{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T21:16:43Z","timestamp":1783199803368,"version":"3.54.6"},"reference-count":87,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T00:00:00Z","timestamp":1780272000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,4,27]],"date-time":"2026-04-27T00:00:00Z","timestamp":1777248000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001732","name":"Danish National Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001732","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001825","name":"Danish Agency for Higher Education and Science","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100009708","name":"Novo Nordisk Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009708","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports Medicine"],"published-print":{"date-parts":[[2026,6]]},"DOI":"10.1016\/j.xcrm.2026.102829","type":"journal-article","created":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T14:37:18Z","timestamp":1779374238000},"page":"102829","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":0,"title":["The proteomics and phosphoproteomics landscape of melanoma under T cell attack"],"prefix":"10.1016","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5309-5558","authenticated-orcid":false,"given":"Giulia","family":"Franciosa","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Agnete W.P.","family":"Jensen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"Martinez-Val","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilaria","family":"Piga","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco","family":"Donia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4747-4938","authenticated-orcid":false,"given":"Jesper V.","family":"Olsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xcrm.2026.102829_bib1","doi-asserted-by":"crossref","first-page":"1535","DOI":"10.1056\/NEJMoa1910836","article-title":"Five-year survival with combined nivolumab and ipilimumab in advanced melanoma","volume":"381","author":"Larkin","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.xcrm.2026.102829_bib2","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1200\/JCO.21.02229","article-title":"Long-term outcomes with nivolumab plus ipilimumab or nivolumab alone versus ipilimumab in patients with advanced melanoma","volume":"40","author":"Wolchok","year":"2022","journal-title":"J. Clin. Oncol."},{"key":"10.1016\/j.xcrm.2026.102829_bib3","doi-asserted-by":"crossref","first-page":"2352","DOI":"10.1002\/ijc.35347","article-title":"How many people in the US are eligible for and respond to checkpoint inhibitors: An empirical analysis","volume":"156","author":"Haslam","year":"2025","journal-title":"Int. J. Cancer"},{"key":"10.1016\/j.xcrm.2026.102829_bib4","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1016\/j.molmed.2025.03.010","article-title":"Acquired resistance to immunotherapy in solid tumors","volume":"31","author":"Verdys","year":"2025","journal-title":"Trends Mol. Med."},{"key":"10.1016\/j.xcrm.2026.102829_bib5","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1038\/s41568-019-0116-x","article-title":"The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy","volume":"19","author":"Havel","year":"2019","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.xcrm.2026.102829_bib6","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.ccell.2021.11.012","article-title":"Multiomic profiling of checkpoint inhibitor-treated melanoma: Identifying predictors of response and resistance, and markers of biological discordance","volume":"40","author":"Newell","year":"2022","journal-title":"Cancer Cell"},{"key":"10.1016\/j.xcrm.2026.102829_bib7","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/nature23477","article-title":"Identification of essential genes for cancer immunotherapy","volume":"548","author":"Patel","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2026.102829_bib8","doi-asserted-by":"crossref","first-page":"553","DOI":"10.1007\/s00262-021-03015-1","article-title":"Transcriptomic signatures of tumors undergoing T cell attack","volume":"71","author":"Gokuldass","year":"2022","journal-title":"Cancer Immunol. Immunother."},{"key":"10.1016\/j.xcrm.2026.102829_bib9","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.cell.2006.09.026","article-title":"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks","volume":"127","author":"Olsen","year":"2006","journal-title":"Cell"},{"key":"10.1016\/j.xcrm.2026.102829_bib10","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1080\/14789450.2021.1976152","article-title":"Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells","volume":"18","author":"Gerritsen","year":"2021","journal-title":"Expert Rev. Proteomics"},{"key":"10.1016\/j.xcrm.2026.102829_bib11","doi-asserted-by":"crossref","first-page":"7016","DOI":"10.1038\/s41467-024-51274-0","article-title":"Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer","volume":"15","author":"Lancaster","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xcrm.2026.102829_bib12","doi-asserted-by":"crossref","DOI":"10.1016\/j.cbpa.2022.102260","article-title":"Recent advances in kinase signaling network profiling by mass spectrometry","volume":"73","author":"Franciosa","year":"2023","journal-title":"Curr. Opin. Chem. Biol."