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ptmRS specifications


Unique identifier OMICS_06877
Name ptmRS
Alternative name phosphoRS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Thermo Scientific Proteome Discoverer
Maintained Yes


No version available


  • person_outline Thomas Koecher

Additional information

Publication for ptmRS

ptmRS citations


The 38K Mediated Specific Dephosphorylation of the Viral Core Protein P6.9 Plays an Important Role in the Nucleocapsid Assembly of Autographa californica Multiple Nucleopolyhedrovirus

J Virol
PMCID: 5899202
PMID: 29444944
DOI: 10.1128/JVI.01989-17

[…] arch was performed with Proteome Discoverer 1.3 (Thermo Scientific) using the SEQUEST program () with the amino acid sequence of AcMNPV P6.9 with search parameters set as previously described (). The phosphoRS algorithm was also employed to evaluate the accuracy of phosphorylation site localizations (). For each phosphorylation site, a phosphoRS probability above 75 indicated that the site actuall […]


Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor

PMCID: 5854290
PMID: 29556515
DOI: 10.18632/oncoscience.395

[…] erance was set to 20 ppm and 0.1 Da, respectively. In addition, decoy database search was carried out to calculate false discovery rate (FDR). FDR of 1% was considered for peptide identification. The PhosphoRS node (Version 3.0) in the Proteome Discoverer was used to calculate the phosphorylation probability at Y residue [] and peptides greater than 75% site localization probability was considered […]


PP5 (PPP5C) is a phosphatase of Dvl2

Sci Rep
PMCID: 5807433
PMID: 29426949
DOI: 10.1038/s41598-018-21124-3
call_split See protocol

[…] sis. Samples were sequentially digested with AspN and chymotrypsin. MS analysis of Dvl2 phosphorylation sites was performed as reported previously. The phosphopeptides were further verified using the phosphoRS 3.1 node in Proteome Discoverer software, which determines the localisation of phosphorylation sites within validated peptide sequences. All MS/MS spectra corresponding to phosphopeptides we […]


UFD 2 is an adaptor assisted E3 ligase targeting unfolded proteins

Nat Commun
PMCID: 5797217
PMID: 29396393
DOI: 10.1038/s41467-018-02924-7
call_split See protocol

[…] set to 2. The result was filtered to 1% FDR using Percolator algorithm integrated in Proteome Discoverer. The localization of the phosphorylation sites within the peptides was performed with the tool phosphoRS.For the mapping of Ub sites shown in Supplementary Table , the nano HPLC system used was an UltiMate 3000 Dual Gradient HPLC system (Dionex, Amsterdam, The Netherlands), equipped with a Prox […]


Arabidopsis serine/threonine/tyrosine protein kinase phosphorylates oil body proteins that regulate oil content in the seeds

Sci Rep
PMCID: 5773694
PMID: 29348626
DOI: 10.1038/s41598-018-19311-3
call_split See protocol

[…] set to 1% for each analysis. The number of unique phosphopeptides and non-phosphopeptides was manually counted and compared. Phosphorylation site localization from CID mass spectra was determined by PhosphoRS scores. For phosphopeptides with inconclusive phosphorylation sites, the one with highest phosphoRS score was selected for further data interpretation. […]


Parallel comparative proteomics and phosphoproteomics reveal that cattle myostatin regulates phosphorylation of key enzymes in glycogen metabolism and glycolysis pathway

PMCID: 5834288
PMID: 29541418
DOI: 10.18632/oncotarget.24250
call_split See protocol

[…] protein.For quantitative phosphopeptides analysis, an additional phosphorylation on Ser, Thr, Tyr residues were specified as variable modifications. To confidently localize phosphorylation sites, the phosphoRS 3.0 node integrated in PD 1.4 workflow was used. The algorithm of phosphoRS 3.0 software enables automated and confident localization of phosphosites by determining individual probability va […]


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ptmRS institution(s)
Research Institute of Molecular Pathology, Vienna, Austria

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