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 20

System / cell line: same ✕ Assay: mass ✕ Clear

Measurement reproducibility in the early stages of biomarker development.

PMID 15665389 · PMC3839328 · Disease markers · 2004 · 6 claims · 3 setups

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Functional PCA can be used as the basis for gauge R&R (repeatability and reproducibility) assessment of mass spectra without prior identification of which spectral features are biomarkers

pooled same registered seldi-tof univariate functional
LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise.

PMID 17386085 · PMC1847688 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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LIMPIC is a computational method for detecting protein peaks from linear-mode MALDI-TOF-MS data using background noise reduction and baseline removal followed by non-uniform threshold peak detection and multi-spectra detection-rate classification.

in-vitro plasma maldi-tof signal baseline
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
Profiling critical cancer gene mutations in clinical tumor samples.

PMID 19924296 · PMC2774511 · PloS one · 2009 · 7 claims · 4 setups

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OncoMap, a panel of ~400 mass-spectrometric genotyping assays targeting 33 cancer genes, enables robust mutation profiling of clinical fresh-frozen and FFPE tumor DNA.

clinical fresh same pediatric mass sanger barcoded
MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

PMID 19850495 · PMC2818324 · Journal of the American Society for Mass Spectrometry · 2010 · 7 claims · 4 setups

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MAZIE is a post-acquisition Perl algorithm that determines precursor ion monoisotopic mass and charge (+1 to +4) from MS1 zoom scan isotopic distributions on a Thermo LTQ-XL

urine same lc-ms2 ms1 comparative
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
Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

PMID 18788775 · PMC3744223 · Journal of proteome research · 2008 · 7 claims · 4 setups

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PeptideProphet's fixed LDA coefficients for combining search scores (Xcorr', ΔCn, SpRank) may not be optimal under all search/instrument conditions.

trypsin-digested mix serum same shotgun sequest lc-ms
GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

PMID 30616647 · PMC6322265 · Genome biology · 2019 · 8 claims · 6 setups

Has reproduction · 96

gBGC conceals the correlation between life-history traits and dN/dS in birds; accounting for it reveals correlations consistent with nearly neutral theory

avian comparative correlation robustness
Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups

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Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.

fresh-frozen same banked resected array mutational pcr
Large-scale and high-confidence proteomic analysis of human seminal plasma.

PMID 16709260 · PMC1779515 · Genome biology · 2006 · 8 claims · 6 setups

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923 proteins were identified with high confidence in seminal plasma from a single individual, combining results from three ejaculate samples

seminal same list combined sds-page database decoy
Hepatocyte dedifferentiation in 2D culture reveals extensive transcriptomic and proteomic rewiring.

PMID 41111196 · PMC12506984 · Hepatology communications · 2025 · 8 claims · 4 setups

Has reproduction · 77

24 hours of 2D culturing changes >10,000 genes and ~3000 proteins in primary hepatocytes compared with freshly isolated cells, reflecting major transcriptomic and proteomic rewiring.

c57bl bulk proteomics single-nucleus
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
Genomic and proteomic profiling I: leiomyomas in African Americans and Caucasians.

PMID 17716379 · PMC2063502 · Reproductive biology and endocrinology : RB&E · 2007 · 7 claims · 6 setups

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268 genes (177 over-expressed, 91 under-expressed) are differentially expressed in leiomyomas of African Americans compared to Caucasians (P<0.01, 2-fold cutoff)

paired same excised paraffin-embedded microarray realtime 2d-page
Pharmaco-proteomic study of hydroxyurea-induced modifications in the sickle red blood cell membrane proteome.

PMID 18849548 · PMC4260454 · Experimental biology and medicine (Maywood, N.J.) · 2008 · 6 claims · 6 setups

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50 μM HU treatment of SS RBC membranes causes statistically significant changes in a discrete set of membrane proteins, distinct from HbF induction.

sickle rbc excised 2d-dige tandem immunoblot
Application of serum SELDI proteomic patterns in diagnosis of lung cancer.

PMID 16029516 · PMC1183195 · BMC cancer · 2005 · 6 claims · 2 setups

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A five-protein-peak SELDI decision-tree pattern (11493, 6429, 8245, 5335, 2538 Da) distinguishes lung cancer sera from healthy control sera with relatively high sensitivity and specificity

serum seldi-tof-ms electrochemiluminescent
Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

PMID 16404425 · PMC2361188 · British journal of cancer · 2006 · 7 claims · 8 setups

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A G274A base substitution in hnRNP K mRNA is present in colorectal tumours and surrounding mucosa but absent from corresponding genomic DNA, indicating an RNA editing event rather than a germline polymorphism.

colorectal cdna matched thyroid rt-pcr restriction genomic
Cannabinoid type-1 receptor gene polymorphisms are associated with central obesity in a Southern Brazilian population.

PMID 18776593 · PMC3827795 · Disease markers · 2008 · 8 claims · 5 setups

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The CNR1 4895G allele is associated with waist-to-hip ratio (WHR)

peripheral same pcr-rflp anthropometric biochemical
Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

PMID 15640441 · PMC546178 · Nucleic acids research · 2005 · 8 claims · 7 setups

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NCL aggregation of DNA-modified gold nanoparticles shows extraordinary selectivity against terminal mismatches at the free ends of surface-bound duplexes

probe-modified probe-gnp synthetic four uv-vis ssdna pcr
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
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

Experiments

Measurement reproducibility in the early stages of biomarker development.

LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise.

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

Profiling critical cancer gene mutations in clinical tumor samples.

MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

Detection of venous thromboembolism by proteomic serum biomarkers.

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

Large-scale and high-confidence proteomic analysis of human seminal plasma.

Hepatocyte dedifferentiation in 2D culture reveals extensive transcriptomic and proteomic rewiring.

Protein expression patterns in primary carcinoma of the vagina.

Genomic and proteomic profiling I: leiomyomas in African Americans and Caucasians.

Pharmaco-proteomic study of hydroxyurea-induced modifications in the sickle red blood cell membrane proteome.

Application of serum SELDI proteomic patterns in diagnosis of lung cancer.

Editing of hnRNP K protein mRNA in colorectal adenocarcinoma and surrounding mucosa.

Cannabinoid type-1 receptor gene polymorphisms are associated with central obesity in a Southern Brazilian population.

Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

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

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.