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).

• Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

  PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups

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  DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)

  standard dsic-labeled immunodepleted serum labeling quantitative in-solution

• A high-temporal resolution technology for dynamic proteomic analysis based on 35S labeling.

  PMID 18714357 · PMC2500177 · PloS one · 2008 · 6 claims · 6 setups

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  35S pulse-labeling (phosphor-imaging) detects more protein spots with higher sensitivity than CBB staining on the same 2-DE gels

  a549 liver 35s electrophoresis paired

• Proteomics analysis of the expression of neurogranin in murine neuroblastoma (Neuro-2a) cells reveals its involvement for cell differentiation.

  PMID 17505539 · PMC1865092 · International journal of biological sciences · 2007 · 6 claims · 5 setups

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  Expression of Ng in Neuro-2a cells causes widespread down-regulation of microtubule components and associated proteins that mediate neurite outgrowth

  neuro-2a hek293 icat western morphology

• 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

• 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

• From genomes to systems.

  PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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  Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

  serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr

• Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

  PMID 15502245 · PMC3839274 · Disease markers · 2004 · 7 claims · 3 setups

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  Standardization of specimen collection, handling, storage, and choice of serum vs. plasma/anticoagulant is essential for comparable proteomic biomarker discovery.

  plasma ppp reference identification quantitative specimen

• Proteomics technologies and challenges.

  PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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  The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.

  serum myeloid formalin-fixed general maldi-tof phage maldi

• 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

• Determination of glycosylation sites and site-specific heterogeneity in glycoproteins.

  PMID 19700364 · PMC2749913 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Mass spectrometry has emerged as the premier tool for structural determination of oligosaccharides/glycans and glycopeptides

  glycoproteins n-linked serum complex maldi tryptic nonspecific

• 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

• Glycomic analysis: an array of technologies.

  PMID 19728746 · PMC3443568 · ACS chemical biology · 2009 · 8 claims · 8 setups

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  Glycosylation is the most prevalent protein post-translational modification, occurring on at least 50% of all proteins

  sera t-cells serum glycoproteins lectin hydrazide bioorthogonal

• Defining the proteome.

  PMID 16356278 · PMC1414090 · Genome biology · 2005 · 8 claims · 8 setups

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  Integration of multi-omics data is an important step toward a systems-biology approach to the proteome

  brain chicken bacillus yeast proteome proteomics two-dimensional