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 15

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

Shotgun proteomics and biomarker discovery.

PMID 12364816 · PMC3851423 · Disease markers · 2002 · 8 claims · 7 setups

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Shotgun (LC/LC-MS/MS, e.g. MudPIT) proteomic approaches show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range.

urine yeast cysteine-containing hemoglobin 2d-ge lc-ms imac
Of mice and men: comparative proteomics of bronchoalveolar fluid.

PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups

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Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.

pooled oxidative unpooled balf shotgun functional protein-protein
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
An initial characterization of the serum phosphoproteome.

PMID 19824718 · PMC2789176 · Journal of proteome research · 2009 · 8 claims · 8 setups

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A TiO2-based phosphopeptide enrichment method coupled with LC-MS/MS (LTQ-Orbitrap CID and LTQ-ETD) was developed and applied to characterize the serum phosphoproteome

u266 serum lc-ms immunoprecipitation sensitivity
Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome.

PMID 19722698 · PMC2783519 · Journal of proteome research · 2009 · 7 claims · 6 setups

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Tandem IgY7-SuperMix separation nearly doubles overall proteome coverage compared to IgY7 flow-through alone (523 vs 263 confidently identified proteins)

plasma identified lc-ms sds-page spike-in
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
Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.

PMID 20005973 · PMC2891339 · The international journal of biochemistry & cell biology · 2010 · 8 claims · 5 setups

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CD45- splenic stem cell-specific proteins are identical to core iPS/ES markers OCT3/4, SOX2, KLF4, c-MYC and NANOG.

spleen cd45 hox11+ lc-ms rt-pcr immunofluorescence
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
Comparing cellular proteomes by mass spectrometry.

PMID 19886975 · PMC2784314 · Genome biology · 2009 · 8 claims · 6 setups

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MS-based proteomics combined with cryo-electron tomography (CET) enables determination of absolute and relative protein abundances and localization

leptospira saccharomyces specified shotgun selected cryo-electron
Urinary proteomic profiling for diagnostic bladder cancer biomarkers.

PMID 19811072 · PMC3422861 · Expert review of proteomics · 2009 · 8 claims · 8 setups

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Single protein biomarkers (e.g., NMP-22, BTA) suffer from high false-positive rates and none have replaced cystoscopy or cytology for bladder cancer detection.

urine page gel 2d-dige
Proteomic-based identification of maternal proteins in mature mouse oocytes.

PMID 19646285 · PMC2730056 · BMC genomics · 2009 · 8 claims · 6 setups

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625 different proteins were identified from 2700 zona pellucida-free mature mouse MII oocytes, the largest oocyte proteome catalog to date

mature mii identified tissues sds-page acid gene
Application of proteomics methods for pathogen discovery.

PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

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Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

hlf sequences synthetic conventional 2d-dige gelc-ms
Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

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Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

serum frozen ig-depleted clinical seldi-tof maldi lc-ms
Comparing protein abundance and mRNA expression levels on a genomic scale.

PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

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Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded
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

Experiments

Shotgun proteomics and biomarker discovery.

Of mice and men: comparative proteomics of bronchoalveolar fluid.

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

An initial characterization of the serum phosphoproteome.

Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome.

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

Proteomics identifies multipotent and low oncogenic risk stem cells of the spleen.

Improved methods for the enrichment and analysis of glycated peptides.

Comparing cellular proteomes by mass spectrometry.

Urinary proteomic profiling for diagnostic bladder cancer biomarkers.

Proteomic-based identification of maternal proteins in mature mouse oocytes.

Application of proteomics methods for pathogen discovery.

Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

Comparing protein abundance and mRNA expression levels on a genomic scale.

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