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Articles tagged: Proteome Discoverer
Identify more proteins using Mascot and Proteome Discoverer with this one small trick
Mascot Server is often used with software packages like Thermo Proteome Discoverer™ (PD). We recently made it possible to enable machine learning on the server side by specifying it in the Mascot instrument definition, which is also the topic of one of our ASMS 2025 posters. An important detail was overlooked in the initial instructions, which is: you should disable [...]
Using machine learning with Mascot and Proteome Discoverer
Update: There is a newer version of this article, Identify more proteins using Mascot and Proteome Discoverer with this one small trick. The PD setup instructions have been updated accordingly. Mascot Server 3.1 is a patch release that enhances integration with Thermo Proteome Discoverer™ and fixes a few important bugs introduced in Mascot Server 3.0. The full list of improvements [...]
Mascot workflows in Proteome Discoverer
For many users of Thermo instruments, Proteome Discoverer (PD) is their primary user interface for database searching, and Mascot is represented by a node in the workflow. This article collects together a few tips and observations concerning Proteome Discoverer 2.3 and Mascot Server 2.6. Proteome Discoverer Configuration Under Administration; Mascot Server, the setting Max. MGF File Size [MB] has a [...]