ArticleProteomics2015
Version 4.0 of PaxDb: Protein abundance data, integrated across model organisms, tissues, and cell-lines.
Article in Proteomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 329 papers, 4 of them syntheses that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
329 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- (Re)defining the human chromatome: an integrated meta-analysis of localization, function, abundance, physical properties, and domain composition of chromatin proteins.Nucleic acids research · 2026Pooled it
- Mapping protein states and interactions across the tree of life with co-fractionation mass spectrometry.Nature communications · 2023Pooled it
- Shift of the insoluble content of the proteome in the aging mouse brain.Proceedings of the National Academy of Sciences of the United States of America · 2023Pooled it
- Meta-analysis defines principles for the design and analysis of co-fractionation mass spectrometry experiments.Nature methods · 2021Pooled it
- CA-IV-directed small-molecule shuttle enables targeted brain delivery of biologics.Nature chemical biology · 2026Article
- The genetic code at the balance point of error and demand.PLoS computational biology · 2026Article
- A pooled image-based CRISPR screen identifies EAF1 as abioRxiv : the preprint server for biology · 2026Article
- Cytosolic PRDX1 acts as an extramitochondrial sink to set mitochondrial HRedox biology · 2026Article
- Translation efficiency covariation identifies conserved coordination patterns across cell types.Nature biotechnology · 2026Article
- The complexome contextualizes proteomics data to fingerprint biological states and highlight perturbed functional modules in disease.NPJ systems biology and applications · 2026Article
- Multi-omic mapping of Drosophila protein secretomes reveals tissue-specific origins and inter-organ trafficking.Nature communications · 2026Article
- Data-Independent Acquisition (DIA) Strategy for Measuring Protein Stability Using Stability of Proteins from Rates of Oxidation (SPROX).Journal of the American Society for Mass Spectrometry · 2026Article
- Pan-cancer analysis reveals differential PERK expression across tumour types and its potential as a therapeutic target.Discover oncology · 2026Article
- Article
- Pathological frataxin deficiency in mice causes tissue-specific alterations in iron homeostasis.iScience · 2026Article
- Evolutionary bioenergetics of sporulation.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Beyond olfaction: New insights into human odorant binding proteins.Protein science : a publication of the Protein Society · 2026Review
- Profiling Glycoproteins Enriched by Multinanoparticle Protein Corona.Analytical chemistry · 2026Article
- Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.The journal of physical chemistry. B · 2026Article
- PaxDb v6.0: reprocessed, LLM-selected, curated protein abundance data across organisms.Nucleic acids research · 2026Article
269 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein quantification at proteome-wide scale is an important aim, enabling insights into fundamental cellular biology and serving to constrain experiments and theoretical models. While proteome-wide quantification is not yet fully routine, many datasets approaching proteome-wide coverage are becoming available through biophysical and MS techniques. Data of this type can be accessed via a variety of sources, including publication supplements and online data repositories. However, access to the data is still fragmentary, and comparisons across experiments and organisms are not straightforward. Here, we describe recent updates to our database resource "PaxDb" (Protein Abundances Across Organisms). PaxDb focuses on protein abundance information at proteome-wide scope, irrespective of the underlying measurement technique. Quantification data is reprocessed, unified, and quality-scored, and then integrated to build a meta-resource. PaxDb also allows evolutionary comparisons through precomputed gene orthology relations. Recently, we have expanded the scope of the database to include cell-line samples, and more systematically scan the literature for suitable datasets. We report that a significant fraction of published experiments cannot readily be accessed and/or parsed for quantitative information, requiring additional steps and efforts. The current update brings PaxDb to 414 datasets in 53 organisms, with (semi-) quantitative abundance information covering more than 300,000 proteins.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.