Awesome Pan-Cancer Phosphoproteomics¶
Pan-cancer phosphoproteomics can identify thousands of sites — but without knowing which kinase, which pathway, and which drug, a catalog is not a map.
Mass spectrometry can now quantify over 100,000 phosphorylation sites across tumor types. Yet fewer than 5% of these sites have a known upstream kinase, and fewer than 3% have established functional roles. The gap between measurement and understanding defines this field.
This site is the companion to the awesome list. While the list provides a curated index of tools, databases, and studies, this site goes deeper — with concept explainers, method comparisons, paper analyses, and synthesis essays that connect the pieces.
The Central Problem¶
| What we can measure | What we know |
|---|---|
| ~240,000 human phosphosites cataloged | <5% have a known upstream kinase |
| 110,274 sites quantified across 10 CPTAC cancers | <3% have established functional roles |
| 518 kinases in the human kinome | 130+ kinases have zero known substrates |
The annotation bottleneck is not just a data problem — it shapes which biological questions can be asked and which therapeutic strategies can be pursued.
How This Site Is Organized¶
- Concepts — Phosphorylation biology, the kinase-substrate inference problem, and how phosphoproteomics complements genomics.
- Methods — Detailed guides for each tool category: identification, kinase inference, pathway reconstruction, functional scoring, pan-cancer integration, and therapeutic response.
- Deep Reads — Honest analyses of landmark papers.
- Benchmarks — The state of evaluation and what metrics actually matter.
- Datasets — Key datasets organized by what analyses they support.
- Timeline — Interactive literature timeline showing how the field evolved.
- Explorer — Interactive maps: a method taxonomy and a kinase-substrate-pathway-drug biology network.
- Synthesis — Cross-cutting essays on the annotation bottleneck and the path from phosphosites to signaling circuits.
- Glossary — Key terms and definitions.
Key Numbers¶
| Statistic | Value | Source |
|---|---|---|
| Human phosphosites cataloged | ~240,000 | PhosphoSitePlus |
| Sites with known upstream kinase | <5% | Community estimate |
| Sites with known function | <3% | Ochoa et al. 2020 |
| Ser/Thr kinases with motif data | 303 | KinaseLibrary (2023) |
| CPTAC cancer types profiled | 10+ | Geffen et al. 2023 |
| Kinase inhibitors FDA-approved | 70+ | As of 2024 |
| Phosphosites per typical experiment | 10,000–40,000 | DIA-NN / MaxQuant |