Complete proteonomics databases publicly available
Executive summary
There is no single publicly available database that contains a definitively "complete" proteome; instead, a network of public repositories and curated resources collectively host mass-spectrometry identifications, expression atlases, PTM maps and proteome annotations that researchers stitch together for near‑comprehensive coverage [1] [2]. Major public resources—PRIDE, PeptideAtlas, MassIVE, ProteomicsDB, UniProt/neXtProt and coordinated portals such as ProteomeXchange and ProteomeCentral—offer complementary datasets and standards but explicitly acknowledge that no one resource fits every use case [3] [4] [5] [6] [7] [8].
1. The ecosystem, not a monolith: public repositories that matter
Public proteomics is an ecosystem of repositories rather than a single monolithic database: PRIDE functions as a core public repository for peptide and protein identifications and PTM evidence [3] [9], PeptideAtlas and MassIVE host extensive spectral and reanalysis resources [1], and ProteomicsDB provides multi‑omics, multi‑organism visualizations and analytics for human and model organisms [4]. Specialized portals such as the NCI Proteomic Data Commons / Office of Cancer Clinical Proteomics Research Data Portal house cancer proteogenomic datasets, while other domain‑specific databases (e.g., saliva, mitochondrial, CHO cell proteomes) fill niche needs [10] [11].
2. Coordination by ProteomeXchange: creating a single submission front door, not a single database
ProteomeXchange and its ProteomeCentral front end were created to standardize submissions and make datasets findable across multiple repositories—PRIDE, PeptideAtlas, MassIVE, jPOST, iProX and Panorama Public are formal members—so users can track identifiers and reuse data, but the output remains distributed across member sites rather than consolidated into a single “complete” file [12] [2] [7].
3. What “complete proteome” means — evidence levels, PTMs and contexts
Claims of a “complete human proteome” are complicated by definitions: sequence existence (cataloged in UniProt/neXtProt), experimental peptide evidence (as archived in PRIDE, PeptideAtlas and MassIVE), and functional/post‑translational annotation (in resources referenced from repositories) are all distinct layers, and repositories report different evidence types and confidence metrics rather than one unified completeness score [5] [6] [1].
4. Complementarity and limits: why one database can’t serve all researchers
The literature and repository teams themselves acknowledge complementarity and limits—no single proteomics resource is ideally suited to every application; repositories differ in focus (shotgun vs targeted datasets), supported metadata standards, and analytical tools, so researchers must combine resources for comprehensive coverage [8] [1].
5. Practical reality: how researchers assemble a near‑complete view
In practice, scientists compile sequence and functional annotations from UniProt/neXtProt, experimental identifications and raw spectra from PRIDE/MassIVE/PeptideAtlas, and curated analytics from ProteomicsDB or domain portals, using ProteomeXchange identifiers and ProteomeCentral to crosswalk datasets and reuse public spectra and PTM catalogs [5] [3] [4] [7] [12].
6. Competing priorities and implicit agendas in the public data world
Open repositories and consortiums promote FAIR data and reuse, but institutional priorities (e.g., cancer data curation at NCI portals, regional members like jPOST/iProX) influence which datasets are emphasized and supported; repositories also balance incentives for data deposit with differing curation resources, creating uneven coverage across organisms, tissues and PTM types [10] [2] [12].
7. Bottom line for users seeking a “complete” proteomics database
A truly complete, single‑file public proteomics database does not exist in the available reporting; instead, researchers rely on a federation of public, interoperable resources—PRIDE, PeptideAtlas, MassIVE, ProteomicsDB, UniProt/neXtProt and others—coordinated by ProteomeXchange and ProteomeCentral to reach near‑comprehensive, evidence‑layered proteome coverage while accepting domain‑specific gaps and varying confidence metrics [3] [1] [4] [5] [2] [7].