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).

• Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

  PMID 18722006 · PMC2566540 · Cell · 2008 · 7 claims · 8 setups

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  A subtiligase-based N-terminal biotinylation and enrichment method enables global identification and sequencing of protease cleavage sites in complex mixtures

  jurkat computational immunoblotting structural protein-protein

• 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

• Determination of glycosylation sites and site-specific heterogeneity in glycoproteins.

  PMID 19700364 · PMC2749913 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Mass spectrometry has emerged as the premier tool for structural determination of oligosaccharides/glycans and glycopeptides

  glycoproteins n-linked serum complex maldi tryptic nonspecific

• High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

  PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups

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  High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.

  tuberculosis sanger spectra lc-ms sds-page signal

• From genomes to systems.

  PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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  Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

  serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr

• Global mapping of the topography and magnitude of proteolytic events in apoptosis.

  PMID 18724940 · PMC2597167 · Cell · 2008 · 7 claims · 6 setups

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  PROTOMAP, a method combining 1D SDS-PAGE fractionation with LC-MS/MS-derived sequence coverage and spectral counting visualized as 'peptographs', enables global mapping of proteolytic topography and magnitude

  jurkat sds-page fragmentation caspase-3

• Methods for the proteomic identification of protease substrates.

  PMID 19729334 · PMC2787889 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Gel-based methods (2D-DiGE, diagonal electrophoresis, PROTOMAP) identify protease substrates by comparing proteolyzed versus control samples via electrophoretic migration differences followed by MS identification

  lysate jurkat apoptotic yeast 2d-dige protomap cofradic

• Differential 14-3-3 affinity capture reveals new downstream targets of phosphatidylinositol 3-kinase signaling.

  PMID 19648646 · PMC2773716 · Molecular & cellular proteomics : MCP · 2009 · 7 claims · 6 setups

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  Four known insulin-regulated proteins (PFK-2, PRAS40, AS160, MYO1C) show high d0/d4 ratios, i.e. increased 14-3-3 binding upon insulin stimulation, validating the screen

  hek293 hela far-western quantitative tio2

• The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.

  PMID 35371105 · PMC8964954 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 50

  HCV E1E2 glycoproteins, and more so E2, down-modulate HIV-1 LTR activation in 293T, TZM-bl and Huh7 cells

  293t tzm-bl tzm-bl-e1e2 hiv-1 pseudo-typed transcriptomic