Mascot Server.

Welcome to the home of Mascot software, the benchmark for identification, characterisation and quantitation of proteins using mass spectrometry data. Here, you can learn more about the tools developed by Matrix Science to get the best out of your data, whatever your chosen instrument.


March 15, 2023

Using Mascot Daemon, Mascot Distiller and Mascot Server A recent paper from Manda et al.[1] describes a pipeline to generate [...]

Mascot Server

Mascot Server is a powerful search engine for identifying proteins and peptides from primary sequence databases using mass spectrometry data. Fast, parallel execution is combined with chemical and post-translational modifications, robust FDR estimation, top-down protein identification, quantitation using isobaric labelling, spectral libraries, intact crosslinking, and more.

The free service running on this website is ideal for evaluation and searching smaller data sets. A selection of popular sequence databases are online, including SwissProt, Uniprot proteomes, and the EST divisions of EMBL. For large scale and routine work, you'll want to license Mascot Server to run in-house.

Mascot Daemon

Mascot Daemon is a batch automation utility, bundled with Mascot Server. In combination with Mascot Distiller, every step of a quantitation experiment can be fully automated.

Mascot Distiller

Mascot Distiller offers a single, graphical user interface to native (binary) data files from Agilent, AB Sciex, Bruker, Shimadzu, Thermo and Waters. Raw data can be processed into high quality, de-isotoped peak lists. Optional toolboxes support Mascot search result review, de novo sequencing, batch processing and quantitation: isobaric labelling, isotopic labelling and label-free. Distiller can be used for free in read-only mode as a project viewer, ideal for distributing search and quantitation results to colleagues.

Mascot Parser

Mascot Parser provides an API (Application Programmer Interface) to Mascot Server result files and Mascot Distiller project files, making it easy to access search results from programs written in C++, C#, Java, Python or Perl. Free for non-commercial use.

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