In addition to these advancements, Kleikamp et al. focused on improving the detection of specific PTMs by incorporating SMSNet into their metaproteomics pipeline. Moreover, SMSNet also enhances de novo sequencing by addressing a key challenge: the absence of robust methods for FDR estimation. While most de novo methods struggle with confidence evaluation due to a lack of decoy sequences , SMSNet refines its low-confidence predictions by incorporating a peptide database, providing an additional layer of validation.