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 13

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

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
A mouse plasma peptide atlas as a resource for disease proteomics.

PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

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A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

plasma peptides fully tissues lc-ms anion database
MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

PMID 19850495 · PMC2818324 · Journal of the American Society for Mass Spectrometry · 2010 · 7 claims · 4 setups

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MAZIE is a post-acquisition Perl algorithm that determines precursor ion monoisotopic mass and charge (+1 to +4) from MS1 zoom scan isotopic distributions on a Thermo LTQ-XL

urine same lc-ms2 ms1 comparative
Decision tree-driven tandem mass spectrometry for shotgun proteomics.

PMID 18931669 · PMC2597439 · Nature methods · 2008 · 8 claims · 5 setups

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A decision tree (DT) algorithm that selects CAD or ETD per precursor based on z and m/z yields more peptide identifications than either CAD or ETD alone

saccharomyces proteome embryonic nlc-ms phosphoproteomics sequential
A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.

PMID 18613715 · PMC2601597 · Journal of proteome research · 2008 · 8 claims · 5 setups

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A NCI source coupled via an added octopole and the c-trap to a QLT-orbitrap enables fast, efficient ETD reagent anion injection (4-8 ms)

saccharomyces histone glioblastoma fluoranthene lc-ms etd anion
Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

PMID 17303479 · PMC7105233 · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2007 · 5 claims · 5 setups

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Pre-fractionation of plasma with immuno-affinity depletion and anion-exchange chromatography prior to 2D-DIGE substantially increases the number of detectable protein spots compared with unfractionated plasma.

plasma excised fractionated 2d-dige multi-dimensional lc-ms
iTRAQ proteomic identification of pVHL-dependent and -independent targets of Egln1 prolyl hydroxylase knockdown in renal carcinoma cells.

PMID 19159641 · PMC2716563 · Advances in enzyme regulation · 2009 · 7 claims · 4 setups

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Egln1 knockdown induces P1465 hydroxylation and Ser5 phosphorylation of Rpb1 only in VHL(+) cells, not VHL(-) cells

786-o itraq-labeled scx-fractionated spectra itraq strong capillary
Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

PMID 18841935 · PMC2716176 · Analytical chemistry · 2008 · 7 claims · 6 setups

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An integrated hardware/software online-offline platform (TriVersa NanoMate + 12T LTQ FT Ultra + AUTOMATION WAREHOUSE) automates collection of high-resolution MS/MS data for polypeptides >3 kDa that cannot be acquired online on a chromatographic timescale

acid-extracted hela online offline
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
Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

PMID 19902006 · PMC2774473 · Journal of biomedicine & biotechnology · 2010 · 8 claims · 5 setups

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iTRAQ labelling combined with 4800 MALDI TOF/TOF can detect quantitative differences in the maternal plasma proteome between DS and euploid pregnancies

maternal tryptic scx-fractionated identified itraq immunodepletion strong
Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

PMID 19848416 · PMC2789179 · Journal of proteome research · 2009 · 6 claims · 6 setups

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Transgelin (TAGLN), transgelin-2 (TAGLN2), and cyclophilin A (PPIA) are overexpressed in lung adenocarcinoma tissue compared to matched normal lung

matched excised additional formalin-fixed 2-d lc-ms quantitative
One-pot shotgun quantitative mass spectrometry characterization of histones.

PMID 19764812 · PMC2798817 · Journal of proteome research · 2009 · 8 claims · 8 setups

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One-pot propionylation and trypsin digestion of unfractionated bulk histones enables quantitative Bottom Up MS characterization of histone PTMs without prior off-line HPLC or SDS-PAGE purification

hela wild-type set2δ yeast bottom rp-hplc one-pot
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

Experiments

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

A mouse plasma peptide atlas as a resource for disease proteomics.

MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.

Decision tree-driven tandem mass spectrometry for shotgun proteomics.

A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.

Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

iTRAQ proteomic identification of pVHL-dependent and -independent targets of Egln1 prolyl hydroxylase knockdown in renal carcinoma cells.

Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

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

Quantitative proteomics analysis of maternal plasma in Down syndrome pregnancies using isobaric tagging reagent (iTRAQ).

Tissue proteomics reveals differential and compartment-specific expression of the homologs transgelin and transgelin-2 in lung adenocarcinoma and its stroma.

One-pot shotgun quantitative mass spectrometry characterization of histones.

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.