ptmRS specifications

Information


Unique identifier OMICS_06877
Name ptmRS
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


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Maintainer


  • person_outline Thomas Koecher <>

Additional information


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

ptmRS article

ptmRS citations

 (7)
2018
PMCID: 5797227

[…] and lysine residues; methionine oxidation; and phosphorylation on serine, threonine and tyrosine were set as variable modifications. the identification of the phosphorylation site was done by the phosphors 3.0 node of proteome discoverer. a probability threshold of at least 0.75 was used for confident phosphosite localization. the 3plex or duplex dimethyl-based quantitation method was chosen […]

2017
PMCID: 5705597

[…] fragment mass tolerance of 0.8 da were used for search analysis. only peptides with high stringency mascot score threshold (identity, fdr < 1%) were selected and used for protein identification. phosphors 3.0 tool was activated in proteomediscoverer software to enable automated and confident localization of phosphorylation sites within validated peptides sequences., five microliters […]

2017
PMCID: 5297695

[…] from the analysis when they were not further supported by additional high-scoring identifications in other replicates or experiments. all phosphopeptide hits were automatically re-analyzed by the phosphors software within the protein discoverer software suite. phosphors probability higher than 90% was required for a phosphorylation site to be considered as localized. only those peptides […]

2016
PMCID: 4806917

[…] ions were analyzed in the orbitrap. the software xcalibur 2.2 was used for lc-ms method programming and data acquisition. the evaluation of phosphorylation site probabilities was performed by using phosphors and for identification of proteins ms/ms2 data were analyzed against the a. nidulans genome database [134] using the sequest and mascot search engine and the proteome discoverer software […]

2015
PMCID: 4613507

[…] threshold < 1% false discovery rate, based on a concatenated decoy database search to calculate the median protein and peptide ratios. localization of phosphotyrosine sites was evaluated using phosphors score and manual inspection., ok cells were grown in glass-bottom dishes and transiently co-transfected with pmeos2–nherf or pflag–meos2-nherf constructs as indicated on the second day post […]

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

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