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).

• Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

  PMID 18788775 · PMC3744223 · Journal of proteome research · 2008 · 7 claims · 4 setups

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  PeptideProphet's fixed LDA coefficients for combining search scores (Xcorr', ΔCn, SpRank) may not be optimal under all search/instrument conditions.

  trypsin-digested mix serum same shotgun sequest lc-ms

• Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.

  PMID 16251401 · PMC1270952 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  ZFNs combining the FokI nuclease domain with custom zinc finger proteins can deliver site-specific double-strand breaks to plant and mammalian genomes.

  foki zif268-derived coli zfns limited foot-printing x-ray

• Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

  PMID 17052327 · PMC1626071 · BMC medical genetics · 2006 · 8 claims · 8 setups

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  RSTS is caused by chromosomal microdeletions and point mutations in one copy of CREBBP (16p13.3), consistent with haploinsufficiency of this dosage-sensitive gene

  peripheral patient-parent genomic crebbp karyotyping bac microsatellite

• 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

• 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

• Large-scale and high-confidence proteomic analysis of human seminal plasma.

  PMID 16709260 · PMC1779515 · Genome biology · 2006 · 8 claims · 6 setups

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  923 proteins were identified with high confidence in seminal plasma from a single individual, combining results from three ejaculate samples

  seminal same list combined sds-page database decoy

• 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

• MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes.

  PMID 17090601 · PMC1781136 · Nucleic acids research · 2007 · 8 claims · 8 setups

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  MAPU is a unified, freely accessible database integrating organellar, cellular, tissue and body fluid proteomes generated by high-resolution mass spectrometry.

  urine tear seminal breast gel lc-ms3 in-depth

• Immunohistochemical and proteomic evaluation of nuclear ubiquitous casein and cyclin-dependent kinases substrate in invasive ductal carcinoma of the breast.

  PMID 20069058 · PMC2801467 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 5 setups

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  NUCKS is highly overexpressed in invasive ductal carcinoma (IDC) of the breast compared to matched normal tissue.

  matched idc nucks rabbits lc-ms sds-page western

• The synovial proteome: analysis of fibroblast-like synoviocytes.

  PMID 15059280 · PMC400437 · Arthritis research & therapy · 2004 · 7 claims · 5 setups

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  2D-PAGE combined with MALDI mass spectrometry can characterize the FLS cellular proteome with high confidence

  fibroblast-like excised fls computational 2d-page in-gel maldi

• 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

• Wiggle-predicting functionally flexible regions from primary sequence.

  PMID 16839194 · PMC1500818 · PLoS computational biology · 2006 · 7 claims · 6 setups

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  A GNM-derived, correlation-weighted 'FF score' can objectively define functionally flexible regions (FFRs) that match experimentally confirmed flexible/functional regions (hinges, recognition loops, catalytic loops).

  hiv bovine calmodulin nonredundant gaussian gnm support

• Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

  PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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  GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.

  coli sds-page glutathione pepck-gst sds-page maldi-tof native

• 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

• Proteomic and phospho-proteomic profile of human platelets in basal, resting state: insights into integrin signaling.

  PMID 19859549 · PMC2762604 · PloS one · 2009 · 8 claims · 8 setups

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  A comprehensive platelet proteome of 1507 unique proteins was identified from ten independent human platelet samples, the most comprehensive platelet proteome assembled to date

  platelets platelet anti-coagulated lc-ms phospho-proteomic membrane

• 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

• Cyclic olefin homopolymer-based microfluidics for protein crystallization and in situ X-ray diffraction.

  PMID 19690369 · PMC2733880 · Acta crystallographica. Section D, Biological crystallography · 2009 · 8 claims · 7 setups

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  A COP-based microfluidics system (SpinX cards, 500 chambers of 320 nl each) was established for protein crystallization and in situ X-ray diffraction.

  chicken bovine p53 arabidopsis microbatch situ vapour-diffusion

• Mass spectrometry-based proteomic analyses of contact lens deposition.

  PMID 18334948 · PMC2254969 · Molecular vision · 2008 · 8 claims · 2 setups

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  Silicone hydrogel contact lenses deposit substantially less total protein than traditional soft (non-silicone) lens materials

  worn bradford nano-lc-ms

• Intracellular sorting and targeting of melanosomal membrane proteins: identification of signals for sorting of the human brown locus protein, gp75.

  PMID 7642699 · PMC2199968 · The Journal of cell biology · 1995 · 7 claims · 7 setups

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  The 36-amino acid cytoplasmic tail of gp75 alone is sufficient to direct intracellular retention and targeting of chimeric CD8 proteins to the endosomal/lysosomal compartment in fibroblasts

  melanoma sk-mel-19 immunoprecipitated coli immunofluorescence immunoelectron protease

• 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