Development of a mass spectrometry-compatible chemical probe for protein citrullination enrichment

Citrullination is a post-translational modification (PTM) on arginine catalyzed by peptidylarginine deiminase (PAD) enzymes. Despite the significance of citrullination in health and disease, the absence of efficient MS-compatible enrichment tools has hindered the exploration of how this modification influences the functions of proteins at the proteome-wide level. Here, we present a cleavable, MS-compatible chemical probe for the enrichment of citrullinated peptides, based on two commercially available compounds, making it readily accessible to the community to explore functional implications in diverse biological contexts. Citrullinated peptides were derivatized by 4-azidophenyl glyoxal, followed by a click reaction with dde-biotin alkyne that adds a biotin residue with a cleavable linker. After enrichment by streptavidin beads, the peptides are cleaved off, leaving a mass tag of 212 Da. The peptides were then measured in LC-MS/MS and analyzed by MSFragger (v20.0) using a custom variable modification. First, we optimized reaction conditions such as incubation time, temperature, probe ratio, etc., using synthetic citrullinated peptides. Then, we spiked them into tryptic HeLa peptides to assess platform sensitivity in a complex background. The detection limit of the single peptide is ~7.8 nmol/µg. Next, we generated in vitro citrullinated HeLa peptides with 0.1 to 2% citrullination content to assess enrichment efficiency. As a result, we identified a 2 to 7-fold increase in citrullinated peptides, and the enrichment selectivity (intensity-based) is up to 90% for the sample with the highest citrullination content. Finally, we extended the capacity to a 96-well format to demonstrate its high-throughput ability and quantitative reproducibility. In conclusion, this study presents a robust enrichment workflow for protein citrullination at the peptide level. This enhances the depth of citrullination proteomics analysis using commercially available probes and enables high-throughput citrullination analysis in various sample types from diverse biological contexts.