IMP Nodes for Proteome Discoverer 2.1 and Proteome Discoverer 2.3

This package contains free nodes for Proteome Discoverer 2.1 and Proteome Discoverer 2.3, including

  • Elutator
  • MS Amanda
  • apQuant (aka PeakJuggler)
  • Normalisation and Limma
  • MS2 Spectrum Processor (PD 2.1 only)
  • ptmRS (PD 2.1 only)

These nodes work with a free version of Proteome Discoverer 2.1 and Proteome Discoverer 2.3. See section Installation for more information.

What's new?

Date Info
2019-09-27 Added PD 2.3 version
2017-09-13 ptmRS updated
2016-11-09 Updated Peakjuggler, MsAmanda and the Normalization Node
2016-06-21 Added ptmRS, updated Peakjuggler
2016-06-16 Elutator and MS2 Spectrum Processor Node now show up if you don't have the base licence of Proteome Discoverer. Also added sample workflows
2106-06-02 Initial release


is a validation node for PSMs, based on Percolator. It is especially optimized for validating matches from MS Amanda.
MS Amanda
is a scoring system for identifying peptides and proteins out of tandem mass spectrometry data, especially designed for high resolution and high accuracy tandem mass spectra. More information
apQuant (aka PeakJuggler)
is a Proteome Discoverer node for label-free quantification of peptides and proteins. More information
Normalisation and Limma
provide different normalisation methods and an interface for limma.
performs site localisation for post translational modifications. More information
MS2 Spectrum Processor
Deisotoping of isotopic clusters and charge deconvolution. More information


For PD 2.1: Installer.exe
For PD 2.3: Installer.exe


To get a free version of Proteome Discoverer, please download the demo software from the ThermoFisher Portal.

After 60 days the demo license expires but Proteome Discoverer can still be used with the nodes in this package.

With an existing Proteome Discoverer 2.1 or Proteome Discoerer 2.3 installation, please download and install the IMP nodes package.


We have a forum. Feel free to ask questions and give feedback!

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