The invention relates to a novel method for identifying a
diagnostic marker peak of
protein citrullination by
mass spectrometry. A
gas phase fragmentation pathway of citrullinated
peptide is explored, a characteristic neutral loss is found, namely, the neutral loss of 43.0058 Da is matched with release of an
isocyanate group of citrullinated ureido, the two modifications can be distinguished when the corresponding neutral loss is detected, and citrullinated modification can be accurately and quickly confirmed. When secondary
mass spectrum data are retrieved, an anti-
library is additionally added to calculate the
false positive rate caused by random matching, and a common
pollution library is added into a
database to eliminate the influence of
pollution protein in an identification result; the
mass error tolerance is set in a targeted manner, and the accuracy of
mass spectrum data retrieval and the diagnosis accuracy of
protein citrullination are improved. The process of converting
arginine into
citrulline can be diagnosed with high specificity, the technology is a key technology for realizing polypeptide sequencing and post-translational modification analysis, and the specific
citrulline part in the protein can be determined.