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).

• Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors.

  PMID 16901338 · PMC1779605 · Genome biology · 2006 · 8 claims · 4 setups

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  491 proteins were identified in human tear fluid using in-gel digestion and LC-MS/MS/MS3 on LTQ-FT and LTQ-Orbitrap instruments

  closed-eye tear analysis sds-page in-solution gene

• Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.

  PMID 17203985 · PMC2664920 · Journal of proteome research · 2007 · 8 claims · 4 setups

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  An information-theoretic log-likelihood scoring method can predict experimentally observed missed cleavage sites from amino acid sequence alone with up to 90% accuracy.

  pepseeker local known swissprot tandem peptide pmf

• Proteomic identification of nitrated brain proteins in amnestic mild cognitive impairment: a regional study.

  PMID 17760844 · PMC3823261 · Journal of cellular and molecular medicine · 2007 · 8 claims · 5 setups

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  Total protein nitration (3-NT immunoreactivity) is significantly increased in MCI hippocampus and IPL compared to age-matched control brain

  postmortem excised mci 2d-page sypro in-gel

• Comparative cytochrome P450 proteomics in the livers of immunodeficient mice using 18O stable isotope labeling.

  PMID 17296599 · PMC2315784 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 5 setups

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  SDS-PAGE combined with post-digest 18O/16O labeling and LC-MS/MS enables relative quantification of multiple P450 proteins from liver microsomes, including highly homologous isoforms

  liver recombinant tryptic sds-page western mascot

• Using proteomic approach to identify tumor-associated antigens as markers in hepatocellular carcinoma.

  PMID 18672925 · PMC2680441 · Journal of proteome research · 2008 · 8 claims · 6 setups

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  34 immunoreactive protein spots were detected in 2DE Western blots probed with HCC patient sera but not normal sera

  hepg2 excised identified recombinant two-dimensional western in-gel

• Investigation of the human tear film proteome using multiple proteomic approaches.

  PMID 18334958 · PMC2268847 · Molecular vision · 2008 · 8 claims · 6 setups

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  Tear collection method (capillary vs. Schirmer strip) significantly impacts which proteins are detected in the tear film proteome.

  tear spectra 1d-sds-page 2d-sds-page mudpit

• 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

• Application of proteomics methods for pathogen discovery.

  PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

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  Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

  hlf sequences synthetic conventional 2d-dige gelc-ms

• High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.

  PMID 18597682 · PMC2483986 · BMC genomics · 2008 · 8 claims · 5 setups

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  High-accuracy MS proteomics (LTQ-Orbitrap) can be used to verify and improve gene annotation by identifying peptides specific to one of two competing annotation datasets.

  tuberculosis sanger spectra lc-ms sds-page signal

• Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

  PMID 18212748 · PMC2243141 · British journal of cancer · 2008 · 5 claims · 6 setups

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  LC-MS/MS proteomic analysis of stage I lung adenocarcinoma specimens identified myosin IIA and vimentin as candidate biomarker proteins with signal intensities that differed significantly among patient outcome groups

  surgically tryptic set lysates lc-ms mascot immunohistochemistry

• The effects of quercetin on SW480 human colon carcinoma cells: a proteomic study.

  PMID 15748282 · PMC555539 · Nutrition journal · 2005 · 8 claims · 4 setups

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  20 μM quercetin treatment of SW480 cells for 48 h consistently decreased expression of three proteins and increased expression of one protein across four independent experiments.

  sw480 excised two-dimensional quantitative mass