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: lines ✕ Assay: peptide ✕ Clear

A new era for proteomics research?

PMID 19014405 · PMC2614486 · Genome biology · 2008 · 8 claims · 8 setups

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Refined mass spectrometry instrumentation and software now make whole-proteome coverage of model organisms in a single experiment conceivable

proteins lines kinases breast mass silac kinase-specific
Tubulin proteomics: towards breaking the code.

PMID 18840397 · PMC4039029 · Analytical biochemistry · 2009 · 8 claims · 8 setups

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Tubulin isotype and posttranslational-modification diversity constitutes a 'tubulin code' that is read by microtubule-associated proteins and translates into specific in vivo functions

bovine mda-mb-231 cancer a549 maldi-tof tandem sds-page
Proteomic and genetic approaches identify Syk as an AML target.

PMID 19800574 · PMC2803063 · Cancer cell · 2009 · 8 claims · 8 setups

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EGFR inhibitors (e.g., gefitinib) induce AML differentiation through a non-EGFR, off-target mechanism

hl-60 aml molm-14 luciferase-labeled phospho-tyrosine kinome-wide secondary
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

Has reproduction · 74

ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot
Pathway analysis of kidney cancer using proteomics and metabolic profiling.

PMID 17123452 · PMC1665458 · Molecular cancer · 2006 · 8 claims · 8 setups

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31 proteins are differentially expressed with high statistical significance (p<0.05) in ccRCC tumor tissue compared to adjacent non-malignant kidney tissue

ccrcc rcc computational random gel immunoblotting immunohistochemistry
Three-dimensional neuroblastoma cell culture: proteomic analysis between monolayer and multicellular tumor spheroids.

PMID 18797883 · PMC2804865 · Pediatric surgery international · 2008 · 7 claims · 3 setups

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18 protein spots were differentially over-expressed in neuroblastoma spheroids compared to monolayers

neuroblastoma excised monolayer 2-d lc-ms fractionation
Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.

PMID 35701420 · PMC9197839 · Scientific data · 2022 · 8 claims · 5 setups

Has reproduction · 50

An open, containerised, Nextflow-orchestrated reanalysis pipeline combining metadata annotation, SWATH-MS analysis, statistical analysis, and Expression Atlas integration was developed for public DIA data.

pooled datasets pxd014194 technical swath-ms dda-based differential
Proteomic solutions for analytical challenges associated with alcohol research.

PMID 23584870 · PMC3860482 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 7 claims · 4 setups

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Protein-level meta-analyses analogous to the transcriptome meta-analysis by Mulligan et al. (2006) are not yet possible because proteins lack a uniform sample preparation/analysis method and span up to 8 orders of magnitude in abundance.

general complex plasma selected shotgun label-free targeted
Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth.

PMID 19920251 · PMC2812789 · Science signaling · 2009 · 7 claims · 8 setups

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Oncogenic FGFR1 directly phosphorylates PKM2 at tyrosine 105 (Y105), inhibiting its enzymatic activity

293t kg-1a recombinant h1299 ms-based co-transfection enzymatic
Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

PMID 19912651 · PMC2784748 · BMC cell biology · 2009 · 7 claims · 7 setups

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hnRNP L is a novel Sam68-interacting protein partner identified by proteomics and confirmed by co-immunoprecipitation

lncap hek293 nih3t3 co-immunoprecipitation sucrose indirect
Pre-operative urinary cathepsin D is associated with survival in patients with renal cell carcinoma.

PMID 19789534 · PMC2768081 · British journal of cancer · 2009 · 8 claims · 7 setups

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Cathepsin D, identified via comparative 2D PAGE of conditioned media from RCC cell lines vs normal renal cultures, is a candidate secreted biomarker of RCC

htb49 excised conditioned urine page maldi western
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
Human Protein Reference Database--2009 update.

PMID 18988627 · PMC2686490 · Nucleic acids research · 2009 · 8 claims · 8 setups

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HPRD is a curated database of experimentally derived human protein-protein interactions, post-translational modifications, and tissue expression data

mastl proteins phosphorylation yeast mass
ZAP targets aberrant mRNA transcripts encoding proteins with defective signal peptides for degradation.

PMID 41820617 · PMC13084044 · The EMBO journal · 2026 · 8 claims · 7 setups

Has reproduction · 50

ZAP (ZC3HAV1/PARP13) is a key component of the RAPP quality control pathway

k562 zap-s rt-qpcr western immunofluorescence
A gene encoding antigenic peptides of human squamous cell carcinoma recognized by cytotoxic T lymphocytes.

PMID 9449708 · PMC2212124 · The Journal of experimental medicine · 1998 · 8 claims · 8 setups

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A gene, SART-1, encoding antigenic peptides recognized by HLA-A2601-restricted CTLs was identified from human squamous cell carcinoma cells.

ke4 normal pbmcs va13 expression northern western
Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response.

PMID 15545352 · PMC2211924 · The Journal of experimental medicine · 2004 · 7 claims · 4 setups

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CD8+ CTL responses contribute to containment of viral replication in acute/early HIV-1 infection, and HIV-1 rapidly selects escape variants within epitope-containing regions beginning within weeks of infection.

pbmcs autologous vaccinia plasma ifn-γ 51cr recombinant
AgBase: a functional genomics resource for agriculture.

PMID 16961921 · PMC1618847 · BMC genomics · 2006 · 8 claims · 7 setups

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AgBase is a curated, web-accessible database providing structural and functional (GO) annotation for agricultural genomes and their pathogens.

pasteurella chicken maize gene proteogenomic mudpit differential
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
Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements.

PMID 18942891 · PMC2570425 · PLoS biology · 2008 · 8 claims · 5 setups

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An unbiased SILAC-based proteomic screen identified a relatively small cohort of γ-secretase substrates among thousands of proteins in HeLa cells, all of which are type I transmembrane proteins.

hela presenilin-1 hek silac western
The dietary bioflavonoid, quercetin, selectively induces apoptosis of prostate cancer cells by down-regulating the expression of heat shock protein 90.

PMID 18726985 · PMC2826114 · The Prostate · 2008 · 7 claims · 8 setups

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Quercetin treatment of prostate cancer cells decreases cell proliferation and viability in a dose-dependent manner

pc-3 excised prostate viability difference nano

Experiments

A new era for proteomics research?

Tubulin proteomics: towards breaking the code.

Proteomic and genetic approaches identify Syk as an AML target.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Pathway analysis of kidney cancer using proteomics and metabolic profiling.

Three-dimensional neuroblastoma cell culture: proteomic analysis between monolayer and multicellular tumor spheroids.

Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas.

Proteomic solutions for analytical challenges associated with alcohol research.

Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth.

Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

Pre-operative urinary cathepsin D is associated with survival in patients with renal cell carcinoma.

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

Human Protein Reference Database--2009 update.

ZAP targets aberrant mRNA transcripts encoding proteins with defective signal peptides for degradation.

A gene encoding antigenic peptides of human squamous cell carcinoma recognized by cytotoxic T lymphocytes.

Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response.

AgBase: a functional genomics resource for agriculture.

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

Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements.

The dietary bioflavonoid, quercetin, selectively induces apoptosis of prostate cancer cells by down-regulating the expression of heat shock protein 90.