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 18

System / cell line: lysate ✕ Assay: gel ✕ Clear

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
Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers.

PMID 15502247 · PMC3839398 · Disease markers · 2004 · 8 claims · 8 setups

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Proteomics approaches (2D Western blot, protein microarray, multiplex ELISA) can identify tumor antigen-directed autoantibodies as candidate cancer biomarkers

lung pancreatic hepatocellular renal gel microarray multiplex
The effects of quercetin on SW480 human colon carcinoma cells: a proteomic study.

PMID 15748282 · PMC555539 · Nutrition journal · 2005 · 8 claims · 4 setups

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20 μM quercetin treatment of SW480 cells for 48 h consistently decreased expression of three proteins and increased expression of one protein across four independent experiments.

sw480 excised two-dimensional quantitative mass
Using proteomic approach to identify tumor-associated antigens as markers in hepatocellular carcinoma.

PMID 18672925 · PMC2680441 · Journal of proteome research · 2008 · 8 claims · 6 setups

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34 immunoreactive protein spots were detected in 2DE Western blots probed with HCC patient sera but not normal sera

hepg2 excised identified recombinant two-dimensional western in-gel
Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

PMID 19859549 · PMC2762604 · PloS one · 2009 · 8 claims · 8 setups

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A comprehensive platelet proteome of 1507 unique proteins was identified from ten independent human platelet samples, the most comprehensive platelet proteome assembled to date

platelets platelet anti-coagulated lc-ms phospho-proteomic membrane
Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells and the dendritic cell-like KG-1 cells reveals distinct characteristics.

PMID 17331236 · PMC1868942 · Genome biology · 2007 · 8 claims · 8 setups

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moDCs and KG-1 cells show significant proteomic differences from primary mDCs, particularly in proteins involved in cell growth/maintenance and cell-cell interaction/integrity.

mdcs mdc freshly peripheral two-dimensional maldi-tof capture
The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.

PMID 18798661 · PMC2746028 · Journal of proteome research · 2008 · 8 claims · 7 setups

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Over half of confidently identified peptides in complex mixtures have S/N ratios below 10 on both FT-ICR and Orbitrap instruments

jurkat silac-based sds-page database
Proteomic surveillance of retinal autoantigens in endogenous uveitis: implication of esterase D and brain-type creatine kinase as novel autoantigens.

PMID 18552983 · PMC2426731 · Molecular vision · 2008 · 7 claims · 6 setups

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Six novel candidate retinal autoantigens (β-actin, esterase D, tubulin β-2, brain-type creatine kinase, VDAC, aspartate aminotransferase) were identified by 2D-WB and mass spectrometry in EAU mice

c57bl retinal recombinant eau two-dimensional maldi-tof one-dimensional
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
Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

PMID 15626334 · PMC5172349 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 5 setups

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Well-resolved, reproducible 2-DE profiles of human lung squamous carcinoma and normal bronchial epithelial tissues were obtained under optimized conditions (0.75-mg protein load, TCA precipitation)

lung scanned excised peptide 2-d 2-de maldi-tof-ms
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
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
Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups

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E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.

e2348 hep-2 blast colony transformation
Point mutations in GLI3 lead to misregulation of its subcellular localization.

PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

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The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

hela immunofluorescence real-time luciferase
Expression patterns of cardiac myofilament proteins: genomic and protein analysis of surgical myectomy tissue from patients with obstructive hypertrophic cardiomyopathy.

PMID 19808356 · PMC2765062 · Circulation. Heart failure · 2009 · 8 claims · 4 setups

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Myofilament protein levels (MYBPC3 and MYH7) are increased, not decreased, in HCM patients carrying a mutation in either gene compared to healthy heart tissue

genomic lysate formalin-fixed myectomy mutational western immunohistochemistry
IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

PMID 19752006 · PMC2808259 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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IDEAL-Q predicts the elution time of peptides unidentified in a given LC-MS/MS run (but identified in others) using a computation-efficient linear regression plus fragmental refining function, avoiding costly whole-dataset pattern recognition

standard thp-1 replicate lc-ms manual cross-instrument
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
Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

placenta five lines huh7 5'-race rt-pcr real-time

Experiments

Methods for the proteomic identification of protease substrates.

Proteomics approaches to identify tumor antigen directed autoantibodies as cancer biomarkers.

The effects of quercetin on SW480 human colon carcinoma cells: a proteomic study.

Using proteomic approach to identify tumor-associated antigens as markers in hepatocellular carcinoma.

Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells and the dendritic cell-like KG-1 cells reveals distinct characteristics.

The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.

Proteomic surveillance of retinal autoantigens in endogenous uveitis: implication of esterase D and brain-type creatine kinase as novel autoantigens.

Application of proteomics methods for pathogen discovery.

Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

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

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

Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

Point mutations in GLI3 lead to misregulation of its subcellular localization.

Expression patterns of cardiac myofilament proteins: genomic and protein analysis of surgical myectomy tissue from patients with obstructive hypertrophic cardiomyopathy.

IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

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.

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.