{"entity":{"id":"mass-spec-proteome","kind":"term","name":"Deep mass-spectrometry proteome (CPTAC)","aka":["mass-spectrometry proteome","mass spectrometry proteomics","deep proteome","global proteome","MS proteomics","TMT proteomics","phospho-proteomics data"],"tldr":"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.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/Mass_spectrometry","links":[{"label":"CPTAC (NCI Office of Cancer Clinical Proteomics Research)","url":"https://proteomics.cancer.gov"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Mass_spectrometry"}],"tags":["cansim-terms"],"related":["cptac","cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":["proteomics","proteomics-platforms"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["rppa","mrna-protein-concordance","pathway-activation-state"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"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."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"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"},"category":"Biomarkers"},"route":"/terms/mass-spec-proteome/","neighbours":{"collection":[{"id":"cptac","kind":"collection","name":"CPTAC (Clinical Proteomic Tumor Analysis Consortium)","route":"/collections/cptac/"}],"term":[{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"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":"rppa","kind":"term","name":"Reverse-phase protein array (RPPA)","route":"/terms/rppa/"}],"technology":[{"id":"proteomics","kind":"technology","name":"Proteomics & phosphoproteomics","route":"/technologies/proteomics/"},{"id":"proteomics-platforms","kind":"technology","name":"Proteomics instruments and affinity platforms","route":"/technologies/proteomics-platforms/"}]}}