A release candidate of the next version of Mascot Server is running on this website. One of the headline features in the preliminary release notes is refining results with machine learning, which includes integration with MS2Rescore. Below is a preview for you to enjoy while we are beta testing the new release. What is MS2Rescore ..read more

This website is now running a Mascot Server 3.0 release candidate, which is undergoing extensive beta testing. What’s new in Mascot Server 3.0 If you spot any bugs or experience any problems, please email support@matrixscience.com with details. No matter how much testing we do ourselves, there will always be some bugs that we miss ..read more

Mascot Server ships with Percolator, which is an algorithm that uses semi-supervised machine learning to improve the discrimination between correct and incorrect spectrum identifications. This is often termed rescoring with machine learning. What exactly does it mean, and how does it work? Identifying correct matches using a score threshold When you submit a search against ..read more

The ASMS 2024 conference was held in Anaheim, California, on 2-6 June 2024. It was great to see many of you at our booth as well as the annual Breakfast Meeting! We presented three talks at the meeting. If you were unable to attend, or want to review any of the material that was presented ..read more

This year we are celebrating 30 years of sequence tags. The technique was developed by Matthias Mann and Matthias Wilm while in the Protein and Peptide group at the European Molecular Biology Laboratory (EMBL). EMBL is itself celebrating its 50th Anniversary and has been an important center for science over that period. The sequence tag ..read more

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