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).

• 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

• Measurement reproducibility in the early stages of biomarker development.

  PMID 15665389 · PMC3839328 · Disease markers · 2004 · 6 claims · 3 setups

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  Functional PCA can be used as the basis for gauge R&R (repeatability and reproducibility) assessment of mass spectra without prior identification of which spectral features are biomarkers

  pooled same registered seldi-tof univariate functional

• 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

• 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

• 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

• An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

  PMID 16872505 · PMC1550395 · BMC medical genetics · 2006 · 7 claims · 7 setups

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  Marginally significant (uncorrected) transmission distortion was found for four SNPs after stratification by HLA-DRB1*1501 status, disease course, or gender.

  pooled australian independent trio pool snapshot snplex

• Identification of serum biomarkers for colon cancer by proteomic analysis.

  PMID 16755300 · PMC2361335 · British journal of cancer · 2006 · 8 claims · 8 setups

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  Complement C3a des-arg, α1-antitrypsin and transferrin were identified as serum proteins with diagnostic potential for CRC.

  serum pooled seldi seldi-tof seldi artificial

• 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

• Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.

  PMID 19055809 · PMC2657802 · BMC bioinformatics · 2008 · 7 claims · 5 setups

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  QC processes for identifying and removing low-quality spectra are often overlooked in proteomic profiling studies

  serum pooled duplicate full seldi-tof principal technical

• 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

• 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

• Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

  PMID 16895448 · PMC1523240 · PLoS genetics · 2006 · 8 claims · 8 setups

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  MALDI-TOF MS-based primer extension assays (hME, iPLEX) enable cost-effective, high-throughput multiplexed SNP genotyping

  genomic domestic pooled colorectal snp pooling microsatellite

• In vivo pharmaco-proteomic analysis of hydroxyurea induced changes in the sickle red blood cell membrane proteome.

  PMID 19914412 · PMC2818491 · Journal of proteomics · 2010 · 8 claims · 4 setups

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  2D-DIGE combined with tandem mass spectrometry identified 32 distinct sickle RBC membrane proteins that significantly changed in abundance after in vivo HU therapy

  sickle excised patients 2d-dige tandem immunoblot

• A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease.

  PMID 19823678 · PMC2757911 · PloS one · 2009 · 6 claims · 4 setups

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  SLC10A2 is a novel susceptibility gene for cholelithiasis in humans

  genomic pooled sanger maldi-tof genotype-phenotype

• Pre-operative urinary cathepsin D is associated with survival in patients with renal cell carcinoma.

  PMID 19789534 · PMC2768081 · British journal of cancer · 2009 · 8 claims · 7 setups

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  Cathepsin D, identified via comparative 2D PAGE of conditioned media from RCC cell lines vs normal renal cultures, is a candidate secreted biomarker of RCC

  htb49 excised conditioned urine page maldi 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

• Target SNP selection in complex disease association studies.

  PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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  A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

  genes pooled primer computational maldi-tof blast

• 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

• 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