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

Mascot Daemon – automate DIA, DDA and PMF data analysis

Mascot Daemon is a Microsoft Windows client application that automates raw file processing and Mascot database searching. When Mascot Distiller is used as the data import filter, Mascot Daemon automates all steps of protein identification and quantitation for DIA, DDA and PMF analysis.

Daemon capabilities

Mascot Daemon functionality includes:

  • Data import filters: automatically convert native (“raw”) mass spectrometry data files.
  • Schedules: configure tasks to run at a pre-set time.
  • Batch mode: an arbitrary group of files can be defined for searching.
  • Real-time monitor mode: trigger a task as new files are created on a pre-defined path.
  • Follow-up tasks: automatically repeat a search at a later date or against a different sequence database.
  • Relational task database: use ODBC connection to relational database of your choice.
  • Exporting results: automatically save identification results in standard formats (mzIdentML, mzTab, Mascot XML, Mascot CSV).
  • Quantitation reports: automatically run quantitation after the database search and generate reports (requires Mascot Distiller).
  • Configurable hooks: run an external process before or after any task.

Mascot Daemon is included free of charge with every Mascot Server installation.

Supported file formats (DIA)

Mascot Distiller is required for DIA. When it is used as the data import filter, Daemon supports data independent acquisition (DIA) experiments using:

Support for Bruker diaPASEF is planned.

Supported file formats (DDA, PMF)

When Mascot Distiller is used as the data import filter, Daemon supports data dependent acquisition (DDA) and peptide mass fingerprint (PMF) experiments from all major instruments used in proteomics research today, including:

When a different data import filter is used, such as ProteoWizard mzConvert or SCIEX MS Data Converter, instrument support depends on the data import filter.

System requirements

Mascot Daemon integrates with Mascot Server for protein identification by database searching. We recommend the latest release of Mascot Server.

Mascot Daemon integrates with Mascot Distiller for raw data processing and protein quantitation. Mascot Distiller is required for DIA support and optional but recommend for DDA and PMF.

Mascot Daemon requires 64-bit Microsoft Windows 10 or later, Server 2016 or later. Daemon is fully compatible with Windows 11/Server 2022/Server 2025. In all cases, the latest service pack should be applied. Mascot Daemon requires .NET Framework 4.7 or later to run.

The default database engine used by Mascot Daemon is VistaDB, which is a database contained in a single disk file. Alternatively, Daemon can be configured to use any database engine which supports ODBC, such as Microsoft SQL Server, PostgreSQL or Oracle, enabling multiple Daemon clients to share a common task database.

Please check the PC hardware requirements for Mascot Server if Daemon is running on the same PC, and Mascot Distiller if you are using Distiller as a data import filter.

Premium Support

Mascot Daemon is covered by Mascot Server Premium Support.

Software and version updates

Mascot Daemon is bundled with Mascot Server. When you update Mascot Server, you can install an updated version of Daemon for free.

Feature overview

Client-server architecture

Multiple Daemon clients can submit searches to the same Mascot server. If you have several mass spectrometers, you can install separate copies of Daemon on each instrument data system or just have a single copy of Daemon somewhere on the internal network processing searches for data from all instruments.

Task configuration

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.

Setting up a task in Daemon

Multiple Daemon clients can share a task database using an ODBC connection, for example Microsoft SQL Server or PostgreSQL.

Search Parameter Editor

Search parameters are defined in the Parameter Editor, which closely resembles the HTML form used for interactive Mascot searches. Fields can also contain HTML-like tags which are automatically substituted at run time with information such as a file name or a sample description.

Search Parameter editor

Task tree

Every time a new task is run, it creates a task node on the status tree. The results from each task are attached to the task node, just like directories and sub-directories in Windows Explorer. Key information for each result can be displayed by clicking on the result node. The full result report can be displayed in a web browser by clicking on the blue hyperlink.

A result on the status tree

Sample map

Studies that use mass spectrometry-based quantitation often contain large numbers of individual analyses: samples from different sources or treatments or time points, possibly fractionated, with replicates and so forth. Using statistical methods to combine the analyses, extract meaningful information, and report it as charts and tables is a complex task that usually requires input in spreadsheet form, called a Quantitation Summary, where the rows correspond to proteins and the columns contain expression data for the various samples in the form of abundances or ratios of abundances.

The facility to create such a spreadsheet is part of Mascot Daemon. Create a Sample Map from a set of search results using label-free and isotopic label quantitation methods, including reporter ion methods (TMT, TMTpro, iTRAQ).

Sample map dialog

Real-time Monitor

By running Mascot Daemon in real-time monitor mode, each raw file can be searched automatically, as soon as acquisition is complete. Simply configure the task with a directory where new raw files are placed.

Real-time monitor example

Follow-up tasks

Daemon’s follow-up function can be used in many different ways. A couple of simple examples would be:

  1. Multiple follow-up tasks can be chained together creating a sieve approach to the analysis. An example of this technique is analysing a Histone dataset.
  2. Sequence databases of increasing size or decreasing quality can be searched serially. For example, a small database of common contaminants might be searched first. Spectra which are unmatched can then be searched against a comprehensive non-redundant protein database, such as TrEMBL. Data which still fail to find a match can then proceed to a search of UniRef100 or an EST database.

Arbitrary numbers of follow-up tasks can be chained together to implement complex decision trees. This is possible because Mascot scores reflect true probabilities, permitting rule-based software to determine whether a match is significant according to user specified criteria.

Histone follow-up tasks

External Processes

The External Processes dialog allows calling programs or scripts before or after a task or search. Daemon uses tokens to pass values such as file names and paths to the external application. This way, you can trigger a program that performs a task after every search is complete, for example sending an email or passing the results to another program for further analysis.

External task example

Example use cases: