ArticleJournal of proteome research2014
State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project.
Article in Journal of proteome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
54 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Salivary and pellicle proteome: A datamining analysis.Scientific reports · 2016Pooled it
- Circulating Neutrophils Exhibit an Altered Immune Response in Chronic LUTS: An Image-Based Deep Learning Analysis.International urogynecology journal · 2026Article
- Abnormalities of IL-12 Family Cytokine Pathways in Autosomal Dominant Polycystic Kidney Disease Progression.Medicina (Kaunas, Lithuania) · 2024Article
- On the Roles of Protein Intrinsic Disorder in the Origin of Life and Evolution.Life (Basel, Switzerland) · 2024Review
- MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search.Journal of proteome research · 2023Article
- Pathway Analysis for Cancer Research and Precision Oncology Applications.Advances in experimental medicine and biology · 2022Article
- Advances and Utility of the Human Plasma Proteome.Journal of proteome research · 2021Review
- A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer.Frontiers in medicine · 2021Article
- Zooming into the Dark Side of Human Annexin-S100 Complexes: Dynamic Alliance of Flexible Partners.International journal of molecular sciences · 2020Review
- Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era.Plants (Basel, Switzerland) · 2020Review
- New technologies to analyse protein function: an intrinsic disorder perspective.F1000Research · 2020Review
- Multi-functionality of proteins involved in GPCR and G protein signaling: making sense of structure-function continuum with intrinsic disorder-based proteoforms.Cellular and molecular life sciences : CMLS · 2019Review
- The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins.The Journal of membrane biology · 2019Review
- Review
- Intrinsic Disorder and Posttranslational Modifications: The Darker Side of the Biological Dark Matter.Frontiers in genetics · 2018Review
- The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.Journal of proteome research · 2017Article
- Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins.Oncotarget · 2017Article
- Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry.Nature protocols · 2017Article
- A comprehensive analysis and annotation of human normal urinary proteome.Scientific reports · 2017Article
- The PeptideAtlas of the Domestic Laying Hen.Journal of proteome research · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
The kidney, urine, and plasma proteomes are intimately related: proteins and metabolic waste products are filtered from the plasma by the kidney and excreted via the urine, while kidney proteins may be secreted into the circulation or released into the urine. Shotgun proteomics data sets derived from human kidney, urine, and plasma samples were collated and processed using a uniform software pipeline, and relative protein abundances were estimated by spectral counting. The resulting PeptideAtlas builds yielded 4005, 2491, and 3553 nonredundant proteins at 1% FDR for the kidney, urine, and plasma proteomes, respectively - for kidney and plasma, the largest high-confidence protein sets to date. The same pipeline applied to all available human data yielded a 2013 Human PeptideAtlas build containing 12,644 nonredundant proteins and at least one peptide for each of ∼14,000 Swiss-Prot entries, an increase over 2012 of ∼7.5% of the predicted human proteome. We demonstrate that abundances are correlated between plasma and urine, examine the most abundant urine proteins not derived from either plasma or kidney, and consider the biomarker potential of proteins associated with renal decline. This analysis forms part of the Biology and Disease-driven Human Proteome Project (B/D-HPP) and is a contribution to the Chromosome-centric Human Proteome Project (C-HPP) special issue.
Indexed as
Identifiers
What OpenQuestion holds
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.