I am trying to generate simulated MS data (Top-down and Bottom-up) for phosphorylated protein such as platelet-derived growth factor receptor (PDGFR-B). There are 10 tyrosine sites which are phosphorylated. Could you kindly tell me if there is any good software application to help me do that?
Also, how can I include in the input file (FASTA) that there are 10 modification sites on the protein sequence?
What are the parameters required to be set for top-down and bottom-up MS separately?