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 11

System / cell line: whole-cell ✕ Assay: proteomics ✕ Clear

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

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Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

gingivalis whole-cell comparative gene
A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

PMID 19997597 · PMC2781549 · PloS one · 2009 · 8 claims · 7 setups

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The majority of proteins expressed in growing and non-growing S. aureus cells can be identified and quantified by a metabolic labeling proteomic approach

aureus 2-d 1-d gelc-ms
Decision tree-driven tandem mass spectrometry for shotgun proteomics.

PMID 18931669 · PMC2597439 · Nature methods · 2008 · 8 claims · 5 setups

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A decision tree (DT) algorithm that selects CAD or ETD per precursor based on z and m/z yields more peptide identifications than either CAD or ETD alone

saccharomyces proteome embryonic nlc-ms phosphoproteomics sequential
Shotgun proteomics and biomarker discovery.

PMID 12364816 · PMC3851423 · Disease markers · 2002 · 8 claims · 7 setups

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Shotgun (LC/LC-MS/MS, e.g. MudPIT) proteomic approaches show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range.

urine yeast cysteine-containing hemoglobin 2d-ge lc-ms imac
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
Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains.

PMID 18560578 · PMC2409963 · PloS one · 2008 · 8 claims · 6 setups

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Ovarian cancer cells exhibit extensive shedding of extra-cellular domains from cell surface proteins into the extracellular milieu.

ovcar3 analysis lc-ms cell-surface silac
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
Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells.

PMID 17949499 · PMC2148065 · BMC genomics · 2007 · 8 claims · 8 setups

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ECM-stimulated hMSC and OS-media-stimulated hMSC represent two distinct intermediate/transitional phenotypes en route to becoming osteoblasts

naive hmsc osteoblasts proteomic lc-ms gene computational
Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

PMID 18654835 · PMC4973579 · Biogerontology · 2009 · 8 claims · 7 setups

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Treatment of HCA3 human diploid fibroblasts with a mild dose of H2O2 (600 μM) induces premature senescence without killing the cells.

hca3 differentially mudpit cdna semi-quantitative
Characterisation and protein expression profiling of annexins in colorectal cancer.

PMID 18071363 · PMC2361450 · British journal of cancer · 2008 · 7 claims · 5 setups

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Annexins A1, A2, A4 and A11 are overexpressed in primary colorectal cancer compared with normal colon

dukes colorectal immunised whole-cell gel immunohistochemistry elisa
Proteomic analysis of tumor necrosis factor-alpha resistant human breast cancer cells reveals a MEK5/Erk5-mediated epithelial-mesenchymal transition phenotype.

PMID 19087274 · PMC2656902 · Breast cancer research : BCR · 2008 · 8 claims · 7 setups

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MEK5 over-expression promotes a TNF-α resistance phenotype in MCF-7 breast cancer cells

mcf-7-mek5 mcf-7 western clonogenic immunofluorescence

Experiments

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.

Decision tree-driven tandem mass spectrometry for shotgun proteomics.

Shotgun proteomics and biomarker discovery.

Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains.

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

Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells.

Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

Characterisation and protein expression profiling of annexins in colorectal cancer.

Proteomic analysis of tumor necrosis factor-alpha resistant human breast cancer cells reveals a MEK5/Erk5-mediated epithelial-mesenchymal transition phenotype.