Implementing the MSFragger Search Engine as a Node in Proteome Discoverer

Here, we describe the implementation
of the fast proteomics search
engine MSFragger as a processing node in the widely used Proteome
Discoverer (PD) software platform. PeptideProphet (via the Philosopher
tool kit) is also implemented as an additional PD node to allow validation
of MSFragger open (mass-tolerant) search results. These two nodes,
along with the existing Percolator validation module, allow users
to employ different search strategies and conveniently inspect search
results through PD. Our results have demonstrated the improved numbers
of PSMs, peptides, and proteins identified by MSFragger coupled with
Percolator and significantly faster search speed compared to the conventional
SEQUEST/Percolator PD workflows. The MSFragger-PD node is available
at https://github.com/nesvilab/PD-Nodes/releases/.