#35 · Tools & infrastructure
Proteomics resources advance FAIR data sharing and reprocessed protein abundance
The dominant thread is the maintenance of shared proteomics infrastructure: reference proteome annotation, reprocessed abundance compendia, and open data standards. The HUPO HPP 2025 report places 19,435 proteins in the reference proteome, with 93.6% detected and 5,562 proteins now carrying FE1 function-level assignments. PaxDb v6.0 reprocesses 1639 public MS datasets from 392 species through a standardized FragPipe pipeline, adding metadata, orthology mappings, and LLM-assisted curation. The ProteomeXchange consortium frames its 2026 contribution around making proteomics data FAIR, while Expression Atlas 2026 reports over 4500 studies across 67 species with expanded proteomics content. A spotted hyena study is less directly aligned: it benchmarks three draft genomes and a Trinity transcriptome for database searches, with 2022-Shao performing best, which bears on database construction for non-model organisms.
Published papers
MouseOmics: a multi-omics database for mouse biological study.
MouseOmics is a web database integrating 21 Mus genomes, transcriptomes, proteomes, metabolomes, metallomes and variomes across 52 inbred strains, with…
International Mouse Phenotyping Consortium Portal: facilitating investigation of gene function and providing insights into human disease.
Cloud-native rebuild of the IMPC mouse phenotype portal; DR23.0 holds >100M data points for 9277 genes, with new API tools.
The mouse Gene Expression Database (GXD): 2026 update.
Update to the Gene Expression Database (GXD), a curated mouse resource adding bulk RNA-Seq data, cell-type-specific expression search, and improved RNA-Seq…
Topic history
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