Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

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Posted by Ville Koskinen (June 11, 2024)

Matrix Science at ASMS 2024

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, the talks are summarised below [...]

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Posted by Richard Jacob (May 20, 2024)

30 years of Sequence Tags

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 paper was published in 1994, [...]

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Posted by Ville Koskinen (April 18, 2024)

Mascot workflow for LC-MS/MS data

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 to mass spectrometry proteomics or [...]

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Posted by Patrick Emery (March 18, 2024)

Tutorial: Creating custom reports in Mascot Distiller

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 can develop your own reports [...]

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Posted by Ville Koskinen (February 16, 2024)

How to run the public Mascot service

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 secrets to running the public [...]

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Posted by Richard Jacob (January 15, 2024)

Mascot security – guest users and administrators

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 the results of other groups. [...]

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Posted by Richard Jacob (December 5, 2023)

ABRF iPRG 2023 crosslinking study

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. The goal is to teach [...]

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Posted by Patrick Emery (November 13, 2023)

Finding unsuspected modifications in narrow-window DIA data using the Mascot Error Tolerant Search

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 to an MS/MS spectrum. Three [...]

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Posted by Patrick Emery (October 13, 2023)

Spectrum-centric searching of narrow window DIA data with Mascot Server

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, and it’s possible to run [...]

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Posted by Ville Koskinen (September 18, 2023)

Mascot Distiller 20th anniversary

This year is the 25th anniversary of Matrix Science and 25 years of Mascot Server, but it’s also the 20th birthday of Mascot Distiller! Mascot Distiller 1.0 was released in June 2003 and it’s still under active development today. Distiller started as a GUI application for browsing and peak picking native (raw, binary) mass spectrometry data files. Let’s have a [...]

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Posted by Ville Koskinen (August 23, 2023)

Identifying peptides from chimeric spectra (DDA, DIA)

Many traditional search engines assume the MS/MS spectrum of a peptide is produced by a single precursor. This is often true when you run a single-species tryptic digest in data dependent acquisition (DDA) mode with a narrow isolation window. Once you change the acquisition strategy or analyse a complex mixture, like an environmental sample, it’s possible for two or more [...]

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Posted by Ville Koskinen (July 13, 2023)

Get better HCD results by matching internal fragments

Mascot ships with several instrument definitions, which define the fragment ion series used for matching and scoring. All of them enable b ions and most enable y ions, and a few like ETD-TRAP also enable c and z+1. Mascot can also match internal fragments, which are formed by double backbone cleavage, a combination of a/b type and y type. Of [...]

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