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 14

System / cell line: proteomics ✕ Assay: statistical ✕ Clear

Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

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Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

pooled computational identified additional label-free lspad pathway-associated
A statistical model to identify differentially expressed proteins in 2D PAGE gels.

PMID 19763172 · PMC2734266 · PLoS computational biology · 2009 · 7 claims · 5 setups

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A mixture likelihood model incorporating both detected and non-detected proteins has higher statistical power to detect differential expression than standard approaches like the Student's t-test.

plasma simulated page simulated
Proteomic characterization of HIV-modulated membrane receptors, kinases and signaling proteins involved in novel angiogenic pathways.

PMID 19712456 · PMC2754444 · Journal of translational medicine · 2009 · 7 claims · 5 setups

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31 HIV-modulated cellular proteins were identified as functionally associated with signaling events involved in angiogenesis

rh9 hiv-infected identified subtractive mass enzyme-linked
A mouse plasma peptide atlas as a resource for disease proteomics.

PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

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A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

plasma peptides fully tissues lc-ms anion database
Salivary proteomics for oral cancer biomarker discovery.

PMID 18829504 · PMC2877125 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 5 setups

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Subtractive salivary proteomics reveals proteins differentially present/expressed between OSCC patients and matched healthy controls.

pooled saliva shotgun two-dimensional elisa
Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells.

PMID 14709176 · PMC395736 · Genome biology · 2003 · 8 claims · 5 setups

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Distinct cellular processes are coregulated by androgen while others are essentially unaffected in LNCaP cells

lncap computational icat western hypergeometric
PromoterPlot: a graphical display of promoter similarities by pattern recognition.

PMID 15980503 · PMC1160174 · Nucleic acids research · 2005 · 7 claims · 4 setups

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PromoterPlot is a web-based tool that displays and processes TransFac transcription factor search results as an interactive SVG page

under set transcription microarray proteomics
Evolution of organelle-associated protein profiling.

PMID 19110081 · PMC2680700 · Journal of proteomics · 2009 · 8 claims · 8 setups

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Traditional biochemical organelle isolation followed by MS cataloguing suffers high false-positive rates because organelles cannot be purified to homogeneity and are structurally heterogeneous

golgi nuclear lipid clathrin-coated density qualitative silac
Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

PMID 19936259 · PMC2775948 · PloS one · 2009 · 8 claims · 8 setups

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Integrated proteomic analysis of a cancer mouse model and human cancer cell populations provides an effective approach to identify potential circulating protein biomarkers.

k-ras ovarian lists tumor quantitative pathway immunoblot
Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

PMID 19691830 · PMC2746235 · BMC genomics · 2009 · 7 claims · 6 setups

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85 proteins are differentially and consistently expressed (>2-fold change, P<0.05) between paired OLK and OSCC tissues, including 52 up-regulated and 33 down-regulated proteins

paired list differentially oscc 2-de gene interaction
Peeling off the layers: skin taping and a novel proteomics approach to study atopic dermatitis.

PMID 19748658 · PMC8648281 · The Journal of allergy and clinical immunology · 2009 · 8 claims · 3 setups

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Noninvasive D-Squame tape stripping coupled with MS proteomics can profile the AD skin proteome

skin extracted lesion skin lc-ms statistical
Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.

PMID 41486154 · PMC12828970 · BMC bioinformatics · 2026 · 8 claims · 8 setups

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Frag'n'Flow is a Nextflow-based pipeline that encapsulates FragPipe, automating manifest/workflow generation, tool dependency management, and downstream analysis for HPC/cloud/cluster environments.

laboratory institutional breast pluripotent ram cpu storage
A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.

PMID 19813771 · PMC2789208 · Journal of proteome research · 2009 · 7 claims · 7 setups

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Coupling DRC (hexapeptide libraries) with 3D peptide fractionation (IEF + SCX + µLC-MS/MS) substantially increases the number of proteins identified in whole saliva

saliva offgel-fractionated identified sds-page trypsin strong
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

Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

A statistical model to identify differentially expressed proteins in 2D PAGE gels.

Proteomic characterization of HIV-modulated membrane receptors, kinases and signaling proteins involved in novel angiogenic pathways.

A mouse plasma peptide atlas as a resource for disease proteomics.

Salivary proteomics for oral cancer biomarker discovery.

Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells.

PromoterPlot: a graphical display of promoter similarities by pattern recognition.

Evolution of organelle-associated protein profiling.

Integrated proteomic analysis of human cancer cells and plasma from tumor bearing mice for ovarian cancer biomarker discovery.

Involvement of potential pathways in malignant transformation from oral leukoplakia to oral squamous cell carcinoma revealed by proteomic analysis.

Peeling off the layers: skin taping and a novel proteomics approach to study atopic dermatitis.

Frag'n'Flow: automated workflow for large-scale quantitative proteomics in high performance computing environments.

A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.

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