},{"key":"10.1016\/j.xcrm.2026.102829_bib13","doi-asserted-by":"crossref","first-page":"1575","DOI":"10.1093\/annonc\/mdy139","article-title":"T cells isolated from patients with checkpoint inhibitor-resistant melanoma are functional and can mediate tumor regression","volume":"29","author":"Andersen","year":"2018","journal-title":"Ann. Oncol."},{"key":"10.1016\/j.xcrm.2026.102829_bib14","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1074\/mcp.M200025-MCP200","article-title":"Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics","volume":"1","author":"Ong","year":"2002","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.xcrm.2026.102829_bib15","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.113598","article-title":"Phosphoprotein dynamics of interacting T cells and tumor cells by HySic","volume":"43","author":"Ib\u00e1\u00f1ez-Molero","year":"2024","journal-title":"Cell Rep."},{"key":"10.1016\/j.xcrm.2026.102829_bib16","doi-asserted-by":"crossref","first-page":"1855","DOI":"10.1038\/s41587-023-02099-7","article-title":"Ultra-fast label-free quantification and comprehensive proteome coverage with narrow-window data-independent acquisition","volume":"42","author":"Guzman","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xcrm.2026.102829_bib17","doi-asserted-by":"crossref","first-page":"2570","DOI":"10.1021\/ac503593d","article-title":"Multiplexed quantification for data-independent acquisition","volume":"87","author":"Minogue","year":"2015","journal-title":"Anal. Chem."},{"key":"10.1016\/j.xcrm.2026.102829_bib18","doi-asserted-by":"crossref","first-page":"1212","DOI":"10.1038\/s41467-017-01422-6","article-title":"Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells","volume":"8","author":"Liu","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xcrm.2026.102829_bib19","doi-asserted-by":"crossref","first-page":"1918","DOI":"10.1021\/acs.jproteome.0c00938","article-title":"Improved SILAC Quantification with Data-Independent Acquisition to Investigate Bortezomib-Induced Protein Degradation","volume":"20","author":"Pino","year":"2021","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.xcrm.2026.102829_bib20","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1038\/s41587-022-01389-w","article-title":"Increasing the throughput of sensitive proteomics by plexDIA","volume":"41","author":"Derks","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.xcrm.2026.102829_bib21","doi-asserted-by":"crossref","first-page":"2433","DOI":"10.1016\/j.cell.2025.03.002","article-title":"Global analysis of protein turnover dynamics in single cells","volume":"188","author":"Sabatier","year":"2025","journal-title":"Cell"},{"key":"10.1016\/j.xcrm.2026.102829_bib22","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.705422","article-title":"Rapid identification of the tumor-specific reactive TIL repertoire via combined detection of CD137, TNF, and IFN\u03b3, following recognition of autologous tumor-antigens","volume":"12","author":"Draghi","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.xcrm.2026.102829_bib23","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1038\/nri1083","article-title":"The ABCs of granule-mediated cytotoxicity: new weapons in the arsenal: Cell death and immunity","volume":"3","author":"Lieberman","year":"2003","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.xcrm.2026.102829_bib24","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","article-title":"DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput","volume":"17","author":"Demichev","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xcrm.2026.102829_bib25","article-title":"QuantUMS: uncertainty minimisation enables confident quantification in proteomics","author":"Kistner","year":"2023","journal-title":"bioRxiv"},{"key":"10.1016\/j.xcrm.2026.102829_bib26","doi-asserted-by":"crossref","DOI":"10.1016\/j.mcpro.2024.100754","article-title":"Systematic optimization of automated phosphopeptide enrichment for high-sensitivity phosphoproteomics","volume":"23","author":"Bortel","year":"2024","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.xcrm.2026.102829_bib27","article-title":"Differential proteomic and metabolic remodelling of CD4+ and CD8+ T cells in mesenteric lymph nodes during colitis-associated