--- Links and information on useful web application ---
Peptide and fragment ion calculator
MZCal is an online tool that calculats physiochemical properties for a given peptides, including monoisotopic mass, MZ values, fragment values and predicted fragment intensities (via MSPIP). The tool supports isotopic labelling and modifications on any amino acid.
HiLight-PTM is an online tool that highlights m/z peaks from peptide fragmentation (MS/MS) spectra that have matching masses, and those which have a predictable mass-shift owing to the incorporation of an isotopic label. Using this tool, we can extract pairs of MS/MS spectra that contain correlative fragments. Coupled to this, we use retention-time matching and compare the ratio of precursor isotopic peaks to match heavy/light peptide at both the MS1 and MS2 level. By doing this, we can interrogate when standard database searching fails (e.g. owing to poor fragmentation scans from co-isolation or low intensity). We also use experimental fragmentation matching to in silico fragment ions independant of precursor mass. For a full description, click here.