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The proteomic landscape of advanced melanoma remains poorly understood, especially regarding proteomic heterogeneity across metastases within patients.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We collected 83 melanoma metastases from 19 different metastatic sites in 24 patients with advanced metastatic melanoma almost exclusively from the pre\u2010immunotherapy era, using semi\u2010rapid autopsies. The metastases were subjected to histopathological evaluation, RNA\u2010sequencing and mass spectrometry\u2010based proteomics for protein quantitation and non\u2010reference peptide (NRP) sequence detection using a proteogenomic data integration approach.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>NRPs associated with mutations frequently occurred in proteins related to focal adhesion, vesicle\u2010mediated transport, MAPK signalling and immune response pathways across the cohort. Intrapatient heterogeneity was negligible when considering morphology and driver gene mutation status but was substantial at the proteogenomic level. This heterogeneity was not driven by metastasis location, albeit liver metastases exhibited distinct proteogenomic patterns, including upregulation of metabolic pathways. Cluster analysis outlined four proteomic clusters (C1\u20134) of the metastases, characterised by the upregulation of cell cycle and RNA\u2010splicing (C1), mitochondrial processes (C3), extracellular matrix (ECM) and immune pathways (C2) and ECM and vesicle\u2010mediated transport pathways (C4). Around two\u2010thirds of patients had metastases that had strongly distinct phenotypes. Patients in our cohort whose metastases were primarily assigned to clusters C1 and C3 exhibited shorter overall survival than patients whose metastases were categorised mainly into the C2 and C4 clusters.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Our unique multi\u2010metastasis cohort captured the proteogenomic heterogeneity of immunotherapy\u2010na\u00efve melanoma distant metastases, establishing a foundation for future studies aimed at identifying novel therapeutic targets to complement current immunotherapies.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Key points<\/jats:title>\n                    <jats:p>\n                      <jats:list list-type=\"bullet\">\n                        <jats:list-item>\n                          <jats:p>Comprehensive proteogenomic profiling of post\u2010mortem melanoma metastases, collected primarily before the immunotherapy era.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>Description of 1177 protein sequence variants predicted by RNA\u2010Seq and validated via mass spectrometry\u2010based proteomics.<\/jats:p>\n                        <\/jats:list-item>\n                        <jats:list-item>\n                          <jats:p>Empirical evidence of prominent intrapatient heterogeneity, driven by heterogeneous protein expression related to cell cycle\u2010 and mitochondrial processes, immune system and extracellular matrix organization.<\/jats:p>\n                        <\/jats:list-item>\n                      <\/jats:list>\n                    <\/jats:p>\n                  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