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Protocols

ptmRS specifications

Information


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
Requirements
Thermo Scientific Proteome Discoverer
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Thomas Koecher

Additional information


http://ms.imp.ac.at/index.php?action=phosphors

Publication for ptmRS

ptmRS citations

 (82)
library_books

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

2018
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 […]

library_books

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

2018
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 […]

call_split

PP5 (PPP5C) is a phosphatase of Dvl2

2018
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 […]

call_split

UFD 2 is an adaptor assisted E3 ligase targeting unfolded proteins

2018
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 […]

call_split

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

2018
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. […]

call_split

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

2018
Oncotarget
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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