informatics (iPRG) and Proteomics Standards (sPRG), have all held interesting studies over the years. This year the iPRG group has put together a crosslinking study ..read more

Mascot’s spectrum-centric approach doesn’t have the constraints on variable modifications, missed cleavages and protein sequences that are required by peptide-centric DIA tools. In fact, it’s nearly trivial to identify unsuspected variable modifications in narrow-window DIA data using the Mascot Error Tolerant Search. There can be many reasons for failing to get a significant sequence match ..read more

Data-independent acquisition (DIA) can be broadly separated into narrow window and wide window strategies depending on the size of the isolation window. There are also two data analysis strategies – peptide-centric and spectrum-centric. Wide window DIA typically requires a peptide-centric approach, but narrow window DIA data can be analysed either way. Mascot Server is spectrum-centric ..read more