Protein methylation, a prevalent post-translational modification, plays crucial roles in chromatin remodeling and gene transcription. A deeper understanding protein methylation in these biological processes necessitates a comprehensive characterization of the methylation sites. However, the methylation group induces minimal changes in the size and electrostatic status of lysine/arginine residues. This significantly increases the difficulty of distinguishing the methylation sites from the non-methylation sites. In this study, we developed a strategy to enrich protein methylation, termed the Negative Enrichment Strategy for Profiling Protein Methylation, to comprehensively analyze lysine/arginine methylation. Initially, proteins were digested using LysargNase to generate peptides containing methylated or non-methylated lysine/arginine at the Nterminus. Subsequently, the N-terminal free α-amines of the LysargiNase-generated peptides were selectively blocked using formaldehyde in an acidic solution. As t