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Posted by Ville Koskinen (September 22, 2021)

Identify more HLA peptides

Endogenous peptides are challenging to identify by database searching. A Mascot no-enzyme search matches every subsequence of a protein to the observed spectrum, which makes a very large search space even if precursor tolerance is tight. As a result, Mascot score thresholds tend to be conservative and sensitivity is reduced. Mascot ships with Percolator, which often improves discrimination between true [...]

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Posted by John Cottrell (April 15, 2019)

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 [...]

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