colorectal cancer","author":"Gonz\u00e1lez-Romero","year":"2025","journal-title":"bioRxiv"},{"key":"10.1016\/j.xcrm.2026.102829_bib28","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2318687121","article-title":"Engineered CD4 T cells for in vivo delivery of therapeutic proteins","volume":"121","author":"Radhakrishnan","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.xcrm.2026.102829_bib29","doi-asserted-by":"crossref","first-page":"374","DOI":"10.1016\/j.immuni.2016.07.009","article-title":"The tumor microenvironment represses T cell mitochondrial biogenesis to drive intratumoral T cell metabolic insufficiency and dysfunction","volume":"45","author":"Scharping","year":"2016","journal-title":"Immunity"},{"key":"10.1016\/j.xcrm.2026.102829_bib30","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1016\/j.molmed.2024.04.014","article-title":"CRISPR\/Cas9 screening: unraveling cancer immunotherapy\u2019s \u201cRosetta Stone.\u201d","volume":"30","author":"Chen","year":"2024","journal-title":"Trends Mol. Med."},{"key":"10.1016\/j.xcrm.2026.102829_bib31","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.aar3451","article-title":"Tumor immune evasion arises through loss of TNF sensitivity","volume":"3","author":"Kearney","year":"2018","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.xcrm.2026.102829_bib32","article-title":"RNF31 inhibition sensitizes tumors to bystander killing by innate and adaptive immune cells","volume":"3","author":"Zhang","year":"2022","journal-title":"Cell Rep. Med."},{"key":"10.1016\/j.xcrm.2026.102829_bib33","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1016\/j.ccell.2020.08.005","article-title":"Conserved interferon-\u03b3 signaling drives clinical response to immune checkpoint blockade therapy in melanoma","volume":"38","author":"Grasso","year":"2020","journal-title":"Cancer Cell"},{"key":"10.1016\/j.xcrm.2026.102829_bib34","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1186\/s12943-025-02276-z","article-title":"IL-4 mediated TAP2 downregulation is a dominant and reversible mechanism of immune evasion and immunotherapy resistance in non-small cell lung cancer","volume":"24","author":"Ranjan","year":"2025","journal-title":"Mol. Cancer"},{"key":"10.1016\/j.xcrm.2026.102829_bib35","doi-asserted-by":"crossref","first-page":"847","DOI":"10.3389\/fimmu.2018.00847","article-title":"Interferon-Gamma at the Crossroads of Tumor Immune Surveillance or Evasion","volume":"9","author":"Castro","year":"2018","journal-title":"Front. Immunol."},{"key":"10.1016\/j.xcrm.2026.102829_bib36","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2022.111153","article-title":"Cancer genes disfavoring T cell immunity identified via integrated systems approach","volume":"40","author":"Kishton","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.xcrm.2026.102829_bib37","doi-asserted-by":"crossref","first-page":"2645","DOI":"10.1158\/0008-5472.CAN-22-3114","article-title":"Targeting KDM2A enhances T-cell infiltration in NSD1-deficient head and neck squamous cell carcinoma","volume":"83","author":"Chen","year":"2023","journal-title":"Cancer Res."},{"key":"10.1016\/j.xcrm.2026.102829_bib38","doi-asserted-by":"crossref","first-page":"984","DOI":"10.1016\/j.cell.2018.09.006","article-title":"A cancer cell program promotes T cell exclusion and resistance to checkpoint blockade","volume":"175","author":"Jerby-Arnon","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.xcrm.2026.102829_bib39","doi-asserted-by":"crossref","first-page":"1879","DOI":"10.1038\/s41401-023-01079-6","article-title":"Predictive biomarkers of immunotherapy response with pharmacological applications in solid tumors","volume":"44","author":"Kov\u00e1cs","year":"2023","journal-title":"Acta Pharmacol. Sin."},{"key":"10.1016\/j.xcrm.2026.102829_bib40","doi-asserted-by":"crossref","first-page":"1550","DOI":"10.1038\/s41591-018-0136-1","article-title":"Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response","volume":"24","author":"Jiang","year":"2018","journal-title":"Nat. Med."},{"key":"10.1016\/j.xcrm.2026.102829_bib41","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/s13073-020-0721-z","article-title":"Large-scale public data reuse to model immunotherapy response and resistance","volume":"12","author":"Fu","year":"2020","journal-title":"Genome Med."