Help > What’s new in Mascot Daemon 3.2

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 the submission of data files to Mascot server. 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 Overview of 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 3.2 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 MS^E. 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: 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.

Other improvements

The patch release also fixes other minor issues, which are listed below.