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 41

System / cell line: fractions ✕ Assay: fractionation ✕ Clear

Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics.

PMID 12213833 · PMC2173151 · The Journal of cell biology · 2002 · 8 claims · 8 setups

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Subcellular proteomics of purified CCVs identifies enthoprotin (encoded by KIAA0171), a novel ENTH domain-containing protein not previously detected at the protein level.

brain cos-7 hek-293 clathrin subcellular western ccv
A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.

PMID 20026476 · PMC2849709 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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A SILAC-based 'spatial proteomics' method can quantitatively measure the relative subcellular distribution of thousands of proteins across cytoplasm, nucleus, and nucleolus.

hct116 silac silac-based immunofluorescence
Comparative proteomics of clathrin-coated vesicles.

PMID 17116749 · PMC2064594 · The Journal of cell biology · 2006 · 8 claims · 4 setups

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A comparative proteomics strategy contrasting CCV fractions from control and clathrin-depleted (CHC siRNA knockdown) HeLa cells can distinguish genuine CCV proteins from copurifying contaminants

hela western sds-page difference
iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.

PMID 19674965 · PMC2773724 · Molecular & cellular proteomics : MCP · 2009 · 6 claims · 5 setups

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Serial transplantation of human GBM xenografts in nude rats converts an initially highly infiltrative, non-angiogenic phenotype into a highly angiogenic phenotype over 4-6 generations.

membrane-enriched xenograft homogenate quantified itraq western bradford
The development of an integrated platform to identify breast cancer glycoproteome changes in human serum.

PMID 19782370 · PMC4142217 · Journal of chromatography. A · 2010 · 8 claims · 6 setups

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M-LAC (multi-lectin affinity chromatography combining Con A, WGA and Jacalin) provides comprehensive capture of glycoproteins from biological fluids based on differing glycan specificities

pooled m-lac excised individual high-performance sds-page lectin
Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome.

PMID 19722698 · PMC2783519 · Journal of proteome research · 2009 · 7 claims · 6 setups

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Tandem IgY7-SuperMix separation nearly doubles overall proteome coverage compared to IgY7 flow-through alone (523 vs 263 confidently identified proteins)

plasma identified lc-ms sds-page spike-in
7SL RNA and signal recognition particle orchestrate a global cellular response to acute thermal stress.

PMID 39952919 · PMC11828898 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 93

Heat shock induces de novo transcription and nuclear accumulation of 7SL RNA together with SRP proteins, which then bind chromatin at promoters

embryonic nih3t3 pro-seq fractionation fluorescence
Sediment Resuspension as a System-Wide Driver of Legacy and Bioavailable Phosphorus Release in Lake Erie.

PMID 41960750 · PMC13130958 · Environmental science & technology · 2026 · 7 claims · 8 setups

Has reproduction · 90

Sediment resuspension is a major episodic internal phosphorus source releasing bioavailable P far exceeding previously reported aerobic diffusive fluxes.

western sediment lake great sediment sequential beryllium-7
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

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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
Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

PMID 18212748 · PMC2243141 · British journal of cancer · 2008 · 5 claims · 6 setups

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LC-MS/MS proteomic analysis of stage I lung adenocarcinoma specimens identified myosin IIA and vimentin as candidate biomarker proteins with signal intensities that differed significantly among patient outcome groups

surgically tryptic set lysates lc-ms mascot immunohistochemistry
H-DBAS: human-transcriptome database for alternative splicing: update 2010.

PMID 19969536 · PMC2808982 · Nucleic acids research · 2010 · 8 claims · 4 setups

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RNA-Seq tags from the polysome fraction identify AS exons that are very likely used for protein synthesis

dld-1 rna-seq western real-time
Use of proteomics for validation of the isolation process of clotting factor IX from human plasma.

PMID 19819359 · PMC2818390 · Journal of proteomics · 2010 · 8 claims · 8 setups

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Proteomic techniques (LC-MS/MS, iTRAQ, immunochemical/biochemical methods) can monitor and validate each production step of pd F IX isolation

plasma in-process chromatographic one-stage competitive elisa
RNA structure maps across mammalian cellular compartments.

PMID 30886404 · PMC6640855 · Nature structural & molecular biology · 2019 · 8 claims · 6 setups

Has reproduction · 45

icSHAPE-based cytotopic RNA structuromes across chromatin, nucleoplasm and cytoplasm in human and mouse cells substantially expand the scope of RNA structural information beyond whole-cell data.

v6.5 mes icshape rt-qpcr western
Proteomic analysis of the mammalian nuclear pore complex.

PMID 12196509 · PMC2173148 · The Journal of cell biology · 2002 · 8 claims · 7 setups

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Mass spectrometry was used to identify all proteins present in a biochemically purified rat liver NPC fraction.

liver empigen transiently mass sds-page electron
Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

PMID 16162288 · PMC1261261 · BMC genomics · 2005 · 8 claims · 5 setups

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A novel rTS protein isoform, rTSγ, exists with a 27-residue longer N-terminus generated from an alternative upstream start codon relative to rTSβ.

rts rtsβ ccrf-cem comparative mitochondrial subcellular
Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

PMID 17124346 · PMC3862287 · Disease markers · 2006 · 8 claims · 5 setups

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SELDI-TOF MS serum profiling can discriminate MM patients with vs without skeletal (bone lesion) involvement using peak biomarkers

serum seldi seldi-tof serum univariate
Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

PMID 18267298 · PMC5054205 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 5 setups

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Out of 20 amino acids, the metabolic pathways of 17 utilize mitochondrial enzymes, and dysfunction of these enzymes causes over 40 known human mitochondrial diseases/disorders

mitoproteome orthologous liver mitochondrial sequence-based computational literature
Glycomic approach for potential biomarkers on prostate cancer: profiling of N-linked glycans in human sera and pRNS cell lines.

PMID 19126968 · PMC3827814 · Disease markers · 2008 · 8 claims · 5 setups

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Glycomic profiling of N-linked glycans in serum can reveal potential biomarkers distinguishing prostate cancer patients from controls

serum prns-1-1 n-linked maldi solid tandem
A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion
Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry

Experiments

Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics.

A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.

Comparative proteomics of clathrin-coated vesicles.

iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype.

The development of an integrated platform to identify breast cancer glycoproteome changes in human serum.

Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome.

7SL RNA and signal recognition particle orchestrate a global cellular response to acute thermal stress.

Sediment Resuspension as a System-Wide Driver of Legacy and Bioavailable Phosphorus Release in Lake Erie.

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

Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

H-DBAS: human-transcriptome database for alternative splicing: update 2010.

Use of proteomics for validation of the isolation process of clotting factor IX from human plasma.

RNA structure maps across mammalian cellular compartments.

Proteomic analysis of the mammalian nuclear pore complex.

Comparative genomic analysis reveals a novel mitochondrial isoform of human rTS protein and unusual phylogenetic distribution of the rTS gene.

Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

Glycomic approach for potential biomarkers on prostate cancer: profiling of N-linked glycans in human sera and pRNS cell lines.

A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.