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).

• Perspectives of targeted mass spectrometry for protein biomarker verification.

  PMID 19818677 · PMC2795387 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  SRM/MRM mass spectrometry can quantify targeted proteotypic peptides as surrogates for candidate biomarker proteins in complex plasma samples

  proteins standard plasma sera srm multiplexed immunoaffinity-srm

• Proteomics as a tool for biomarker discovery.

  PMID 18057524 · PMC3851415 · Disease markers · 2007 · 8 claims · 7 setups

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  A useful clinical biomarker must be easily attainable, have adequate sensitivity, have adequate specificity, and lead to patient benefit through intervention

  serum laser ovarian seldi-tof two-dimensional gene

• Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

  PMID 18490959 · PMC2386506 · Molecular vision · 2008 · 7 claims · 6 setups

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  A novel affinity-enrichment strategy using UV cross-linked protease inhibitor peptides on Protein A/G columns improves capture of the TM protease proteome compared to SDS-PAGE fractionation alone

  cytosolic affinity-eluted porcine affinity-enriched affinity western sds-page

• A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.

  PMID 18613715 · PMC2601597 · Journal of proteome research · 2008 · 8 claims · 5 setups

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  A NCI source coupled via an added octopole and the c-trap to a QLT-orbitrap enables fast, efficient ETD reagent anion injection (4-8 ms)

  saccharomyces histone glioblastoma fluoranthene lc-ms etd anion

• Proteomic analysis of ovarian cancer cells reveals dynamic processes of protein secretion and shedding of extra-cellular domains.

  PMID 18560578 · PMC2409963 · PloS one · 2008 · 8 claims · 6 setups

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  Ovarian cancer cells exhibit extensive shedding of extra-cellular domains from cell surface proteins into the extracellular milieu.

  ovcar3 analysis lc-ms cell-surface silac

• 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

• Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

  PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups

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  A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity

  serum hplc-purified trypsin-digested crude seldi-tof-ms solid-phase maldi-tof-ms

• Methods for the proteomic identification of protease substrates.

  PMID 19729334 · PMC2787889 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Gel-based methods (2D-DiGE, diagonal electrophoresis, PROTOMAP) identify protease substrates by comparing proteolyzed versus control samples via electrophoretic migration differences followed by MS identification

  lysate jurkat apoptotic yeast 2d-dige protomap cofradic

• The use of neuroproteomics in drug abuse research.

  PMID 19926406 · PMC3947580 · Drug and alcohol dependence · 2010 · 8 claims · 8 setups

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  Neuroproteomic technologies (2D-DIGE, iTRAQ, ICAT, etc.) enable identification of protein-level changes underlying effects of drugs of abuse such as amphetamine, morphine, cocaine, and alcohol.

  rodent brain postmortem sectioned 2d-dige itraq heat

• 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

• Toxicoproteomics: a parallel approach to identifying biomarkers.

  PMID 12940285 · PMC1241639 · Environmental health perspectives · 2003 · 8 claims · 8 setups

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  Combining parallel DNA microarray and proteomic analyses on the same tissues merges microarray's gene discovery power with proteomics' ability to exploit post-translational modifications for biomarker identification.

  liver serum peptide digested two-dimensional seldi maldi

• Modification-specific proteomics: strategies for characterization of post-translational modifications using enrichment techniques.

  PMID 19743430 · PMC2892724 · Proteomics · 2009 · 8 claims · 8 setups

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  Lack of efficient enrichment procedures for PTM peptides is a major bottleneck in PTM proteomic research

  cytosolic cellular unspecified yeast immunoaffinity azide chemical

• 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