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).

• 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

• A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation.

  PMID 19888438 · PMC2771280 · Journal of biomedicine & biotechnology · 2010 · 6 claims · 6 setups

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  iTRAQ labelling combined with OFFGEL fractionation improves proteome coverage of human plasma compared to iTRAQ alone or no iTRAQ

  pooled plasma prefractionated immunodepleted itraq 1-dimensional fluorescence-based

• Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.

  PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups

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  A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.

  pooled genome est novel tandem whole-genome est

• 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

• 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

• Proteomic analysis of human aqueous humor using multidimensional protein identification technology.

  PMID 20019884 · PMC2793904 · Molecular vision · 2009 · 8 claims · 4 setups

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  Albumin/IgG depletion combined with MudPIT (2D-LC-MS/MS) enables high-confidence, extensive characterization of the human AH proteome

  pooled albumin-bound analysis mudpit immunoaffinity bca

• A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.

  PMID 16321154 · PMC1326206 · BMC neurology · 2005 · 7 claims · 6 setups

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  CFS, PGI and fibromyalgia are highly overlapping symptom complexes likely reflecting a shared underlying pathophysiological mechanism rather than distinct diseases

  pooled individual cerebrospinal subjects capillary trypsin elisa

• Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

  PMID 16403238 · PMC1351203 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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  No NPC proteome database existed prior to this work despite availability of other cancer proteome databases

  nasopharyngeal excised subset monoisotopic 2-de maldi-tof q-tof

• Comparative analysis of the tear protein profile in mycotic keratitis patients.

  PMID 18385783 · PMC2268856 · Molecular vision · 2008 · 8 claims · 5 setups

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  A glutaredoxin-related protein is expressed only in the tears of fungal keratitis patients and is absent in control tears.

  pooled in-gel peptide 2de two-dimensional maldi-tof post

• Proteomic profiling of amniotic fluid in preterm labor using two-dimensional liquid separation and mass spectrometry.

  PMID 19012186 · PMC3163445 · The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians · 2008 · 8 claims · 6 setups

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  Amniotic fluid protein composition can be analyzed by combining 2D liquid chromatography and mass spectrometry to identify differentially expressed proteins in preterm labor

  pooled amniotic two-dimensional sds-page maldi-tof

• 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

• Proteomic analysis identifies MMP-9, DJ-1 and A1BG as overexpressed proteins in pancreatic juice from pancreatic ductal adenocarcinoma patients.

  PMID 18706098 · PMC2528014 · BMC cancer · 2008 · 7 claims · 6 setups

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  MMP-9, DJ-1 and A1BG are overexpressed in pancreatic juice and tissue from PDAC patients compared with cancer-free/normal controls

  pooled individual trypsin-digested pancreatic two-dimensional difference maldi-tof-ms

• Proteomics analysis reveals novel components in the detergent-insoluble subproteome in Alzheimer's disease.

  PMID 19746990 · PMC2784247 · Journal of proteome research · 2009 · 8 claims · 5 setups

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  A label-free XIC-based LC-MS/MS quantitation strategy, combined with an FTLD-U comparator cohort, can be used to identify AD-specific changes in the detergent-insoluble brain subproteome.

  pooled postmortem individual detergent-insoluble lc-ms sequential sds-page

• Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.

  PMID 19693676 · PMC2824116 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 7 setups

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  Proteomic screening of human synaptosomes identifies a set of proteins differentially expressed in HIV/AIDS brain

  frontal excised synaptosome paraffin-embedded 2d-page maldi-tof western

• Differential proteome analysis of the preeclamptic placenta using optimized protein extraction.

  PMID 19756160 · PMC2742651 · Journal of biomedicine & biotechnology · 2010 · 8 claims · 5 setups

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  Solubilization with urea/CHAPS combined with dichloromethane/methanol or acidified acetone precipitation gives the best 2D-PAGE protein separation for placental tissue

  placental excised placenta 1d-page 2d-page maldi-tof

• 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

• 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

• Differential protein expression in human corneal endothelial cells cultured from young and older donors.

  PMID 18852868 · PMC2565687 · Molecular vision · 2008 · 8 claims · 5 setups

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  Cultured HCEC protein profiles show age-related differences between young and older donors

  corneal 2-d trypsin-digested confluent 2-d gel maldi-tof

• 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

• 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