},{"key":"10.1016\/j.xcrm.2026.102829_bib42","doi-asserted-by":"crossref","first-page":"D512","DOI":"10.1093\/nar\/gku1267","article-title":"PhosphoSitePlus, 2014: mutations, PTMs and recalibrations","volume":"43","author":"Hornbeck","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xcrm.2026.102829_bib43","doi-asserted-by":"crossref","first-page":"698","DOI":"10.1016\/j.molcel.2017.05.003","article-title":"MK2 phosphorylates RIPK1 to prevent TNF-induced cell death","volume":"66","author":"Jaco","year":"2017","journal-title":"Mol. Cell"},{"key":"10.1016\/j.xcrm.2026.102829_bib44","doi-asserted-by":"crossref","first-page":"1237","DOI":"10.1038\/ncb3608","article-title":"MK2 phosphorylation of RIPK1 regulates TNF-mediated cell death","volume":"19","author":"Dondelinger","year":"2017","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.xcrm.2026.102829_bib45","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1038\/ncb3614","article-title":"p38MAPK\/MK2-dependent phosphorylation controls cytotoxic RIPK1 signalling in inflammation and infection","volume":"19","author":"Menon","year":"2017","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.xcrm.2026.102829_bib46","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1038\/s41467-017-00406-w","article-title":"Regulation of RIPK1 activation by TAK1-mediated phosphorylation dictates apoptosis and necroptosis","volume":"8","author":"Geng","year":"2017","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xcrm.2026.102829_bib47","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1074\/mcp.TIR118.000943","article-title":"A Curated Resource for Phosphosite-specific Signature Analysis","volume":"18","author":"Krug","year":"2019","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.xcrm.2026.102829_bib48","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1038\/nmeth.2646","article-title":"pLogo: a probabilistic approach to visualizing sequence motifs","volume":"10","author":"O\u2019Shea","year":"2013","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xcrm.2026.102829_bib49","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1038\/s41586-022-05575-3","article-title":"An atlas of substrate specificities for the human serine\/threonine kinome","volume":"613","author":"Johnson","year":"2023","journal-title":"Nature"},{"key":"10.1016\/j.xcrm.2026.102829_bib50","doi-asserted-by":"crossref","first-page":"37538","DOI":"10.1074\/jbc.274.53.37538","article-title":"Substrate specificities and identification of putative substrates of ATM kinase family members","volume":"274","author":"Kim","year":"1999","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.xcrm.2026.102829_bib51","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1038\/s41467-021-21211-6","article-title":"Robust inference of kinase activity using functional networks","volume":"12","author":"Y\u0131lmaz","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xcrm.2026.102829_bib52","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13578-020-0376-x","article-title":"ATM, ATR and DNA-PKcs kinases-the lessons from the mouse models: inhibition \u2260 deletion","volume":"10","author":"Menolfi","year":"2020","journal-title":"Cell Biosci."},{"key":"10.1016\/j.xcrm.2026.102829_bib53","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.canlet.2020.09.016","article-title":"Reality CHEK: Understanding the biology and clinical potential of CHK1","volume":"497","author":"Neizer-Ashun","year":"2021","journal-title":"Cancer Lett."},{"key":"10.1016\/j.xcrm.2026.102829_bib54","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1128\/MMBR.00013-12","article-title":"Activation and function of the MAPKs and their substrates, the MAPK-activated protein kinases","volume":"76","author":"Cargnello","year":"2012","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"10.1016\/j.xcrm.2026.102829_bib55","doi-asserted-by":"crossref","first-page":"510","DOI":"10.1038\/s41467-024-55533-y","article-title":"PTMNavigator: interactive visualization of differentially regulated post-translational modifications in cellular signaling pathways","volume":"16","author":"M\u00fcller","year":"2025","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xcrm.2026.102829_bib56","doi-asserted-by":"crossref","first-page":"1227","DOI":"10.1093\/intimm\/dxh299","article-title":"Heterotypic interaction of CRTAM with Necl2 induces cell adhesion on activated NK cells and CD8+ T cells","volume":"17","author":"Arase","year":"2005","journal-title":"Int. Immunol."},{"key":"10.1016\/j.xcrm.2026.102829_bib57","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1182\/blood-2005-02-0817","article-title":"The tumor suppressor TSLC1\/NECL-2 triggers NK-cell and CD8+ T-cell responses through the cell-surface receptor CRTAM","volume":"106","author":"Boles","year":"2005","journal-title":"Blood"},{"key":"10.1016\/j.xcrm.2026.102829_bib58","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1038\/s41698-024-00655-1","article-title":"Secrets of DNA-PKcs beyond DNA repair","volume":"8","author":"Camfield","year":"2024","journal-title":"npj Precis. Oncol."},{"key":"10.1016\/j.xcrm.2026.102829_bib59","doi-asserted-by":"crossref","DOI":"10.1126\/sciimmunol.aba4219","article-title":"Human DNA-PK activates a STING-independent DNA sensing pathway","volume":"5","author":"Burleigh","year":"2020","journal-title":"Sci. Immunol."