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).

• High-accuracy proteome maps of human body fluids.

  PMID 17140426 · PMC1794581 · Genome biology · 2006 · 8 claims · 5 setups

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  Large-scale, high-accuracy MS analyses of tear fluid, urine, and seminal plasma provide high-quality datasets useful for biomarker discovery

  tear-duct urine seminal blood lc-ms large-scale decoy

• 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

• The use of proteomics in biomarker discovery in neurodegenerative diseases.

  PMID 15920295 · PMC3850612 · Disease markers · 2005 · 8 claims · 8 setups

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  A combination of low CSF-β-amyloid(1-42) with high CSF-tau and high CSF-phospho-tau is associated with an AD diagnosis

  csf serum two-dimensional seldi liquid-phase

• Proteomic approaches to cancer biomarkers.

  PMID 19931265 · PMC2873613 · Gastroenterology · 2010 · 8 claims · 8 setups

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  Combining abundant-protein depletion, offline fractionation, and subproteome (e.g., glycoproteome) enrichment with 2D LC-MS/MS increases the dynamic range and depth of blood proteome analysis for biomarker discovery.

  plasma serum capan-2 apcδ580 lectin silac elisa

• A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

  PMID 19087293 · PMC2636810 · BMC bioinformatics · 2008 · 6 claims · 6 setups

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  A theoretical exon-exon junction protein database accounting for all in-phase (frame-preserving) exon combinations can be built from the Ensembl Core Database using Perl/Bioperl/MySQL/Ensembl API.

  ensembl liver candidate same database tandem decoy

• 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 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

• 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

• The cancer secretome: a reservoir of biomarkers.

  PMID 18796163 · PMC2562990 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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  Cancer secretome analysis is a promising reservoir for identifying novel, non-invasive cancer biomarkers, addressing limitations of whole blood/serum proteomics

  a549 m-be sw480 neoplastic 2-de dige icat

• 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 European focus on proteomics.

  PMID 15128441 · PMC416463 · Genome biology · 2004 · 8 claims · 8 setups

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  MALDI-MS and ESI-MS are complementary techniques that identify overlapping but distinct subsets of proteins

  ribosomal breast ovarian prostate maldi-ms laser-capture fticr-ms