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


This tool enables automated and confident localization of modification sites within validated peptide sequences and can be applied to all commonly used fragmentation techniques (CID, ETD and HCD). It calculates individual probability values for each putatively modified site based on the given MS/MS data. For further information on the algorithm of the software, please refer to the corresponding publication.

What's new?

The ptmRS node is the latest version of this modification-site localization algorithm and is compatible with both Thermo Scientific Proteome Discoverer 1.4, 2.0 and 2.1. The new features of this update are:


The analysis of a HeLa dataset revealed that ptmRS is able to localize more phosphorylation sites compared to the preliminary version (distributed with Thermo Scientific Proteome Discoverer 1.3), which is attributed to the novel individual peak depth approach and the optimization of scoring parameters. Repeating the validation of the algorithm by analyzing chemically synthesized modification-peptides with precisely known sites ensured that the empirical false localization rate (FLR) is always lower than indicated by the applied ptmRS site probability cutoff. All results are identical between ptmRS 1.4 and 2.0/2.1.
Download & Installation

The ptmRS node can be installed easily for Thermo Scientific Proteome Discoverer 1.4/2.0/2.1 and will replace its preliminary version by following these steps: