Post-Search Recalibrator Node

Download and Installation

1. Save all your files and shutdown Thermo Scientific Proteome Discoverer.
2. Download the node’s DLL (for PD 1.3.x or PD 1.4.x)
3. Copy the downloaded DLLs to the Proteome Discoverer Release folder, e.g.: "C:\Program Files\Thermo\Discoverer Demo 1.3\System\Release".
4. For each DLL: Right-click the DLL, open its properties window and click the Unblock botton, if available.
   
5. Open a command prompt and navigate to the Proteome Discoverer Release folder.
6. Enter “Thermo.Magellan.Server –install” (without the quotes).
7. You should see the message, indicating that the installation worked sucessfully: "INFO - ProcessingNodeManager: Node: Post Search Mass Recalibrator registered."

Functionality

The node performs a recalibration of the precursor masses based on the results of a previous search. The (precursor-m/z, ppm error)-pairs of the high-scoring PSMs are extracted and a regression curve is fitted through these data points. This curve is used to adjust all precursor-m/z values in preparation of a second search. It is possible to define the degree of the polynomial to be used for the fitting.

Usage

Although it is possible to append the Post-Search Mass Recalibrator node to a search and directly add the second search in one workflow, it is not recommended to do so. The structure of the .msf files generated by PD does not allow the removal of the results of the first search. Therefore both search results would occur in the results. Figure 1 shows the workflow to create an input file whose spectra have recalibrated precursor masses by using the Spectrum Exporter node. This file can then be used as input for another workflow where the actual search is conducted.

Figure 1: Proposed workflow for the usage of the Post-Search Mass Recalibrator node to generate a recalibrated input file