Detection of protein mutations is still a very challenging analytical task mainly due to two reasons: first, a genetically modified protein may contain any changes (point mutation, deletion, insertion, gene conversion) with unlimited possibilities; and there is often information before hand about the structural changes. 2). For low-level mutations (SV), there is always a background of low-level chemical modifications of proteins that give the same mass change as an amino acid substitution. One has to distinguish mutations from chemical modifications to avoid false-positive.

To overcome those difficulties, we have to develop a complex process and novel computer algorism for protein mutation analysis. With our technology, we can detect heavily mutated proteins, and we can detect very low-level mutations due to translational errors.