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 52

System / cell line: peptide ✕ Assay: trypsin ✕ Clear

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
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
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
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
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
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
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
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
Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.

PMID 17203985 · PMC2664920 · Journal of proteome research · 2007 · 8 claims · 4 setups

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An information-theoretic log-likelihood scoring method can predict experimentally observed missed cleavage sites from amino acid sequence alone with up to 90% accuracy.

pepseeker local known swissprot tandem peptide pmf
Tags for labeling protein N-termini with subtiligase for proteomics.

PMID 18762420 · PMC2590642 · Bioorganic & medicinal chemistry letters · 2008 · 6 claims · 4 setups

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Arginine-rich peptide esters (3, 4, 5) are markedly more soluble than the original TEVest2 ester (1) and give significantly higher N-terminal tagging of proteins by subtiligase at higher concentrations.

jurkat neutravidin-coated synthetic proteomic sds-page sandwich aqueous
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
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
Stable isotope labeling tandem mass spectrometry (SILT): integration with peptide identification and extension to data-dependent scans.

PMID 18774841 · PMC2707264 · Journal of proteome research · 2008 · 8 claims · 5 setups

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Using MS/MS ion intensities with stable isotope labeling (SILT) decreases the effects of contamination from unrelated co-eluting compounds compared to precursor ion intensity methods.

astrocytes hepg2 app695δnl labeled nano-lc sds-page immunoprecipitation
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
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 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
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
The synovial proteome: analysis of fibroblast-like synoviocytes.

PMID 15059280 · PMC400437 · Arthritis research & therapy · 2004 · 7 claims · 5 setups

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2D-PAGE combined with MALDI mass spectrometry can characterize the FLS cellular proteome with high confidence

fibroblast-like excised fls computational 2d-page in-gel maldi
Identification of novel citrullinated autoantigens of synovium in rheumatoid arthritis using a proteomic approach.

PMID 17125526 · PMC1794520 · Arthritis research & therapy · 2006 · 8 claims · 6 setups

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51 citrullinated protein spots were detected in RA synovial tissue, of which 30 (58.8%) were autoantigenic (reactive with RA sera)

synovial excised coli recombinant two-dimensional maldi-tof recombinant
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

Experiments

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

Improved methods for the enrichment and analysis of glycated peptides.

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

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

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

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

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

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

Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.

Tags for labeling protein N-termini with subtiligase for proteomics.

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

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

Stable isotope labeling tandem mass spectrometry (SILT): integration with peptide identification and extension to data-dependent scans.

Defining the proteome.

Tubulin proteomics: towards breaking the code.

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

Mass spectrometry-based proteomic analyses of contact lens deposition.

The synovial proteome: analysis of fibroblast-like synoviocytes.

Identification of novel citrullinated autoantigens of synovium in rheumatoid arthritis using a proteomic approach.

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