{"entity":{"id":"proteomics","kind":"technology","name":"Proteomics & phosphoproteomics","aka":[],"tldr":"Measuring the proteins in a tumour, which is what drugs actually hit, rather than the genes that encode them.","summary":"Proteomics measures the proteins and phosphorylation sites in a tumour directly, using liquid chromatography tandem mass spectrometry with isobaric labelling to quantify thousands of proteins and phosphosites at once. Mass-spectrometry proteomics (CPTAC) reveals pathway activity and ADC target abundance that transcript levels do not predict, since RNA and protein levels often disagree. Quantitative IHC and mass-spec assays of HER2 and TROP2 aim to improve ADC patient selection by measuring the actual antigen the drug binds rather than a proxy. Throughput and standardisation remain the barriers to routine clinical use, and it is still open whether protein-level selection will outperform established IHC scoring in trials. For a newcomer, proteomics measures what drugs actually hit, the proteins, rather than the genes that encode them.","status":"emerging","asOf":"2026-09-04","wikipedia":"https://en.wikipedia.org/wiki/Proteomics","links":[{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Proteomics"}],"tags":[],"related":[],"cancers":[],"sections":["diagnostics","drug-discovery"],"technologies":[],"targets":[],"drugs":[],"companies":["elucidate-bio","acrivon-therapeutics","biodesix","helio-genomics","nonagen-bioscience","omanta","oncohost"],"institutions":[],"pathways":[],"terms":[],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":[],"principle":"Liquid chromatography tandem mass spectrometry with isobaric labelling quantifies proteins and phosphosites.","strengths":["Direct measurement of drug targets and signalling"],"limitations":["Throughput and standardisation"]},"route":"/technologies/proteomics/","neighbours":{"section":[{"id":"diagnostics","kind":"section","name":"Diagnostics & Biomarkers","route":"/fronts/diagnostics/"},{"id":"drug-discovery","kind":"section","name":"Drug Discovery Platforms","route":"/fronts/drug-discovery/"}],"company":[{"id":"acrivon-therapeutics","kind":"company","name":"Acrivon Therapeutics","route":"/companies/acrivon-therapeutics/"},{"id":"biodesix","kind":"company","name":"Biodesix","route":"/companies/biodesix/"},{"id":"bruker","kind":"company","name":"Bruker (Bruker Spatial Biology)","route":"/companies/bruker/"},{"id":"elucidate-bio","kind":"company","name":"Elucidate Bio","route":"/companies/elucidate-bio/"},{"id":"helio-genomics","kind":"company","name":"Helio Genomics","route":"/companies/helio-genomics/"},{"id":"nonagen-bioscience","kind":"company","name":"Nonagen Bioscience","route":"/companies/nonagen-bioscience/"},{"id":"omanta","kind":"company","name":"Omanta","route":"/companies/omanta/"},{"id":"oncohost","kind":"company","name":"OncoHost","route":"/companies/oncohost/"}],"cancer":[{"id":"pancreatic","kind":"cancer","name":"Pancreatic ductal adenocarcinoma","route":"/cancers/pancreatic/"}],"paper":[{"id":"paper-cohen-ctdna-protein-liquid-biopsy-pancreatic-pnas-2017","kind":"paper","name":"Combined circulating tumor DNA and protein biomarker-based liquid biopsy for the earlier detection of pancreatic cancers","route":"/key-papers/paper-cohen-ctdna-protein-liquid-biopsy-pancreatic-pnas-2017/"},{"id":"paper-cohen-cancerseek-multi-analyte-blood-test-science-2018","kind":"paper","name":"Detection and localization of surgically resectable cancers with a multi-analyte blood test","route":"/key-papers/paper-cohen-cancerseek-multi-analyte-blood-test-science-2018/"},{"id":"paper-tcga-pancreatic-integrated-characterisation-cancer-cell-2017","kind":"paper","name":"Integrated genomic characterization of pancreatic ductal adenocarcinoma","route":"/key-papers/paper-tcga-pancreatic-integrated-characterisation-cancer-cell-2017/"},{"id":"paper-fahrmann-ca19-9-lead-time-gastroenterology-2021","kind":"paper","name":"Lead-Time Trajectory of CA19-9 as an Anchor Marker for Pancreatic Cancer Early Detection","route":"/key-papers/paper-fahrmann-ca19-9-lead-time-gastroenterology-2021/"},{"id":"paper-worthington-precede-early-detection-biomarkers-ijc-2026","kind":"paper","name":"Pancreatic cancer early detection biomarkers for high-risk individuals: insights from the PRECEDE consortium","route":"/key-papers/paper-worthington-precede-early-detection-biomarkers-ijc-2026/"}],"roadmap":[{"id":"diagnostics-roadmap","kind":"roadmap","name":"Diagnostics roadmap: stains → gene panels → blood tests that decide