},{"key":"10.1016\/j.xcrm.2026.102829_bib60","doi-asserted-by":"crossref","DOI":"10.1172\/JCI180278","article-title":"DNA-PK inhibition enhances neoantigen diversity and increases T cell responses to immunoresistant tumors","volume":"134","author":"Nielsen","year":"2024","journal-title":"J. Clin. Investig."},{"key":"10.1016\/j.xcrm.2026.102829_bib61","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1056\/NEJMoa1604958","article-title":"Mutations associated with acquired resistance to PD-1 blockade in melanoma","volume":"375","author":"Zaretsky","year":"2016","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.xcrm.2026.102829_bib62","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1186\/s12915-025-02237-4","article-title":"Tyrosinase in melanoma inhibits anti-tumor activity of PD-1 deficient T cells","volume":"23","author":"Huang","year":"2025","journal-title":"BMC Biol."},{"key":"10.1016\/j.xcrm.2026.102829_bib63","doi-asserted-by":"crossref","first-page":"1524","DOI":"10.1158\/2159-8290.CD-20-0812","article-title":"Therapeutically increasing MHC-I expression potentiates immune checkpoint blockade","volume":"11","author":"Gu","year":"2021","journal-title":"Cancer Discov."},{"key":"10.1016\/j.xcrm.2026.102829_bib64","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1016\/j.cell.2019.06.014","article-title":"Augmenting immunotherapy impact by lowering tumor TNF cytotoxicity threshold","volume":"178","author":"Vredevoogd","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.xcrm.2026.102829_bib65","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1186\/s12964-022-00998-x","article-title":"CD6-mediated inhibition of T cell activation via modulation of Ras","volume":"20","author":"Henriques","year":"2022","journal-title":"Cell Commun. Signal."},{"key":"10.1016\/j.xcrm.2026.102829_bib66","doi-asserted-by":"crossref","first-page":"8627","DOI":"10.1073\/pnas.96.15.8627","article-title":"Dipeptidyl peptidase I is required for the processing and activation of granzymes A and B in vivo","volume":"96","author":"Pham","year":"1999","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"10.1016\/j.xcrm.2026.102829_bib67","doi-asserted-by":"crossref","DOI":"10.1126\/scisignal.aau8645","article-title":"Illuminating the dark phosphoproteome","volume":"12","author":"Needham","year":"2019","journal-title":"Sci. Signal."},{"key":"10.1016\/j.xcrm.2026.102829_bib68","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/s41592-023-01802-5","article-title":"Sampling the proteome by emerging single-molecule and mass spectrometry methods","volume":"20","author":"MacCoss","year":"2023","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xcrm.2026.102829_bib69","doi-asserted-by":"crossref","first-page":"288","DOI":"10.3390\/biom16020288","article-title":"Comparative analysis of lysis buffers for enhanced proteomic and glycoproteomic profiling","volume":"16","author":"Chu","year":"2026","journal-title":"Biomolecules"},{"key":"10.1016\/j.xcrm.2026.102829_bib70","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1080\/14789450.2025.2604157","article-title":"Middle-down proteomics: the pursuit for longer peptides","volume":"22","author":"Hovey","year":"2025","journal-title":"Expert Rev. Proteomics"},{"key":"10.1016\/j.xcrm.2026.102829_bib71","doi-asserted-by":"crossref","first-page":"8837","DOI":"10.1021\/acs.analchem.5b01833","article-title":"Comparing multistep immobilized metal affinity chromatography and multistep TiO2 methods for phosphopeptide enrichment","volume":"87","author":"Yue","year":"2015","journal-title":"Anal. Chem."},{"key":"10.1016\/j.xcrm.2026.102829_bib72","doi-asserted-by":"crossref","first-page":"D1539","DOI":"10.1093\/nar\/gkac1040","article-title":"The ProteomeXchange consortium at 10 years: 2023 update","volume":"51","author":"Deutsch","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xcrm.2026.102829_bib73","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1038\/s41592-020-0955-0","article-title":"MassIVE.quant: a community resource of quantitative mass spectrometry\u2013based proteomics datasets","volume":"17","author":"Choi","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xcrm.2026.102829_bib85","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.xcrm.2026.102829_bib77","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1021\/acs.jproteome.8b00702","article-title":"Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data","volume":"18","author":"Doncheva","year":"2019","journal-title":"J. Proteome Res."},{"key":"10.1016\/j.xcrm.2026.102829_bib87","doi-asserted-by":"crossref","first-page":"157","DOI":"10.12688\/f1000research.22280.1","article-title":"Visualize omics data on networks with Omics Visualizer, a Cytoscape App","volume":"9","author":"Legeay","year":"2020","journal-title":"F1000Res."