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 16

System / cell line: labeled ✕ Assay: page ✕ Clear

Tags for labeling protein N-termini with subtiligase for proteomics.

PMID 18762420 · PMC2590642 · Bioorganic & medicinal chemistry letters · 2008 · 6 claims · 4 setups

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Arginine-rich peptide esters (3, 4, 5) are markedly more soluble than the original TEVest2 ester (1) and give significantly higher N-terminal tagging of proteins by subtiligase at higher concentrations.

jurkat neutravidin-coated synthetic proteomic sds-page sandwich aqueous
Stable isotope labeling tandem mass spectrometry (SILT): integration with peptide identification and extension to data-dependent scans.

PMID 18774841 · PMC2707264 · Journal of proteome research · 2008 · 8 claims · 5 setups

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Using MS/MS ion intensities with stable isotope labeling (SILT) decreases the effects of contamination from unrelated co-eluting compounds compared to precursor ion intensity methods.

astrocytes hepg2 app695δnl labeled nano-lc sds-page immunoprecipitation
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

genomic ecotilling non-synonymous ecotilling sanger universal-primer
Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins.

PMID 18936059 · PMC2649815 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 5 setups

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DMOG pretreatment acts as a pharmacological 'substrate trap' that stabilizes transient FIH-substrate interactions, enabling their identification by SILAC-based proteomics

hek293 u2os 293t 293t-expressed co-immunoprecipitation silac-based co-immunoprecipitation-immunoblotting
A novel approach to tag and identify geranylgeranylated proteins.

PMID 19784953 · PMC2855049 · Electrophoresis · 2009 · 7 claims · 7 setups

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Metabolic incorporation of azido-GG alcohol followed by Cu(I)-catalyzed click reaction with TAMRA-alkyne selectively labels geranylgeranylated proteins for fluorescence detection

jurkat cos-7 mcf-7 embryonic metabolic comparative fractionation
Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.

PMID 16542425 · PMC1431555 · BMC cancer · 2006 · 8 claims · 5 setups

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ICAT tandem MS can identify and quantify differences in specific protein expression between NAF from tumor-bearing and disease-free breasts

paired icat-labeled spectra naf icat sds-page liquid
Intracellular sorting and targeting of melanosomal membrane proteins: identification of signals for sorting of the human brown locus protein, gp75.

PMID 7642699 · PMC2199968 · The Journal of cell biology · 1995 · 7 claims · 7 setups

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The 36-amino acid cytoplasmic tail of gp75 alone is sufficient to direct intracellular retention and targeting of chimeric CD8 proteins to the endosomal/lysosomal compartment in fibroblasts

melanoma sk-mel-19 immunoprecipitated coli immunofluorescence immunoelectron protease
Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

PMID 17303479 · PMC7105233 · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2007 · 5 claims · 5 setups

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Pre-fractionation of plasma with immuno-affinity depletion and anion-exchange chromatography prior to 2D-DIGE substantially increases the number of detectable protein spots compared with unfractionated plasma.

plasma excised fractionated 2d-dige multi-dimensional lc-ms
Mutational analysis of the preferential binding of human topoisomerase I to supercoiled DNA.

PMID 19740104 · PMC3107988 · The FEBS journal · 2009 · 8 claims · 4 setups

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Human topoisomerase I (topo70) does not dimerize either free in solution or when covalently bound to DNA, ruling out dimerization as the source of a second DNA binding site

gst-topo70 topo70 32p-labeled 3h-labeled gst gel 32p-labeled
Apolipoprotein A-IV, a putative satiety/antiatherogenic factor, rises after gastric bypass.

PMID 18948973 · PMC2627784 · Obesity (Silver Spring, Md.) · 2009 · 6 claims · 7 setups

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Apolipoprotein A-IV (apo A-IV) is significantly increased in fasting plasma after RYGBP compared to pre-operative levels

fasting plasma itraq-labeled subjects itraq immunoblot sds-page
Spatial separation and bidirectional trafficking of proteins using a multi-functional reporter.

PMID 18384686 · PMC2359743 · BMC cell biology · 2008 · 8 claims · 8 setups

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β1Int-HaloTag fusion protein localizes to the cell membrane in a pattern similar to endogenous β1 integrin, indicating the fusion does not disrupt normal integrin surface expression

hela hek293 live immunocytochemistry live fluorescence
The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern.

PMID 19908860 · PMC2787777 · Journal of the American Chemical Society · 2009 · 8 claims · 6 setups

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The full-length bcl-2 C-rich promoter sequence (Py39WT) forms one major intramolecular i-motif structure with a transitional pH of 6.6

py39wt fam 32p-labeled circular melting fret
Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells.

PMID 19834888 · PMC4302342 · Proteomics · 2009 · 7 claims · 7 setups

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BioCAT (biotin tagging + AACT) enables highly sensitive and accurate single-step screening of mammalian protein-protein interactions without establishing a stable cell line

293t standard nk92mi list western sds-page nanolc-ms
Application of proteomics methods for pathogen discovery.

PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

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Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

hlf sequences synthetic conventional 2d-dige gelc-ms
The cancer secretome: a reservoir of biomarkers.

PMID 18796163 · PMC2562990 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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Cancer secretome analysis is a promising reservoir for identifying novel, non-invasive cancer biomarkers, addressing limitations of whole blood/serum proteomics

a549 m-be sw480 neoplastic 2-de dige icat
Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

falciparum coli native falciparum-infected rt-pcr recombinant peptide

Experiments

Tags for labeling protein N-termini with subtiligase for proteomics.

Stable isotope labeling tandem mass spectrometry (SILT): integration with peptide identification and extension to data-dependent scans.

High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins.

A novel approach to tag and identify geranylgeranylated proteins.

Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.

Intracellular sorting and targeting of melanosomal membrane proteins: identification of signals for sorting of the human brown locus protein, gp75.

Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

Mutational analysis of the preferential binding of human topoisomerase I to supercoiled DNA.

Apolipoprotein A-IV, a putative satiety/antiatherogenic factor, rises after gastric bypass.

Spatial separation and bidirectional trafficking of proteins using a multi-functional reporter.

The i-motif in the bcl-2 P1 promoter forms an unexpectedly stable structure with a unique 8:5:7 loop folding pattern.

Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells.

Application of proteomics methods for pathogen discovery.

The cancer secretome: a reservoir of biomarkers.

Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.