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 65

System / cell line: sds-page ✕ Assay: gel ✕ Clear

Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

PMID 18989384 · PMC2579937 · Molecular vision · 2008 · 8 claims · 4 setups

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Worn silicone hydrogel contact lenses deposit a wide array of proteins from the tear film and other sources.

deposit excised pooled worn sds-page in-gel lc-ms-ms
Cellular proteins in influenza virus particles.

PMID 18535660 · PMC2390764 · PLoS pathogens · 2008 · 8 claims · 6 setups

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Purified influenza virions contain 36 host-encoded cellular proteins in addition to the 9 previously known viral proteins.

influenza deglycosylated sucrose lc-ms mudpit electron
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
Potential biomarkers of human salivary function: a modified proteomic approach.

PMID 18804197 · PMC2633945 · Archives of oral biology · 2009 · 6 claims · 6 setups

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Two SDS-PAGE bands, identified by MS-MS as statherin and a truncated (N-terminal 8-aa-missing) cystatin S, are the strongest and most consistent predictors of HAA/LAA group membership and clinical/microbiological outcomes

resting pooled saliva quantified preparative sds-page western
Post-translational modifications of histones H3 and H4 associated with the histone methyltransferases Suv39h1 and G9a.

PMID 18096052 · PMC2246272 · Genome biology · 2007 · 6 claims · 4 setups

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Suv39h1 and G9a associate with previously reported methylation states (Suv39h1 with H3K9me3; G9a with H3K9me/me2)

crude hela-suv39h1 suv39h1 normal propionylation-based double maldi-tof
Comparative cytochrome P450 proteomics in the livers of immunodeficient mice using 18O stable isotope labeling.

PMID 17296599 · PMC2315784 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 5 setups

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SDS-PAGE combined with post-digest 18O/16O labeling and LC-MS/MS enables relative quantification of multiple P450 proteins from liver microsomes, including highly homologous isoforms

liver recombinant tryptic sds-page western mascot
Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.

coli sds-page glutathione pepck-gst sds-page maldi-tof native
Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma.

PMID 18839982 · PMC3204659 · Journal of proteome research · 2008 · 7 claims · 4 setups

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Golgi membrane protein 1 (GOLM1/GP73), Annexin IV, and Eps8 are validated candidate biomarkers for cholangiocarcinoma

membrane bile 18o-labeling sds-page western
Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

PMID 18490959 · PMC2386506 · Molecular vision · 2008 · 7 claims · 6 setups

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A novel affinity-enrichment strategy using UV cross-linked protease inhibitor peptides on Protein A/G columns improves capture of the TM protease proteome compared to SDS-PAGE fractionation alone

cytosolic affinity-eluted porcine affinity-enriched affinity western sds-page
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins.

PMID 16948836 · PMC1794545 · Genome biology · 2006 · 8 claims · 6 setups

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Identified 1543 proteins in urine from ten healthy donors while essentially eliminating false-positive identifications

urine pooled urinary identified sds-page albumin decoy
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
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
Immunohistochemical and proteomic evaluation of nuclear ubiquitous casein and cyclin-dependent kinases substrate in invasive ductal carcinoma of the breast.

PMID 20069058 · PMC2801467 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 5 setups

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NUCKS is highly overexpressed in invasive ductal carcinoma (IDC) of the breast compared to matched normal tissue.

matched idc nucks rabbits lc-ms sds-page western
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
High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups

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High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.

tuberculosis sanger spectra lc-ms sds-page signal
Proteomic analyses associate cystatin B with restricted HIV-1 replication in placental macrophages.

PMID 18951626 · PMC3867668 · Placenta · 2008 · 6 claims · 6 setups

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Placental macrophages support significantly lower HIV-1 replication than monocyte-derived macrophages

placental mdm hiv-1 seldi-tof sds-page
Tracheobronchial air-liquid interface cell culture: a model for innate mucosal defense of the upper airways?

PMID 18931053 · PMC2636953 · American journal of physiology. Lung cellular and molecular physiology · 2009 · 8 claims · 5 setups

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A mass spectrometry approach based on prior density-gradient separation of mucins from other proteins enables comprehensive identification of mucins in mucous secretions, overcoming underrepresentation in prior proteomic studies

tracheobronchial normal apical lc-ms isopycnic sds-page
Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.

PMID 17392682 · PMC2642915 · Molecular vision · 2007 · 8 claims · 8 setups

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MLF accumulation more closely reflects the onset of AMD than LF accumulation

donor arpe-19 mlf sucrose phototoxicity fluorescence
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
IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

PMID 19752006 · PMC2808259 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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IDEAL-Q predicts the elution time of peptides unidentified in a given LC-MS/MS run (but identified in others) using a computation-efficient linear regression plus fragmental refining function, avoiding costly whole-dataset pattern recognition

standard thp-1 replicate lc-ms manual cross-instrument

Experiments

Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

Cellular proteins in influenza virus particles.

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

Potential biomarkers of human salivary function: a modified proteomic approach.

Post-translational modifications of histones H3 and H4 associated with the histone methyltransferases Suv39h1 and G9a.

Comparative cytochrome P450 proteomics in the livers of immunodeficient mice using 18O stable isotope labeling.

Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

Differential membrane proteomics using 18O-labeling to identify biomarkers for cholangiocarcinoma.

Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins.

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

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

Immunohistochemical and proteomic evaluation of nuclear ubiquitous casein and cyclin-dependent kinases substrate in invasive ductal carcinoma of the breast.

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

High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

Proteomic analyses associate cystatin B with restricted HIV-1 replication in placental macrophages.

Tracheobronchial air-liquid interface cell culture: a model for innate mucosal defense of the upper airways?

Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.

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.

IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.