# Deep mass-spectrometry proteome (CPTAC)

Source: https://onco.cc/terms/mass-spec-proteome/  
OnCo record `mass-spec-proteome` (Term). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

Mass spectrometry weighs fragments of every protein in a sample to identify and quantify thousands of proteins and their phosphorylation sites, the closest measurement to what a cell is actually doing.

## Summary

Mass spectrometry measures the mass-to-charge ratio of ions and is used to identify molecules (Wikipedia); in proteomics, peptides from digested proteins are quantified, often with isobaric tags across samples. CPTAC applied this genome-scale proteomics and phosphoproteomics to TCGA-linked tumours through several processing centres, giving paired RNA and protein for about a thousand tumours. It is the reference for mRNA-protein concordance and the only route to phosphosite-level pathway activity.

## Fields

- Kind: Term
- Last checked: 2026-09-24
- Also known as: mass-spectrometry proteome; mass spectrometry proteomics; deep proteome; global proteome; MS proteomics; TMT proteomics; phospho-proteomics data
- Tags: cansim-terms

## Notes

- Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/deep-ms-proteome.

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/Mass_spectrometry
- CPTAC (NCI Office of Cancer Clinical Proteomics Research): https://proteomics.cancer.gov
- Wikipedia: https://en.wikipedia.org/wiki/Mass_spectrometry

## Connected records

- collections: [CPTAC (Clinical Proteomic Tumor Analysis Consortium)](https://onco.cc/collections/cptac/)
- terms: [Cancer AI vocabulary (CanSim terms map)](https://onco.cc/terms/cancer-ai-vocabulary/), [mRNA to protein concordance](https://onco.cc/terms/mrna-protein-concordance/), [Pathway activation state (phosphosignalling)](https://onco.cc/terms/pathway-activation-state/), [Reverse-phase protein array (RPPA)](https://onco.cc/terms/rppa/)
- technologies: [Proteomics & phosphoproteomics](https://onco.cc/technologies/proteomics/), [Proteomics instruments and affinity platforms](https://onco.cc/technologies/proteomics-platforms/)

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