Optimizing the identification of citrullinated peptides by mass spectrometry: utilizing the inability of trypsin to cleave after citrullinated amino acids

Citrullinated proteins have been associated with several diseases and citrullination can most likely function as a target for novel diagnostic agents and unravel disease etiologies. The correct identification of citrullinated proteins is therefore of most importance. Mass spectrometry (MS) driven proteomics can with bottom up strategies analyze protein profiles and PTMs in complex samples. However, the site-specific characterization of citrullination using MS remains problematic, especially in complex samples where no sensitive chemical modification technique exists. A tryptic missed cleavage after citrulline is therefore often used as a marker for citrullination post processing. However, C-terminal tryptic citrullinated peptides have also been reported. In this study, we therefore aimed at optimizing the identification of citrullinated peptides in complex samples.

To assess the cleavage properties of trypsin, digestion was performed on synthetic peptide sets containing either arginine or citrulline. The peptide sequences originated from disease-associated in vivo citrullinated proteins; some reported as being C-terminal tryptic citrullinated peptides. Furthermore, the proteolytic activity was verified using digested synovial fluid samples from a rheumatoid arthritis patient. The samples were analyzed using liquid chromatography/tandem MS with electrospray ionization.

Our in vivo and in vitro studies clearly demonstrate the inability of trypsin to cleave after citrulline residues. Based on our findings, we present a strategy for verifying citrullinated sites in complex samples post processing, in proteomics shotgun experiments. By requiring a missed cleavage for the identification of citrullinated peptides, we demonstrate that 64% of false-positively annotated citrullination sites could be removed. We furthermore demonstrated likely pitfalls of applying the strategy.

In conclusion, manual annotation of citrullinated peptide spectra remains essential to ensure correct annotation. Implementing a missed cleavage requirement significantly reduces the number of spectra needing manual verification with minimal loss. This method may help future proteomics studies identify citrullinated proteins in complex samples.