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


phosphoRS 3.1

This tool enables automated and confident localization of phosphorylation 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 phosphorylated 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 phosphoRS 3.1 node is the latest version of this phospho-site localization algorithm and is compatible with both Thermo Scientific Proteome Discoverer 1.3 and 1.4. The new features of this update are:

Further we provide an easy-to-use Microsoft Excel macro, which facilitates the analysis of your phosphoRS 3.1 node results. First, the filtered results have to be exported from Thermo Scientific Proteome Discoverer to Microsoft Excel and then the data can be copied to the downloadable template for further processing.

Easy-to-use Microsoft Excel macro

Performance

The analysis of a HeLa dataset revealed that phosphoRS 3.1 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 phospho-peptides with precisely known sites ensured that the empirical false localization rate (FLR) is always lower than indicated by the applied phosphoRS site probability cutoff. All results are identical between phosphoRS 2.0 and 3.1.

Performance of phosphoRS

Design

As previously mentioned, the phosphoRS 3.1 code has been seperated into two DLLs, one containing the actual site localization functionality (IMP.PhosphoRS.dll) and the other being the interface to Thermo Scientific Proteome Discoverer (IMP.PhosphoRS2Nodes.dll). This new software architecture allows bioinformaticians now to integrate phosphoRS into their individual data analysis workflows. We provide a simple demo showing how to access the complete functionality of phosphoRS here. Please do not hesitate to contact us in case of questions regarding phosphoRS.

Design

Download & Installation

The phosphoRS 3.1 node can be installed easily for Thermo Scientific Proteome Discoverer 1.3/1.4 and will replace its preliminary version by following these steps: