What’s new in Mascot Daemon 3.2 (pre-release draft)
Note: This is a pre-release draft and the details may change before the final release.
Mascot Daemon is a Microsoft Windows client application that automates raw file processing and Mascot database searching. Mascot Daemon 3.2 is shipped with Mascot Server 3.2.
Mascot DIA
Mascot Server and Mascot Distiller can now be used for identifying and quantifying proteins from Data Independent Acquisition (DIA) runs. This is enabled by two key features:
- New in Mascot Distiller 3.0: Novel peak detection for Thermo DIA and SCIEX SWATH (see What’s new in Mascot Distiller 3.0)
- New in Mascot Server 3.2: Noise-resistant scoring for DIA spectra (see What’s new in Mascot Server 3.2)
Mascot DIA is a spectrum-centric solution and uses the same analysis workflow for DDA and DIA identification and quantitation. Read more in Mascot DIA.
New: Process DIA files using Mascot Distiller
Mascot Daemon can now process DIA files using Mascot Distiller as the data import filter. When Mascot Distiller 3.0 or later is installed on the same computer as Daemon, the option is available in the dropdown menu as shown below.
Mascot Distiller 3.0 supports any Thermo Orbitrap instrument that saves raw data in Thermo Xcalibur format, any SCIEX instrument in wiff format and Waters MSE. Support for Bruker diaPASEF is being planned.
Improved: Create quantitation summary using Replicate LFQ [DDA, DIA]
Daemon 3.2 now allows creating a quantitation summary report using Replicate label-free quantitation. Daemon passes the sample map via command line to Mascot Distiller, which now generates the report. Replicate quantitation requires Mascot Distiller 3.0 or later.
Improved: Quantitation summary with Top-3 average intensity [DDA, DIA]
The quantitation summary report can now output Top-3 average intensity for the channels alongside the total summed intensity. Grouping method can be switched between unique sequence, unique Mr or unique m/z just as for the Average quantitation method.
Improved: Refine results with machine learning in the quantitation summary report [DDA, DIA]
Daemon 3.2 can use results refined with machine learning for the quantitation summary report. This functionality is enabled by selecting machine learning in the parameter editor.
When the search parameters are set, Mascot Server automatically refines the results at the end of the database search, and the refined results are imported into Daemon. Enabling machine learning can easily increase the number of quantified peptides by 25% while maintaining the same accuracy. Automatic refining requires Mascot Server 3.1 or later.
Improved: Select modification classifications for error tolerant search
Mascot Server 3.0 introduced a search parameter for modification classifications for error tolerant (ET) search. Mascot Daemon now has a user interface for selecting these.
The ET search is a two-pass search. In the second pass, Mascot Server tries to identify unmatched spectra by iterating over unexpected modifications in all the selected modification classes.
Improved: Allow deleting multiple tasks at a time
A Delete Task(s) menu item has been added to the root status context menu item above the quantitation summary menu items. The option is enabled if one or more tasks are selected in the table and have a status of either “completed” or “cancelled”.
Removal of obsolete functionality
Support for Windows 8.1 and Server 2012 R2 has been dropped. On Windows, Mascot Daemon 3.2 requires Windows 10 or later, or Windows Server 2016 or later. We recommend Windows 11/Server 2025.
Daemon now requires Microsoft .NET 4.7 or later.
Daemon now requires Distiller 2.7 or later. Support for Distiller 2.6 and earlier has been dropped. We recommend Mascot Distiller 3.0 or later.
Other improvements
The patch release also fixes other minor issues, which are listed in Mascot Server release notes.
