# Proteomics & phosphoproteomics

Source: https://onco.cc/technologies/proteomics/  
OnCo record `proteomics` (Technology). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

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.

## Fields

- Kind: Technology
- Status: emerging
- Last checked: 2026-09-04
- 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

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/Proteomics
- Wikipedia: https://en.wikipedia.org/wiki/Proteomics

## Connected records

- fronts: [Diagnostics & Biomarkers](https://onco.cc/fronts/diagnostics/), [Drug Discovery Platforms](https://onco.cc/fronts/drug-discovery/)
- companies: [Acrivon Therapeutics](https://onco.cc/companies/acrivon-therapeutics/), [Biodesix](https://onco.cc/companies/biodesix/), [Bruker (Bruker Spatial Biology)](https://onco.cc/companies/bruker/), [Elucidate Bio](https://onco.cc/companies/elucidate-bio/), [Helio Genomics](https://onco.cc/companies/helio-genomics/), [Nonagen Bioscience](https://onco.cc/companies/nonagen-bioscience/), [Omanta](https://onco.cc/companies/omanta/), [OncoHost](https://onco.cc/companies/oncohost/)
- cancers: [Pancreatic ductal adenocarcinoma](https://onco.cc/cancers/pancreatic/)
- key papers: [Combined circulating tumor DNA and protein biomarker-based liquid biopsy for the earlier detection of pancreatic cancers](https://onco.cc/key-papers/paper-cohen-ctdna-protein-liquid-biopsy-pancreatic-pnas-2017/), [Detection and localization of surgically resectable cancers with a multi-analyte blood test](https://onco.cc/key-papers/paper-cohen-cancerseek-multi-analyte-blood-test-science-2018/), [Integrated genomic characterization of pancreatic ductal adenocarcinoma](https://onco.cc/key-papers/paper-tcga-pancreatic-integrated-characterisation-cancer-cell-2017/), [Lead-Time Trajectory of CA19-9 as an Anchor Marker for Pancreatic Cancer Early Detection](https://onco.cc/key-papers/paper-fahrmann-ca19-9-lead-time-gastroenterology-2021/), [Pancreatic cancer early detection biomarkers for high-risk individuals: insights from the PRECEDE consortium](https://onco.cc/key-papers/paper-worthington-precede-early-detection-biomarkers-ijc-2026/)
- roadmaps: [Diagnostics roadmap: stains → gene panels → blood tests that decide treatment](https://onco.cc/roadmaps/diagnostics-roadmap/), [Drug discovery roadmap: screening in mice → maps of dependency → designing in silico](https://onco.cc/roadmaps/drug-discovery-roadmap/), [Early detection roadmap: organ screening → blood tests for many cancers](https://onco.cc/roadmaps/early-detection-roadmap/)
- collections: [CPTAC (Clinical Proteomic Tumor Analysis Consortium)](https://onco.cc/collections/cptac/), [Human Protein Atlas](https://onco.cc/collections/hpa/)
- technologies: [Proteomics instruments and affinity platforms](https://onco.cc/technologies/proteomics-platforms/), [Spatial-omics-guided treatment selection](https://onco.cc/technologies/spatial-omics-guided-therapy/)
- people: [Eric B. Haura](https://onco.cc/people/eric-haura/), [Li Ding](https://onco.cc/people/li-ding/), [Yi-Zhou Jiang](https://onco.cc/people/jiang-yi-zhou/)
- ideas: [A blood test for the pre-metastatic niche](https://onco.cc/ideas/idea-bio2-premetastatic-niche-assay/), [A commons for leftover trial biospecimens with standard access for approved research](https://onco.cc/ideas/idea-fund-trial-biospecimen-commons/), [A global rapid tissue donation network for metastatic disease](https://onco.cc/ideas/idea-bio2-rapid-autopsy-commons/), [A public biomarker validation utility with pre-diagnostic biobanks and blinded testing](https://onco.cc/ideas/idea-moon-biomarker-validation-utility/), [An open map of which cancer proteins any drug can stick to](https://onco.cc/ideas/idea-bio1-covalent-ligandability-atlas/), [Find E3 ligases that only tumours have, and build degraders around them](https://onco.cc/ideas/idea-bio1-tumour-restricted-e3-atlas/), [Find the parts of a tumour the drug never reaches](https://onco.cc/ideas/idea-bio1-drug-exposure-sanctuary-mapping/), [Keep a freshly removed tumour alive on a pump and test drugs in it](https://onco.cc/ideas/idea-bio1-ex-vivo-perfused-tumour/), [Screen glue-like compounds against every cancer cell line and publish it](https://onco.cc/ideas/idea-bio1-glue-degrader-atlas/), [Select cachexia trial patients by the hormone driving their wasting](https://onco.cc/ideas/idea-bio2-gdf15-stratified-enrolment/), [Shared splice-derived neoantigens as off-the-shelf vaccine targets](https://onco.cc/ideas/idea-splice-neoantigens/), [Time immunotherapy to the moment targeted drugs make tumours visible](https://onco.cc/ideas/idea-bio1-immunopeptidome-timing/)
- terms: [Deep mass-spectrometry proteome (CPTAC)](https://onco.cc/terms/mass-spec-proteome/), [mRNA to protein concordance](https://onco.cc/terms/mrna-protein-concordance/), [Pathway activation state (phosphosignalling)](https://onco.cc/terms/pathway-activation-state/), [Protein](https://onco.cc/terms/protein/), [Reverse-phase protein array (RPPA)](https://onco.cc/terms/rppa/)
- institutions: [EMBL's European Bioinformatics Institute](https://onco.cc/institutions/embl-ebi/), [Frederick National Laboratory for Cancer Research](https://onco.cc/institutions/frederick-national-lab/), [Uppsala University Hospital / Uppsala University](https://onco.cc/institutions/uppsala-akademiska/), [Weizmann Institute of Science](https://onco.cc/institutions/weizmann/)

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JSON: https://onco.cc/api/v1/entities/proteomics.json