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 25

System / cell line: proteins ✕ Assay: peak ✕ Clear

Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups

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DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)

standard dsic-labeled immunodepleted serum labeling quantitative in-solution
Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.

PMID 17166507 · PMC7094463 · Journal of chromatography. A · 2007 · 8 claims · 8 setups

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Standardizing sample preparation procedures for serum/plasma profiling is critical for obtaining reliable biomarkers, since slight procedural changes can produce very different protein profiles.

serum aqueous maldi-tof seldi-tof peak
Adipose proteome analysis: focus on mediators of insulin resistance.

PMID 19086862 · PMC2651673 · Expert review of proteomics · 2008 · 8 claims · 5 setups

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Ectopic lipid accumulation in liver and muscle, resulting from impaired adipose tissue lipid-storage capacity, is more directly associated with insulin resistance than adipose tissue mass itself.

3t3-l1 adipose visceral 35s-radiolabeling gel seldi-tof
Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups

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A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity

serum hplc-purified trypsin-digested crude seldi-tof-ms solid-phase maldi-tof-ms
Systems biology and the host response to viral infection.

PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

lung cd4 rhesus kshv microarray quantitative genomic
Multidimensional proteomics analysis of amniotic fluid to provide insight into the mechanisms of idiopathic preterm birth.

PMID 18431506 · PMC2315798 · PloS one · 2008 · 7 claims · 7 setups

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A novel 5-peak SELDI proteomic signature (Q-profile) in the 10-12.5 kDa mass range identifies a subgroup of women at risk for preterm birth without intra-amniotic inflammation or bleeding.

amniotic excised spot differentially seldi-tof fluorescence robotic
Improved methods for the enrichment and analysis of glycated peptides.

PMID 18989935 · PMC2752342 · Analytical chemistry · 2008 · 7 claims · 4 setups

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Replacing off-line desalting with an online 50 mM NH4OAc wash (10 min) of boronate-bound glycated proteins improves the enrichment workflow while minimizing sample loss

glucose-glycated tryptic glycated lc-ms boronate lc-etd-ms database
Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups

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HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162

monocyte-derived mdm mdms western p24 seldi-tof sds-page
Biomarker discovery in neurodegenerative diseases: a proteomic approach.

PMID 18938247 · PMC2939006 · Neurobiology of disease · 2009 · 6 claims · 8 setups

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Proteomic profiling of CSF and plasma can identify candidate protein biomarkers that distinguish AD patients from controls with high sensitivity and specificity

csf plasma brain 2-dge lc-ms seldi-tof-ms
Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

PMID 18922787 · PMC3523710 · Science signaling · 2008 · 8 claims · 8 setups

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VILIP1 was identified via a proteomic (GST pull-down) approach as a protein interacting with the P2X2 receptor C-terminal tail

brain hek gst co-immunoprecipitation immunocytochemistry
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
The synovial proteome: analysis of fibroblast-like synoviocytes.

PMID 15059280 · PMC400437 · Arthritis research & therapy · 2004 · 7 claims · 5 setups

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2D-PAGE combined with MALDI mass spectrometry can characterize the FLS cellular proteome with high confidence

fibroblast-like excised fls computational 2d-page in-gel maldi
Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

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The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

sequence genes proteins sequences snp interspecies sequence
Induction of calcification by serum depletion in cell culture: a model for focal calcification in aortas related to atherosclerosis.

PMID 18230165 · PMC2248577 · Lipids in health and disease · 2008 · 8 claims · 8 setups

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Serum depletion induces calcification (mineral Ca/P deposition) in rabbit aortic smooth muscle cell culture

rabbit calcifying alizarin fourier-transform dose-response
High-throughput genomic technology in research and clinical management of breast cancer. Plasma-based proteomics in early detection and therapy.

PMID 17184556 · PMC1797031 · Breast cancer research : BCR · 2006 · 8 claims · 8 setups

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Plasma is well suited to proteomic biomarker discovery because it is easily obtained, routinely used diagnostically, and has a rich proteome.

plasma serum maldi-tof seldi-tof tandem
Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.

PMID 19121650 · PMC2706936 · Journal of proteomics · 2009 · 7 claims · 5 setups

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A new MRM worksheet was implemented in The Global Proteome Machine database (GPMDB) that provides all information needed to design MRM transitions based solely on archived observations from previous experiments by other researchers.

platelet proteins reaction midas mrm
Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

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PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

porcine paec umbilical huvec methyltransferase sds-page fragmentation
Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

PMID 19930686 · PMC3091328 · Genome biology · 2009 · 8 claims · 6 setups

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The human mitochondrial proteome expanded via two prevailing gene duplication modes: intra-mitochondrial and inter-compartmental duplication

cerevisiae mitocarta mitochondrial tissues comparative subcellular gene
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
PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.

PMID 34093998 · PMC8142020 · Computational and structural biotechnology journal · 2021 · 7 claims · 8 setups

Has reproduction · 77

PredTAD, a Gradient Boosting Machine model using epigenomic and genomic features plus neighboring-bin information, classifies 10 kb genomic regions as TAD boundary or non-boundary across normal and breast cancer cell lines.

mcf10a t47d gm12878 mcf7 hi-c chip-seq atac-seq

Experiments

Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.

Adipose proteome analysis: focus on mediators of insulin resistance.

Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

Systems biology and the host response to viral infection.

Multidimensional proteomics analysis of amniotic fluid to provide insight into the mechanisms of idiopathic preterm birth.

Improved methods for the enrichment and analysis of glycated peptides.

Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

Biomarker discovery in neurodegenerative diseases: a proteomic approach.

Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

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.

The synovial proteome: analysis of fibroblast-like synoviocytes.

Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

Induction of calcification by serum depletion in cell culture: a model for focal calcification in aortas related to atherosclerosis.

High-throughput genomic technology in research and clinical management of breast cancer. Plasma-based proteomics in early detection and therapy.

Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.

Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

Expansion of the human mitochondrial proteome by intra- and inter-compartmental protein duplication.

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

PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines.