Updated publication reference for PubMed record(s): 34870237. In this project, a cohort of early stage NSCLC samples (141) were analyzed by MS-based proteomics in order to identify molecular subtypes at the phenotype level. In total, close to 14 000 proteins were identified and quantified across samples by HiRIEF-LC-MS and TMT based relative quantification. Further, six identified NSCLC proteome subtypes were investigated in relation to cancer driver pathways, immune phenotypes and neoantigen expression based on the generated MS-data.