ABSTRACT: Multiple post-translational modification (PTM) proteomics generally relies on combining the enrichment of various PTMs with multiplex isobaric labeling and extensive peptide fractionation. However, effective methods for sequentially enriching multiple PTMs from a single sample for data-independent acquisition mass spectrometry (DIA-MS) are still lacking. Here, we present SCASP-PTM, a novel approach enabling desalting-free enrichment of diverse PTMs—including phosphopeptides, ubiquitinated peptides, acetylated peptides, glycopeptides, and biotinylated peptides. SCASP-PTM utilizes SDS for protein denaturation, which is sequestered by cyclodextrins before trypsin digestion, allowing sequential PTM enrichment without additional purification steps. By combing SCASP-PTM with DIA-MS, we quantified the proteome, ubiquitinome, phosphoproteome, and glycoproteome from 18 poly(I:C)-treated HeLa-S3 cell samples, identifying serine 28 phosphorylation as the key driver of poly(I:C)-induced p62 degradation. Additionally, this method enabled the quantification of proteome, ubiquitinome, acetylomes, phosphoproteome, and glycoproteome from 32 clinical tissue samples, revealing that ubiquitination/acetylation of lysine 330 on ALDOA is critical for tumor progression. In summary, SCASP-PTM is a robust method by enabling desalting-free, sequential enrichment of multiple PTMs from a single sample, offering a streamlined workflow for comprehensive PTM analysis when combined with DIA-MS in both basic research and clinical application.
Chuanqi Zhong 
