Mass spectrometry, Protein Chemistry Facility
Research Institute of Molecular Pathology (IMP)
Institute of molecular biotechnology of the Austrian Academy of Sciences (IMBA)
Gregor Mendel Institute of Molecular Plant Biology (GMI)

PD-Nodes SimpatiQCo Software Tools Publications


Peakjuggler is a Proteome Discoverer node for label-free quantification of peptides and proteins.

Features Prequisites Installation

Sample Workflow

This sample workflow should make you ready to go. It is the workflow to analyse the Ramus et al data set which is also used in the performance comparison further down in the Performance section.


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


We benchmarked Peakjuggler on a publicly available dataset (Ramus et al). The original raw files are available on PRIDE (PXD001819). The samples are comprised of UPS1 protein mix spiked in at different concentrations into a 1:1 yeast background. This dataset was used in a comparison for different LFQ algorithms (Veit et al). We used results published there as Supplementary Data in order to compare the performance of Peakjuggler to LFQProfiler(OpenMS), MaxQuant, MFPaQ and Skyline. Peakjuggler outperforms these tools by enabling the detection of more differentially abundant UPS proteins at the same number of falsely identified (unregulated) yeast proteins.

The Proteome Discoverer workflow to reproduce this result is available for download and provides a starting point for easy incorporation of Peakjuggler in your workflow. Furthermore the final results file is also available here.


Please use right-click and "Save Link as" to download the files to your computer.

What's new? Manual Screenshots
Processing Node Workflow
Consensus Node Workflow
Processing Node Parameters
Consensus Node Parameters

Peptide Table
Protein Table
Extracted ion chromatogram a peptide in two samples. Integration boundaries are shown in orange and the peaks center of gravity is shown in blue.
Other Sample Data

To get you started, we provide you with a sample workflow and also the raw and result files. The sample consists of 0.1 µg Hela measured on a QExHF.

Please use right-click and "Save Link as" to download the files to your computer.