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).
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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
An information-theoretic log-likelihood scoring method can predict experimentally observed missed cleavage sites from amino acid sequence alone with up to 90% accuracy.
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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
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.
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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
491 proteins were identified in human tear fluid using in-gel digestion and LC-MS/MS/MS3 on LTQ-FT and LTQ-Orbitrap instruments
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Cellular proteins in influenza virus particles.
PMID 18535660 · PMC2390764 · PLoS pathogens · 2008 · 8 claims · 6 setups
Purified influenza virions contain 36 host-encoded cellular proteins in addition to the 9 previously known viral proteins.
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Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.
PMID 19912651 · PMC2784748 · BMC cell biology · 2009 · 7 claims · 7 setups
hnRNP L is a novel Sam68-interacting protein partner identified by proteomics and confirmed by co-immunoprecipitation
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Synaptic proteins linked to HIV-1 infection and immunoproteasome induction: proteomic analysis of human synaptosomes.
PMID 19693676 · PMC2824116 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 7 setups
Proteomic screening of human synaptosomes identifies a set of proteins differentially expressed in HIV/AIDS brain
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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
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
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Investigation of the human tear film proteome using multiple proteomic approaches.
PMID 18334958 · PMC2268847 · Molecular vision · 2008 · 8 claims · 6 setups
Tear collection method (capillary vs. Schirmer strip) significantly impacts which proteins are detected in the tear film proteome.
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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
51 citrullinated protein spots were detected in RA synovial tissue, of which 30 (58.8%) were autoantigenic (reactive with RA sera)
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High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.
PMID 20037647 · PMC2793016 · PloS one · 2009 · 7 claims · 7 setups
A dirty genome approach using unfinished, unclosed genome sequences combined with proteomics can rapidly identify immunogenic proteins useful for diagnostic tool development
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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
34 immunoreactive protein spots were detected in 2DE Western blots probed with HCC patient sera but not normal sera
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Dissociation of the carbohydrate-binding and splicing activities of galectin-1.
PMID 18662664 · PMC2590671 · Archives of biochemistry and biophysics · 2008 · 7 claims · 7 setups
GST-Gal3 and GST-Gal1 pull down the general transcription factor TFII-I from HeLa nuclear extract, identified by mass spectrometry and confirmed by immunoblot
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Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.
PMID 16403238 · PMC1351203 · BMC bioinformatics · 2006 · 8 claims · 4 setups
No NPC proteome database existed prior to this work despite availability of other cancer proteome databases
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Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.
PMID 17303479 · PMC7105233 · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2007 · 5 claims · 5 setups
Pre-fractionation of plasma with immuno-affinity depletion and anion-exchange chromatography prior to 2D-DIGE substantially increases the number of detectable protein spots compared with unfractionated plasma.
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Proteomic analysis of RCL2 paraffin-embedded tissues.
PMID 19012729 · PMC4506168 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups
RCL2-fixed paraffin-embedded (RCL2P) tissue consistently gives the highest protein yield compared to FFPE and frozen tissue across extraction protocols