Your main problem here will be finding software that works with the mzIdentML output from MS-GF+. I don't think any of the software I list support this format. I know you can export as tsv from MS-GF+, so maybe you can work with that?

The easiest approach would be to use Proteome Discoverer as this has phosphoRS (http://dx.doi.org/10.1021/pr200611n) built into the latest version (http://ms.imp.ac.at/?goto=phosphors). But you obviously need ProteomeDiscoverer and it costs $$$.

You can get a standalone version of phosphoRS here (http://cores.imp.ac.at/protein-chemistry/download/).

Other alternatives are to use Delta score (DOI: 10.1074/mcp.M110.003830) which is now implemented in Mascot. A-score (https://gygi.med.harvard.edu/lab/software.php) is ever popular. There's also C-score (http://composition.sdu.dk/), FragMixer (http://proteomics.fr/FragMixer/) and SLoMo (http://massspec.bham.ac.uk/slomo/).

I'd also suggest you take a look at PeptideShaker (https://code.google.com/p/peptide-shaker/) as this implements both Delta score and A-score. I suspect the next version of PeptideShaker will implement D-score (DOI: 10.1002/pmic.201200408). The software is brilliant and free. It works with SearchGUI (https://code.google.com/p/searchgui/). The only trick here is that you need to generate an MGF from your RAW data file. This is not hard to do, but the method you choose WILL affect the result.

Which one you can use will depend on several factors including how the data was acquired. Take a look and see what suits and what works for your data.

Peter

Thanks a lot for your valuable information and Good review on Site Localization am trying to read and work on that from today..Thanks Peter