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).

• Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

  PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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  P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

  falciparum coli native falciparum-infected rt-pcr recombinant peptide

• Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

  PMID 19011008 · PMC2719557 · Investigative ophthalmology & visual science · 2009 · 6 claims · 5 setups

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  TGFBIp (multiple molecular weight forms) is significantly overexpressed in FECD HCEC-DM complex compared to normal endothelium

  pooled hcec-dm corneal 2-d western real-time

• Biomarkers of lupus nephritis determined by serial urine proteomics.

  PMID 18596723 · PMC2614389 · Kidney international · 2008 · 7 claims · 6 setups

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  SELDI-TOF-MS screening of the LMW urine proteome identifies protein ions that are differentially expressed across phases of the lupus nephritis flare cycle (baseline, pre-flare, flare, post-flare)

  low-molecular-weight lmw urine kidney seldi-tof-ms on-chip capillary

• Characterization of the 3a protein of SARS-associated coronavirus in infected vero E6 cells and SARS patients.

  PMID 15312778 · PMC7127270 · Journal of molecular biology · 2004 · 8 claims · 7 setups

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  ORF3a of SARS-CoV encodes an actual 31 kDa, 274-residue protein detected in infected cells and virions

  vero crude sera sars-cov 2d-lc-ms sds-page western

• The process chain for peptidomic biomarker discovery.

  PMID 16410650 · PMC3850862 · Disease markers · 2006 · 8 claims · 3 setups

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  Peptidomics (comprehensive analysis of peptides and small proteins <20 kDa) fills a methodological gap left by standard proteomics, which mainly addresses proteins in the ~10-200 kDa range.

  general body patients 2d-gel peptidomics peptidomic

• A catalog of human cDNA expression clones and its application to structural genomics.

  PMID 15345055 · PMC522878 · Genome biology · 2004 · 8 claims · 7 setups

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  A high-throughput screening approach can identify human cDNA clones from the hEx1 library that express soluble protein in E. coli

  hex1 ensembl coli recombinant small-scale tag-sequencing blastp

• Mass spectrometry for proteomics.

  PMID 18718552 · PMC2642903 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups

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  New instrumentation (Orbitrap) and new fragmentation methods (ETD) have enabled exciting new areas of proteomic application

  digested intact yeast large shotgun top-down quantitative

• The use of laser capture microscopy in proteomics research--a review.

  PMID 15502248 · PMC3839334 · Disease markers · 2004 · 8 claims · 8 setups

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  LCM allows purification of specific, histologically defined cell populations from heterogeneous tissue for downstream proteomic analysis

  breast prostate esophageal head maldi-tof automated two-dimensional

• Serum protein profile in systemic-onset juvenile idiopathic arthritis differentiates response versus nonresponse to therapy.

  PMID 15987476 · PMC1175022 · Arthritis research & therapy · 2005 · 8 claims · 8 setups

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  SELDI-TOF MS can differentiate serum protein profiles of active versus well-controlled SJIA

  serum clustered pooled trypsin-digested seldi-tof cart immunoprecipitation

• A new family of giardial cysteine-rich non-VSP protein genes and a novel cyst protein.

  PMID 17183673 · PMC1762436 · PloS one · 2006 · 8 claims · 7 setups

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  HCNCp is a novel invariant (non-variant) cyst protein belonging to a new family of high-cysteine membrane proteins (HCMp) abundant in the Giardia genome

  giardia serial northern western

• Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.

  PMID 17166507 · PMC7094463 · Journal of chromatography. A · 2007 · 8 claims · 8 setups

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  Standardizing sample preparation procedures for serum/plasma profiling is critical for obtaining reliable biomarkers, since slight procedural changes can produce very different protein profiles.

  serum aqueous maldi-tof seldi-tof peak

• Preclinical and post-treatment changes in the HCC-associated serum proteome.

  PMID 17060939 · PMC2360589 · British journal of cancer · 2006 · 7 claims · 6 setups

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  SELDI proteomic profiling of serum reveals consistent, statistically significant changes associated with the development of HCC in hepatitis C patients

  serum pooled excised seldi-tof anion lc-ms

• Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum.

  PMID 16980117 · PMC7159276 · Lancet (London, England) · 2006 · 8 claims · 5 setups

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  An SVM classifier trained on serum proteomic profiles discriminated patients with active tuberculosis from controls with clinically overlapping conditions

  serum computational kda spin-column seldi-tof supervised peptide

• 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 protein deposits on worn daily wear silicone hydrogel contact lenses.

  PMID 18989384 · PMC2579937 · Molecular vision · 2008 · 8 claims · 4 setups

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  Worn silicone hydrogel contact lenses deposit a wide array of proteins from the tear film and other sources.

  deposit excised pooled worn sds-page in-gel lc-ms-ms

• 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

• Developmental and genetic regulation of human surfactant protein B in vivo.

  PMID 18776725 · PMC2765709 · Neonatology · 2009 · 8 claims · 7 setups

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  Pro-SP-B peptides are more common in developmentally less mature humans (amniotic fluid, neonatal tracheal aspirates) than in adults

  amniotic tracheal bronchoalveolar simultaneous immunoblotting reducing gene

• Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.

  PMID 18616825 · PMC2492849 · BMC medical informatics and decision making · 2008 · 7 claims · 5 setups

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  An LAD classification model built from a support-set of 3 peptide peaks can distinguish stroke patients from controls with 75% accuracy on an independent validation set

  plasma discretized seldi-tof serum logical

• 93rd Annual Meeting of the American Association for Cancer Research, San Francisco, CA, USA, 6-10 April 2002.

  PMID 12100742 · PMC138737 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

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  Serial analysis of gene expression identifies genes preferentially expressed in ductal carcinoma in situ

  breast laser serum bladder cdna western seldi-tof

• Genetic Dissection of Tissue-Specific Apolipoprotein E Function for Hypercholesterolemia and Diet-Induced Obesity.

  PMID 26695075 · PMC4687855 · PloS one · 2015 · 8 claims · 8 setups

  Has reproduction

  Hepatocyte apoE is required for normal VLDL production and protects against diet-induced dyslipidemia

  liver plasma pooled real-time western elisa