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 41

System / cell line: analysis ✕ Assay: maldi-tof ✕ Clear

Comparative proteomic analysis of cell lines and scrapings of the human intestinal epithelium.

PMID 17407598 · PMC1852558 · BMC genomics · 2007 · 8 claims · 7 setups

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Global protein expression profiles of cultured intestinal epithelial cell lines differ from those of intestinal epithelial scrapings in vivo

caco-2 ht-29 hep muscle 2-d 2-de principal
Proteomic analysis of serum in lung cancer induced by 3-methylcholanthrene.

PMID 19794824 · PMC2753780 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 4 setups

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141 protein spots are differentially expressed between normal rat sera and MCA-induced lung cancer rat sera (82 overexpressed, 59 underexpressed)

serum lung excised two-dimensional maldi-tof-ms histopathology
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
Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

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A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

inhbb cloned same fresh-frozen rnase masscleave clonal
Identification of two late acyltransferase genes responsible for lipid A biosynthesis in Moraxella catarrhalis.

PMID 18795947 · PMC2585779 · The FEBS journal · 2008 · 8 claims · 8 setups

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Two late acyltransferase genes, lpxX and lpxL, were identified in M. catarrhalis O35E by informatics analysis of the partial genome sequence

lipid proteinase catarrhalis suspensions maldi-tof fatty sds-page
MALDI profiling of human lung cancer subtypes.

PMID 19890392 · PMC2767501 · PloS one · 2009 · 8 claims · 8 setups

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PIMAC/MALDI-TOF peptide profiles combined with classification models can distinguish normal lung from tumor and differentiate NSCLC histological subtypes

lung tryptic peak ffpe maldi-tof parallel stepwise
Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

PMID 19763266 · PMC2740864 · PloS one · 2009 · 8 claims · 8 setups

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Androgen treatment alters the whole-cell proteome of LNCaP prostate cancer cells

lncap androgen prostate itraq mudpit immunoblot
Protein expression patterns in primary carcinoma of the vagina.

PMID 15199389 · PMC2409807 · British journal of cancer · 2004 · 5 claims · 4 setups

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Cluster analysis of 2-DE proteomic data allows accurate discrimination between normal vaginal mucosa, primary vaginal carcinoma and primary cervical carcinoma

fresh-frozen excised normal same two-dimensional matrix-assisted hierarchical
Comparative proteome analysis of breast cancer and adjacent normal breast tissues in human.

PMID 17127214 · PMC5054074 · Genomics, proteomics & bioinformatics · 2006 · 8 claims · 7 setups

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15 differential protein spots were detected in 11 of 12 (91.7%) breast cancer tissue samples compared with adjacent normal tissue

breast spots 2d-page stained sds-page 2d-page maldi-tof
Detection of venous thromboembolism by proteomic serum biomarkers.

PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups

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A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays

serum anova-selected citrated depleted direct artificial d-dimer
VEGF, FGF1, FGF2 and EGF gene polymorphisms and psoriatic arthritis.

PMID 17204151 · PMC1781940 · BMC musculoskeletal disorders · 2007 · 7 claims · 5 setups

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The T allele of VEGF +936 (rs3025039) is significantly less frequent in PsA cases than in controls, suggesting a protective effect against PsA.

blood same subject psa snp allele hardy-weinberg
93rd Annual Meeting of the American Association for Cancer Research, San Francisco, CA, USA, 6-10 April 2002.

PMID 12100742 · PMC138737 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

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Serial analysis of gene expression identifies genes preferentially expressed in ductal carcinoma in situ

breast laser serum bladder cdna western seldi-tof
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
KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

PMID 19094223 · PMC2646283 · Genome biology · 2008 · 8 claims · 8 setups

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KEGG spider, using a global 'pathway-free' metabolic network framework, provides deeper insight into metabolism variations than existing enrichment-based methods.

diffuse-type liver renal anaplastic differential proteomic proteomics
A protein-based set of reference markers for liver tissues and hepatocellular carcinoma.

PMID 19725976 · PMC2742551 · BMC cancer · 2009 · 7 claims · 5 setups

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Three protein spots (beta-actin, HSP60, PDI) show low expression variability across tumourous, non-tumourous cirrhotic, and normal liver tissues by 2-DE (ANOVA p>0.99 ranking)

liver 2-de western immunohistochemistry
A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data.

PMID 19681055 · PMC2782493 · Proteomics · 2009 · 8 claims · 2 setups

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PDA_stFFT is a novel automatic peak detection method for prOTOF MS data that does not require a priori knowledge of protein masses

peptide serum maldi-tof
Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam.

PMID 41156725 · PMC12565876 · Microorganisms · 2025 · 7 claims · 8 setups

Has reproduction · 86

HPVN24 is an avian pathogenic E. coli serotype O78:H9, sequence type ST23, with a 5.05 Mb genome and 50.57% GC content.

coli hpvn24 strain hemolysis antibiotic
Association of polymorphisms in cyclooxygenase (COX)-2 with coronary and carotid calcium in the Diabetes Heart Study.

PMID 18768181 · PMC2699582 · Atherosclerosis · 2009 · 8 claims · 6 setups

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COX-2 promoter SNP rs689466 is associated with lower coronary calcified plaque (CorCP)

whole-blood-derived subjects dhs unrelated snp coronary carotid
A proteomic approach to differentiate histologically classified stable and unstable plaques from human carotid arteries.

PMID 18715566 · PMC2659534 · Atherosclerosis · 2009 · 6 claims · 4 setups

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Stable and unstable carotid plaque extracts show distinct 2D-PAGE protein expression profiles, with nine proteins significantly differing in abundance between the two groups

carotid excised 2-dimensional maldi-tof western
HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.

PMID 18714345 · PMC2500163 · PloS one · 2008 · 7 claims · 4 setups

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HIV infection of a human T-cell line differentially regulates 18 proteins involved in lipid metabolism.

t-cell identified gel maldi-tof bioinformatics

Experiments

Comparative proteomic analysis of cell lines and scrapings of the human intestinal epithelium.

Proteomic analysis of serum in lung cancer induced by 3-methylcholanthrene.

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

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

Identification of two late acyltransferase genes responsible for lipid A biosynthesis in Moraxella catarrhalis.

MALDI profiling of human lung cancer subtypes.

Proteomic interrogation of androgen action in prostate cancer cells reveals roles of aminoacyl tRNA synthetases.

Protein expression patterns in primary carcinoma of the vagina.

Comparative proteome analysis of breast cancer and adjacent normal breast tissues in human.

Detection of venous thromboembolism by proteomic serum biomarkers.

VEGF, FGF1, FGF2 and EGF gene polymorphisms and psoriatic arthritis.

93rd Annual Meeting of the American Association for Cancer Research, San Francisco, CA, USA, 6-10 April 2002.

Characterisation and protein expression profiling of annexins in colorectal cancer.

KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

A protein-based set of reference markers for liver tissues and hepatocellular carcinoma.

A novel peak detection approach with chemical noise removal using short-time FFT for prOTOF MS data.

Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam.

Association of polymorphisms in cyclooxygenase (COX)-2 with coronary and carotid calcium in the Diabetes Heart Study.

A proteomic approach to differentiate histologically classified stable and unstable plaques from human carotid arteries.

HIV replication enhances production of free fatty acids, low density lipoproteins and many key proteins involved in lipid metabolism: a proteomics study.