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MSFragger, an ultrafast database search tool, has been increasingly used for peptide identification. In an attempt to allow the easy manipulation of MSFragger, we implement this tool as a processing node in Thermo Scientific Proteome Discoverer (PD) such that it can be operated through the graphical user interface of PD. Since Percolator currently lacks the capability of performing peptide-spectrum match (PSM) validation on open searches, we also implemented Philosopher’s PeptideProphet as a PD processing node. Comparing the search results of SequestHT and Percolator using a public HEK293 data set (PXD001468), using MSFragger and PeptideProphet(Philosopher) makes the processing speed at least four times faster and identifies more proteins/peptide/PSMs.
The MSFragger node can be used with Thermo Scientific Proteome Discoverer 2.2. Please follow the steps belwo for the installation:
Step 1. Download the latest version of PDNode.dll from our github repository.
Step 2. Make sure that Thermo Scientific Proteome Discoverer in your computer is closed.
Step 3. Open the folder where Thermo Scientific Proteome Discoverer is installed.
To find out the folder location of Thermo Scientific Proteome Discoverer, please right click on your Thermo Scientific Proteome Discoverer desktop icon and then click on "Properties". The folder path is shown in the field of Target (as the figure shown in below).
Step 4. Copy the "PDNode.dll" to the folder. (Please ensure that the old version of PDNode.dll is deleted.)
Step 5. Open Thermo Scientific Proteome Discoverer, select the licensing page and click on Scan for Missing Features.
Step 6. Restart Thermo Scientific Proteome Discoverer.
MSFragger
Step1. File conversion
PeptideProphet(Philosopher)