MzidLib - A library of routines for manipulating data in the PSI's mzIdentML standard. 
ProteoAnnotator is a completely automated software pipeline for integration of mass spectrometry (MS) based proteomic evidence into genome databases. 
  

  
Citation:

If you use any of these resources in your work, please cite:

MzidLib:

Ghali, F., Krishna, R., Lukasse, P., Martinez-Bartolome, S. et al., A toolkit for the mzIdentML standard: the ProteoIDViewer, the mzidLibrary and the mzidValidator. Mol. Cell Proteomics 2013, 12, 3026–3035.

ProteoAnnotator:
Ghali, F., Krishna, R., Perkins, S., Collins, A. et al., ProteoAnnotator—open source proteogenomics annotation software supporting PSI standards. Proteomics 2014, 14, 2731–2741.