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 36

System / cell line: lc-ms ✕ Assay: trypsin ✕ Clear

Mass spectrometry-based proteomic analyses of contact lens deposition.

PMID 18334948 · PMC2254969 · Molecular vision · 2008 · 8 claims · 2 setups

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Silicone hydrogel contact lenses deposit substantially less total protein than traditional soft (non-silicone) lens materials

worn bradford nano-lc-ms
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
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
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
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
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
MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes.

PMID 17090601 · PMC1781136 · Nucleic acids research · 2007 · 8 claims · 8 setups

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MAPU is a unified, freely accessible database integrating organellar, cellular, tissue and body fluid proteomes generated by high-resolution mass spectrometry.

urine tear seminal breast gel lc-ms3 in-depth
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
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
Investigation of the human tear film proteome using multiple proteomic approaches.

PMID 18334958 · PMC2268847 · Molecular vision · 2008 · 8 claims · 6 setups

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Tear collection method (capillary vs. Schirmer strip) significantly impacts which proteins are detected in the tear film proteome.

tear spectra 1d-sds-page 2d-sds-page mudpit
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
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
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
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
Defining the proteome.

PMID 16356278 · PMC1414090 · Genome biology · 2005 · 8 claims · 8 setups

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Integration of multi-omics data is an important step toward a systems-biology approach to the proteome

brain chicken bacillus yeast proteome proteomics two-dimensional
Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors.

PMID 16901338 · PMC1779605 · Genome biology · 2006 · 8 claims · 4 setups

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491 proteins were identified in human tear fluid using in-gel digestion and LC-MS/MS/MS3 on LTQ-FT and LTQ-Orbitrap instruments

closed-eye tear analysis sds-page in-solution gene
Improved methods for the enrichment and analysis of glycated peptides.

PMID 18989935 · PMC2752342 · Analytical chemistry · 2008 · 7 claims · 4 setups

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Replacing off-line desalting with an online 50 mM NH4OAc wash (10 min) of boronate-bound glycated proteins improves the enrichment workflow while minimizing sample loss

glucose-glycated tryptic glycated lc-ms boronate lc-etd-ms database
Identification of beta-secretase (BACE1) substrates using quantitative proteomics.

PMID 20041192 · PMC2793532 · PloS one · 2009 · 7 claims · 5 setups

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Quantitative proteomics of conditioned medium from BACE1-overexpressing HEK and HeLa cells identified 68 putative β-secretase substrates

hek293 hela hek concentrated silac western sds-page
Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.

PMID 16542425 · PMC1431555 · BMC cancer · 2006 · 8 claims · 5 setups

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ICAT tandem MS can identify and quantify differences in specific protein expression between NAF from tumor-bearing and disease-free breasts

paired icat-labeled spectra naf icat sds-page liquid
Shotgun proteomic analysis of cerebrospinal fluid using off-gel electrophoresis as the first-dimension separation.

PMID 18778093 · PMC4582942 · Journal of proteome research · 2008 · 6 claims · 4 setups

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OGE first-dimension fractionation enabled identification of 156 unique CSF proteins compared to 115 identified using SCX fractionation on the same CSF pool

pooled csf spectra shotgun trypsin peptide

Experiments

Mass spectrometry-based proteomic analyses of contact lens deposition.

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

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

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

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

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

MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes.

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

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

Investigation of the human tear film proteome using multiple proteomic approaches.

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

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

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

Cellular proteins in influenza virus particles.

Defining the proteome.

Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors.

Improved methods for the enrichment and analysis of glycated peptides.

Identification of beta-secretase (BACE1) substrates using quantitative proteomics.

Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.

Shotgun proteomic analysis of cerebrospinal fluid using off-gel electrophoresis as the first-dimension separation.