Deep proteome profiling promotes whole proteome characterization and drug discovery for esophageal squamous cell carcinoma

Proteins are key players in various cellular processes. As the ultimate executors of cellular processes, they play essen-tial roles in linking genotypes to phenotypes. Abnormalities in protein expression and post-translational modifications (PTMs) are closely associated with the initiation and devel-opment of cancer, and they carry biological information inaccessible to genomics and transcriptomics1. Proteomics complements genomic and transcriptomic data, thus ena-bling comprehensive analysis of cancer pathogenesis and accelerating biomedical research2. Owing to the limitations of protein quantification instrumentation and methods, the development of proteomics has substantially lagged behind that of genomics and transcriptomics. Fortunately, recent technological advances in mass spectrometry-based proteom-ics have substantially increased the number of proteins that can be quantified (at high resolution) and the number of samples that can be profiled within a reasonable time frame (high throughput)3. Consequently, whole proteome quantifi-cation can now be performed on a large scale, thereby enabling proteome characterization with greater statistical significance, identification of proteomic subtypes, and discovery of poten-tial drugs. We refer to the high-resolution, high-throughput proteomics profiling of large-scale samples as deep proteome profiling.