},{"key":"10.1016\/j.xcrm.2026.102829_bib78","doi-asserted-by":"crossref","first-page":"3344","DOI":"10.3390\/cancers12113344","article-title":"Qualitative analysis of tumor-infiltrating lymphocytes across human tumor types reveals a higher proportion of bystander CD8+ T cells in non-melanoma cancers compared to melanoma","volume":"12","author":"Gokuldass","year":"2020","journal-title":"Cancers (Basel)"},{"key":"10.1016\/j.xcrm.2026.102829_bib79","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1111\/j.1365-3083.2011.02640.x","article-title":"Characterization and comparison of \u201cstandard\u201d and \u201cyoung\u201d tumour-infiltrating lymphocytes for adoptive cell therapy at a Danish translational research institution","volume":"75","author":"Donia","year":"2012","journal-title":"Scand. J. Immunol."},{"key":"10.1016\/j.xcrm.2026.102829_bib80","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1097\/CMR.0b013e3283390696","article-title":"Establishment of stable cell lines for personalized melanoma cell vaccine","volume":"20","author":"Selvan","year":"2010","journal-title":"Melanoma Res."},{"key":"10.1016\/j.xcrm.2026.102829_bib81","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1097\/CJI.0b013e31818403d5","article-title":"Minimally cultured tumor-infiltrating lymphocytes display optimal characteristics for adoptive cell therapy","volume":"31","author":"Tran","year":"2008","journal-title":"J. Immunother."},{"key":"10.1016\/j.xcrm.2026.102829_bib82","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1074\/mcp.TIR119.001906","article-title":"A compact quadrupole-orbitrap mass spectrometer with FAIMS Interface improves proteome coverage in short LC gradients","volume":"19","author":"Bekker-Jensen","year":"2020","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.xcrm.2026.102829_bib83","doi-asserted-by":"crossref","DOI":"10.1016\/j.xpro.2023.102536","article-title":"Protocol for high-throughput semi-automated label-free- or TMT-based phosphoproteome profiling","volume":"4","author":"Koenig","year":"2023","journal-title":"STAR Protoc."},{"key":"10.1016\/j.xcrm.2026.102829_bib84","doi-asserted-by":"crossref","first-page":"2284","DOI":"10.1074\/mcp.TIR118.000853","article-title":"A novel LC system embeds analytes in pre-formed gradients for rapid, ultra-robust proteomics","volume":"17","author":"Bache","year":"2018","journal-title":"Mol. Cell. Proteomics"},{"key":"10.1016\/j.xcrm.2026.102829_bib74","doi-asserted-by":"crossref","first-page":"2269","DOI":"10.1038\/s41467-023-38035-1","article-title":"DeepFLR facilitates false localization rate control in phosphoproteomics","volume":"14","author":"Zong","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.xcrm.2026.102829_bib86","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1214\/16-AOAS920","article-title":"Robust hyperparameter estimation protects against hypervariable genes and improves power to detect differential expression","volume":"10","author":"Phipson","year":"2016","journal-title":"Ann. Appl. Stat."},{"key":"10.1016\/j.xcrm.2026.102829_bib75","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1093\/bioinformatics\/bti270","article-title":"Use of within-array replicate spots for assessing differential expression in microarray experiments","volume":"21","author":"Smyth","year":"2005","journal-title":"Bioinformatics"},{"key":"10.1016\/j.xcrm.2026.102829_bib76","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The STRING database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res."}],"container-title":["Cell Reports Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666379126002466?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666379126002466?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,7,4]],"date-time":"2026-07-04T20:42:48Z","timestamp":1783197768000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666379126002466"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6]]},"references-count":87,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2026,6]]}},"alternative-id":["S2666379126002466"],"URL":"https:\/\/doi.org\/10.1016\/j.xcrm.2026.102829","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2025.09.12.675787","asserted-by":"object"}]},"ISSN":["2666-3791"],"issn-type":[{"value":"2666-3791","type":"print"}],"subject":[],"published":{"date-parts":[[2026,6]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"The proteomics and phosphoproteomics landscape of melanoma under T cell attack","name":"articletitle","label":"Article Title"},{"value":"Cell Reports Medicine","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xcrm.2026.102829","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"102829"}}