Download

PhosphoRS.zip

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. The download contains a stand-alone version of phosphoRS, as well as some example data. Xml-files serve as input and output for the software.
The application can be executed given the input-file and the location, where to write the output-file.In order to retrieve a detailed description of phosphoRS please refer to the related publication.
Since phosphoRS is implemented in Java programming language (6.0.240, Oracle), please make sure that you have at least Java 6 installed. Free download of Java is provided at java.com.

QuantMerge.exe

V 1.21 This tool is capable of merging reporter ion intensities from HCD or IRMPD scans into CID scans. Currently 4plex and 8plex is supported. Later Versions will include TMT. The input and resulting fileformat is MGF. (Windows executable) ATTENTION: MGF-file must be generated by MSnExtract or Bioworks. Disoverer MGF exports will not work yet.

MGFdummyPeakInsertion.exe

This tool is capable of inserting peaks at any m/z value and any intensity into MGF files.

MS_cleaner_v_1.3.zip

Cleaning of raw peptide MS/MS spectra: Improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise. Including the related publication (Proteomics 2006).