Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

Publications 1.3k Datasets 392.5k Experiments 15

System / cell line: proteomics ✕ Assay: density ✕ Clear

HUPO Highlights.

PMID 19862759 · PMC4594800 · Proteomics · 2009 · 8 claims · 8 setups

Full-text index only

Mass spectrometry analysis of human liver reference samples (French Reference liver + Huh7 hepatoma cells) achieves substantial human genome coverage via PeptideAtlas processing

liver subcellular models fetal mass antibody-based quantitative
Proteomics of the lysosome.

PMID 18977398 · PMC2684028 · Biochimica et biophysica acta · 2009 · 8 claims · 8 setups

Full-text index only

The mammalian lysosome has been shown to contain ~60 soluble luminal proteins and ~25 transmembrane proteins

liver placenta brain conditioned lc-ms n-terminal man6-p
Evolution of organelle-associated protein profiling.

PMID 19110081 · PMC2680700 · Journal of proteomics · 2009 · 8 claims · 8 setups

Full-text index only

Traditional biochemical organelle isolation followed by MS cataloguing suffers high false-positive rates because organelles cannot be purified to homogeneity and are structurally heterogeneous

golgi nuclear lipid clathrin-coated density qualitative silac
Tracheobronchial air-liquid interface cell culture: a model for innate mucosal defense of the upper airways?

PMID 18931053 · PMC2636953 · American journal of physiology. Lung cellular and molecular physiology · 2009 · 8 claims · 5 setups

Full-text index only

A mass spectrometry approach based on prior density-gradient separation of mucins from other proteins enables comprehensive identification of mucins in mucous secretions, overcoming underrepresentation in prior proteomic studies

tracheobronchial normal apical lc-ms isopycnic sds-page
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq).

PMID 33793824 · PMC8136920 · The Plant cell · 2021 · 8 claims · 6 setups

Has reproduction · 100

Grad-seq resolves complexes with overlapping subunits, such as CpcG1-type versus CpcL-type phycobilisomes or PsaK1 versus PsaK2 photosystem I (pre)complexes, validating the approach.

synechocystis gradient proteins grad-seq grad-seq denaturing sds-polyacrylamide
Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

PMID 17127212 · PMC5054077 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 6 setups

Full-text index only

GMFG is a cytokine-responsive protein in EPO-induced (erythroid) and G-CSF-induced (myeloid) hematopoietic lineage development

ac133+ excised e14 tissues 2-de lc-ms rt-pcr
Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.

PMID 17392682 · PMC2642915 · Molecular vision · 2007 · 8 claims · 8 setups

Full-text index only

MLF accumulation more closely reflects the onset of AMD than LF accumulation

donor arpe-19 mlf sucrose phototoxicity fluorescence
Proteomic profiling of human plasma exosomes identifies PPARgamma as an exosome-associated protein.

PMID 19028452 · PMC2633355 · Biochemical and biophysical research communications · 2009 · 7 claims · 6 setups

Full-text index only

Developed a multi-step fractionation scheme (gel exclusion chromatography, rate zonal sucrose gradient centrifugation, high-speed centrifugation) to purify exosomes from human plasma

plasma-derived plasma lc-ms sds-page western
LIMCH1-enriched extracellular vesicles promote vascular permeability in early-onset preeclampsia.

PMID 41604492 · PMC12851021 · Science advances · 2026 · 8 claims · 8 setups

Full-text index only

LIMCH1 is identified as an Eo-PE-associated EV protein via serum sEV proteomics combined with GEO placental transcriptome datasets

serum placenta jar huvecs lc-ms exoview nanoflow
A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

PMID 18414481 · PMC2387231 · Molecular systems biology · 2008 · 8 claims · 6 setups

Full-text index only

Comparing human mRNA co-expression with co-expression of orthologous gene pairs in five other organisms identifies proteins that physically associate

genes hela proteins worm co-expression quantitative functional
Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.

PMID 29921844 · PMC6008431 · Nature communications · 2018 · 8 claims · 8 setups

Has reproduction · 96

ID-seq combines DNA-tagged antibodies with high-throughput sequencing to enable large-scale, high-dimensional, multiplexed (phospho-)protein phenotyping in fixed cell populations across many samples in parallel.

epidermal id-seq immuno-pcr colony
ZAP targets aberrant mRNA transcripts encoding proteins with defective signal peptides for degradation.

PMID 41820617 · PMC13084044 · The EMBO journal · 2026 · 8 claims · 7 setups

Has reproduction · 50

ZAP (ZC3HAV1/PARP13) is a key component of the RAPP quality control pathway

k562 zap-s rt-qpcr western immunofluorescence
Neuroscience in the era of functional genomics and systems biology.

PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

Full-text index only

Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

developing hippocampus bac-transgenic fetal situ gene bac-transgenic
Temporal multiomics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation.

PMID 41545424 · PMC12920657 · Scientific data · 2026 · 8 claims · 8 setups

Full-text index only

Generated a high-resolution, time-resolved multi-omics dataset (RNA-seq, ribosome profiling, and quantitative proteomics) tracking mRNA, translation, and protein dynamics across hESC differentiation into definitive endoderm and polyhormonal pancreatic cells

hesc-derived rues2 extracted star-aligned rna-seq ribosome quantitative
Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death.

PMID 19889237 · PMC2783166 · BMC genomics · 2009 · 8 claims · 8 setups

Full-text index only

scNT-MUC exhibit complete occlusive thrombi and absence of columnar epithelial layers not seen in control or scNT-N umbilical cords

umbilical porcine puvec histology immunostaining real-time

Experiments

HUPO Highlights.

Proteomics of the lysosome.

Evolution of organelle-associated protein profiling.

Tracheobronchial air-liquid interface cell culture: a model for innate mucosal defense of the upper airways?

Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq).

Glia maturation factor gamma (GMFG): a cytokine-responsive protein during hematopoietic lineage development and its functional genomics analysis.

Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.

Proteomic profiling of human plasma exosomes identifies PPARgamma as an exosome-associated protein.

LIMCH1-enriched extracellular vesicles promote vascular permeability in early-onset preeclampsia.

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs.

Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.

ZAP targets aberrant mRNA transcripts encoding proteins with defective signal peptides for degradation.

Neuroscience in the era of functional genomics and systems biology.

Temporal multiomics gene expression data across human embryonic stem cell-derived polyhormonal cell differentiation.

Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death.