Mascot Daemon

Mascot Daemon is a Microsoft Windows client application developed by Matrix Science that automates the submission of mass spectrometry data files to Mascot Server. It is designed for proteomics researchers, core laboratories, and industry users who need to streamline and scale protein identification, characterisation, and quantitation workflows without manual intervention.

The functional unit of Mascot Daemon is a task, which is defined by the data source (a list of data files or a file path), how the data are to be searched, when the searches are to take place, and any follow-up activities such as conditional repeat searches. Multiple Daemon clients can submit searches to the same Mascot Server, making it suitable for facilities running several mass spectrometers — each instrument can have its own Daemon installation, or a single copy can be deployed on the LAN to process data from all instruments.

Core Operating Modes

• Batch mode: An arbitrary group of files can be defined for searching, either immediately or at a pre-set time, enabling scheduled, unattended processing of large datasets.
• Real-time monitor mode: New files appearing on a pre-defined file path are automatically searched as they are created, supporting continuous data acquisition workflows.
• Data-dependent follow-up tasks: Searches can be automatically repeated at a later date or against a different sequence database based on the results of a prior search.

Task Configuration and Search Parameters

• Search parameters are defined in the Parameter Editor, which closely resembles the HTML form used for interactive Mascot searches, providing a familiar interface for experienced users.
• Fields in the Parameter Editor can contain HTML-like tags that are automatically substituted at run time with contextual information such as a file name or sample description, enabling dynamic and flexible task configuration.

Results Management

• Every time a new task is run, it creates a task node on a status tree, with results attached to the task node in a structure similar to directories and sub-directories in Windows Explorer.
• Key information for each result can be viewed by clicking on the result node, and the full result report can be opened in a web browser via a blue hyperlink.

Follow-Up and Decision Tree Capabilities

• A batch of data files can be searched at specified intervals against database updates, with each file remaining in the loop until its score exceeds a pre-set threshold.
• Sequence databases of increasing size or decreasing quality can be searched serially — for example, a small database of common contaminants can be searched first, unmatched spectra can then be searched against a comprehensive non-redundant protein database such as NCBIprot, and data still failing to find a match can proceed to an EST database search.
• Arbitrary numbers of follow-up tasks can be chained together to implement complex decision trees, made possible because Mascot scores reflect true probabilities, allowing rule-based logic to determine match significance according to user-specified criteria.

Database and Deployment Options

• The default database engine is Microsoft Jet 4.0 (the engine used by Microsoft Access), suitable for single-client deployments.
• Daemon can alternatively be configured to use any database engine supporting OLE DB or ODBC, such as Microsoft SQL Server or Oracle, enabling multiple Daemon clients to share a common task database across an organisation.

Mascot Daemon runs on Microsoft Windows and integrates directly with Mascot Server, making it a powerful automation layer for high-throughput proteomics environments. It is available with licensing options suited to researchers, core labs, industry users, and educators.