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 28

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

Proteomic profiling of human plasma exosomes identifies PPARgamma as an exosome-associated protein.

PMID 19028452 · PMC2633355 · Biochemical and biophysical research communications · 2009 · 7 claims · 6 setups

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Developed a multi-step fractionation scheme (gel exclusion chromatography, rate zonal sucrose gradient centrifugation, high-speed centrifugation) to purify exosomes from human plasma

plasma-derived plasma lc-ms sds-page western
Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

PMID 18974882 · PMC2570797 · PLoS pathogens · 2008 · 8 claims · 6 setups

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Midgut (oocyst-derived) and salivary gland sporozoite proteomes are markedly different despite near-identical morphology, consistent with their differing hepatocyte infectivity

falciparum berghei nano-lc-ms targeted gene
Comparison of multidimensional shotgun technologies targeting tissue proteomics.

PMID 19960471 · PMC3465977 · Electrophoresis · 2009 · 6 claims · 4 setups

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CITP-based multidimensional separation achieves superior overall proteome performance (more total peptide, distinct peptide, and distinct protein identifications) than SCX/MuDPIT under matched conditions

glioblastoma peptide shotgun spectral database
Serum S100A6 concentration predicts peritoneal tumor burden in mice with epithelial ovarian cancer and is associated with advanced stage in patients.

PMID 19888321 · PMC2765613 · PloS one · 2009 · 8 claims · 8 setups

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Serum S100A6 concentration correlates with peritoneal tumor burden in a mouse OVCA xenograft model, based on inverse regression calibration against bioluminescent imaging data.

serum skov-3 pooled ovca lc-ms antigen whole-animal
CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.

PMID 16892042 · PMC2360640 · British journal of cancer · 2006 · 6 claims · 6 setups

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CD70 was identified by proteomic analysis of plasma membrane preparations as highly expressed in A498 and SW839 RCC-derived cell lines

a498 frozen normal proteomics flow immunohistochemistry
An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation.

PMID 34772928 · PMC8590018 · Nature communications · 2021 · 8 claims · 5 setups

Has reproduction · 92

PISA-Express is a method that simultaneously measures protein expression and thermal stability (solubility) changes using only two samples per replicate per cell type

hi12 ipsc ht29 foreskin pisa expression cellular
A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups

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Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.

washed platelets tryptic hek293t lc-ms free longsage
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
Proteomic characterization of plasma-derived clotting factor VIII-von Willebrand factor concentrates.

PMID 19768705 · PMC3030255 · Electrophoresis · 2009 · 8 claims · 8 setups

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Commercial plasma-derived FVIII/VWF concentrates contain significant amounts of non-FVIII/VWF plasma proteins as impurities

plasma-derived octanate sec fviii sds-page size-exclusion lc-esi-ms
The Proteomics Identifications database: 2010 update.

PMID 19906717 · PMC2808904 · Nucleic acids research · 2010 · 8 claims · 6 setups

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PRIDE has become one of the main repositories for MS-based proteomics data, with substantial growth in data holdings over the last two years.

species plasma caenorhabditis secretory ms-based quantitative
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
Enhanced protein isoform characterization through long-read proteogenomics.

PMID 35241129 · PMC8892804 · Genome biology · 2022 · 6 claims · 4 setups

Has reproduction · 79

A long-read proteogenomics pipeline integrating PacBio long-read RNA-seq with MS-based proteomics enhances isoform-resolved protein characterization

jurkat jurkat-derived long-read transcript orf
Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer.

PMID 36232369 · PMC9569723 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

Has reproduction · 87

Common genes shared across five cancer types differ from those found in nonmalignant tissue-resident T-cells for each subset (CD4-T, CD8-T, Treg)

breast lung colorectal melanoma single-cell gene reactome
Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

PMID 19859549 · PMC2762604 · PloS one · 2009 · 8 claims · 8 setups

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A comprehensive platelet proteome of 1507 unique proteins was identified from ten independent human platelet samples, the most comprehensive platelet proteome assembled to date

platelets platelet anti-coagulated lc-ms phospho-proteomic membrane
Pleiotropic effects of MORC2 derive from its epigenetic signature.

PMID 40302207 · PMC12782172 · Brain : a journal of neurology · 2026 · 8 claims · 8 setups

Has reproduction

A MORC2-specific DNA methylation episignature exists that is universal across all MORC2-associated phenotypes and conserved across blood and fibroblast tissue

blood fibroblasts fibroblast patient-derived methylation svm phenotype-specific
Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death.

PMID 19889237 · PMC2783166 · BMC genomics · 2009 · 8 claims · 8 setups

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scNT-MUC exhibit complete occlusive thrombi and absence of columnar epithelial layers not seen in control or scNT-N umbilical cords

umbilical porcine puvec histology immunostaining real-time
Novel insights into adipogenesis from omics data.

PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

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Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based
MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.

PMID 40450001 · PMC12126529 · Nature communications · 2025 · 8 claims · 8 setups

Has reproduction · 70

MACanalyzeR is a novel computational scRNAseq framework (with FoamSpotteR, MacPolarizeR, and PathAnalyzeR modules) for comprehensive monocyte/macrophage metabolic and phenotypic profiling

bat stromal paraffin-embedded aortic bulk proteomics scrnaseq
Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

PMID 18515841 · PMC2447758 · Nucleic acids research · 2008 · 8 claims · 5 setups

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Babelomics is a web suite offering both conventional functional enrichment methods and more advanced gene set analysis (GSA) methods, a combination offered by only one other tool (FuncAssociate) among competitors.

user-supplied ranked gene fasta-formatted functional gene novo
Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.

PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups

Has reproduction · 71

DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue

ucec ishikawa rna-seq proteomics immunohistochemistry

Experiments

Proteomic profiling of human plasma exosomes identifies PPARgamma as an exosome-associated protein.

Proteomic profiling of Plasmodium sporozoite maturation identifies new proteins essential for parasite development and infectivity.

Comparison of multidimensional shotgun technologies targeting tissue proteomics.

Serum S100A6 concentration predicts peritoneal tumor burden in mice with epithelial ovarian cancer and is associated with advanced stage in patients.

CD70 (TNFSF7) is expressed at high prevalence in renal cell carcinomas and is rapidly internalised on antibody binding.

An integrative proteomics method identifies a regulator of translation during stem cell maintenance and differentiation.

A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

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

Proteomic characterization of plasma-derived clotting factor VIII-von Willebrand factor concentrates.

The Proteomics Identifications database: 2010 update.

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

Enhanced protein isoform characterization through long-read proteogenomics.

Analysis of Tumor-Infiltrating T-Cell Transcriptomes Reveal a Unique Genetic Signature across Different Types of Cancer.

Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

Pleiotropic effects of MORC2 derive from its epigenetic signature.

Comparative proteomic analysis of malformed umbilical cords from somatic cell nuclear transfer-derived piglets: implications for early postnatal death.

Novel insights into adipogenesis from omics data.

MACanalyzeR scRNAseq analysis tool reveals PPARγ(HIGH)/GDF15(HIGH) lipid-associated macrophages facilitate thermogenic expansion in BAT.

Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments.

Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.