treatment","route":"/roadmaps/diagnostics-roadmap/"},{"id":"drug-discovery-roadmap","kind":"roadmap","name":"Drug discovery roadmap: screening in mice → maps of dependency → designing in silico","route":"/roadmaps/drug-discovery-roadmap/"},{"id":"early-detection-roadmap","kind":"roadmap","name":"Early detection roadmap: organ screening → blood tests for many cancers","route":"/roadmaps/early-detection-roadmap/"}],"collection":[{"id":"cptac","kind":"collection","name":"CPTAC (Clinical Proteomic Tumor Analysis Consortium)","route":"/collections/cptac/"},{"id":"hpa","kind":"collection","name":"Human Protein Atlas","route":"/collections/hpa/"}],"technology":[{"id":"proteomics-platforms","kind":"technology","name":"Proteomics instruments and affinity platforms","route":"/technologies/proteomics-platforms/"},{"id":"spatial-omics-guided-therapy","kind":"technology","name":"Spatial-omics-guided treatment selection","route":"/technologies/spatial-omics-guided-therapy/"}],"person":[{"id":"eric-haura","kind":"person","name":"Eric B. Haura","route":"/people/eric-haura/"},{"id":"li-ding","kind":"person","name":"Li Ding","route":"/people/li-ding/"},{"id":"jiang-yi-zhou","kind":"person","name":"Yi-Zhou Jiang","route":"/people/jiang-yi-zhou/"}],"idea":[{"id":"idea-bio2-premetastatic-niche-assay","kind":"idea","name":"A blood test for the pre-metastatic niche","route":"/ideas/idea-bio2-premetastatic-niche-assay/"},{"id":"idea-fund-trial-biospecimen-commons","kind":"idea","name":"A commons for leftover trial biospecimens with standard access for approved research","route":"/ideas/idea-fund-trial-biospecimen-commons/"},{"id":"idea-bio2-rapid-autopsy-commons","kind":"idea","name":"A global rapid tissue donation network for metastatic disease","route":"/ideas/idea-bio2-rapid-autopsy-commons/"},{"id":"idea-moon-biomarker-validation-utility","kind":"idea","name":"A public biomarker validation utility with pre-diagnostic biobanks and blinded testing","route":"/ideas/idea-moon-biomarker-validation-utility/"},{"id":"idea-bio1-covalent-ligandability-atlas","kind":"idea","name":"An open map of which cancer proteins any drug can stick to","route":"/ideas/idea-bio1-covalent-ligandability-atlas/"},{"id":"idea-bio1-tumour-restricted-e3-atlas","kind":"idea","name":"Find E3 ligases that only tumours have, and build degraders around them","route":"/ideas/idea-bio1-tumour-restricted-e3-atlas/"},{"id":"idea-bio1-drug-exposure-sanctuary-mapping","kind":"idea","name":"Find the parts of a tumour the drug never reaches","route":"/ideas/idea-bio1-drug-exposure-sanctuary-mapping/"},{"id":"idea-bio1-ex-vivo-perfused-tumour","kind":"idea","name":"Keep a freshly removed tumour alive on a pump and test drugs in it","route":"/ideas/idea-bio1-ex-vivo-perfused-tumour/"},{"id":"idea-bio1-glue-degrader-atlas","kind":"idea","name":"Screen glue-like compounds against every cancer cell line and publish it","route":"/ideas/idea-bio1-glue-degrader-atlas/"},{"id":"idea-bio2-gdf15-stratified-enrolment","kind":"idea","name":"Select cachexia trial patients by the hormone driving their wasting","route":"/ideas/idea-bio2-gdf15-stratified-enrolment/"},{"id":"idea-splice-neoantigens","kind":"idea","name":"Shared splice-derived neoantigens as off-the-shelf vaccine targets","route":"/ideas/idea-splice-neoantigens/"},{"id":"idea-bio1-immunopeptidome-timing","kind":"idea","name":"Time immunotherapy to the moment targeted drugs make tumours visible","route":"/ideas/idea-bio1-immunopeptidome-timing/"}],"term":[{"id":"mass-spec-proteome","kind":"term","name":"Deep mass-spectrometry proteome (CPTAC)","route":"/terms/mass-spec-proteome/"},{"id":"mrna-protein-concordance","kind":"term","name":"mRNA to protein concordance","route":"/terms/mrna-protein-concordance/"},{"id":"pathway-activation-state","kind":"term","name":"Pathway activation state (phosphosignalling)","route":"/terms/pathway-activation-state/"},{"id":"protein","kind":"term","name":"Protein","route":"/terms/protein/"},{"id":"rppa","kind":"term","name":"Reverse-phase protein array (RPPA)","route":"/terms/rppa/"}],"institution":[{"id":"embl-ebi","kind":"institution","name":"EMBL's European Bioinformatics Institute","route":"/institutions/embl-ebi/"},{"id":"frederick-national-lab","kind":"institution","name":"Frederick National Laboratory for Cancer Research","route":"/institutions/frederick-national-lab/"},{"id":"uppsala-akademiska","kind":"institution","name":"Uppsala University Hospital / Uppsala University","route":"/institutions/uppsala-akademiska/"},{"id":"weizmann","kind":"institution","name":"Weizmann Institute of Science","route":"/institutions/weizmann/"}]}}