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

• Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

  PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

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  Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

  pooled computational identified additional label-free lspad pathway-associated

• 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

• Identification of beta-secretase (BACE1) substrates using quantitative proteomics.

  PMID 20041192 · PMC2793532 · PloS one · 2009 · 7 claims · 5 setups

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  Quantitative proteomics of conditioned medium from BACE1-overexpressing HEK and HeLa cells identified 68 putative β-secretase substrates

  hek293 hela hek concentrated silac western sds-page

• IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

  PMID 19752006 · PMC2808259 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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  IDEAL-Q predicts the elution time of peptides unidentified in a given LC-MS/MS run (but identified in others) using a computation-efficient linear regression plus fragmental refining function, avoiding costly whole-dataset pattern recognition

  standard thp-1 replicate lc-ms manual cross-instrument

• Cellular proteins in influenza virus particles.

  PMID 18535660 · PMC2390764 · PLoS pathogens · 2008 · 8 claims · 6 setups

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  Purified influenza virions contain 36 host-encoded cellular proteins in addition to the 9 previously known viral proteins.

  influenza deglycosylated sucrose lc-ms mudpit electron

• 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

• Enthoprotin: a novel clathrin-associated protein identified through subcellular proteomics.

  PMID 12213833 · PMC2173151 · The Journal of cell biology · 2002 · 8 claims · 8 setups

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  Subcellular proteomics of purified CCVs identifies enthoprotin (encoded by KIAA0171), a novel ENTH domain-containing protein not previously detected at the protein level.

  brain cos-7 hek-293 clathrin subcellular western ccv

• The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins.

  PMID 16948836 · PMC1794545 · Genome biology · 2006 · 8 claims · 6 setups

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  Identified 1543 proteins in urine from ten healthy donors while essentially eliminating false-positive identifications

  urine pooled urinary identified sds-page albumin decoy

• 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

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  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.

  plasma excised fractionated 2d-dige multi-dimensional lc-ms

• 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

• A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation.

  PMID 19888438 · PMC2771280 · Journal of biomedicine & biotechnology · 2010 · 6 claims · 6 setups

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  iTRAQ labelling combined with OFFGEL fractionation improves proteome coverage of human plasma compared to iTRAQ alone or no iTRAQ

  pooled plasma prefractionated immunodepleted itraq 1-dimensional fluorescence-based

• The development of an integrated platform to identify breast cancer glycoproteome changes in human serum.

  PMID 19782370 · PMC4142217 · Journal of chromatography. A · 2010 · 8 claims · 6 setups

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  M-LAC (multi-lectin affinity chromatography combining Con A, WGA and Jacalin) provides comprehensive capture of glycoproteins from biological fluids based on differing glycan specificities

  pooled m-lac excised individual high-performance sds-page lectin

• Proteomic analysis of the mammalian nuclear pore complex.

  PMID 12196509 · PMC2173148 · The Journal of cell biology · 2002 · 8 claims · 7 setups

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  Mass spectrometry was used to identify all proteins present in a biochemically purified rat liver NPC fraction.

  liver empigen transiently mass sds-page electron

• Comparative proteomics of clathrin-coated vesicles.

  PMID 17116749 · PMC2064594 · The Journal of cell biology · 2006 · 8 claims · 4 setups

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  A comparative proteomics strategy contrasting CCV fractions from control and clathrin-depleted (CHC siRNA knockdown) HeLa cells can distinguish genuine CCV proteins from copurifying contaminants

  hela western sds-page difference

• A novel approach to tag and identify geranylgeranylated proteins.

  PMID 19784953 · PMC2855049 · Electrophoresis · 2009 · 7 claims · 7 setups

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  Metabolic incorporation of azido-GG alcohol followed by Cu(I)-catalyzed click reaction with TAMRA-alkyne selectively labels geranylgeranylated proteins for fluorescence detection

  jurkat cos-7 mcf-7 embryonic metabolic comparative fractionation

• 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

• One-pot shotgun quantitative mass spectrometry characterization of histones.

  PMID 19764812 · PMC2798817 · Journal of proteome research · 2009 · 8 claims · 8 setups

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  One-pot propionylation and trypsin digestion of unfractionated bulk histones enables quantitative Bottom Up MS characterization of histone PTMs without prior off-line HPLC or SDS-PAGE purification

  hela wild-type set2δ yeast bottom rp-hplc one-pot

• Proteomics analysis reveals novel components in the detergent-insoluble subproteome in Alzheimer's disease.

  PMID 19746990 · PMC2784247 · Journal of proteome research · 2009 · 8 claims · 5 setups

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  A label-free XIC-based LC-MS/MS quantitation strategy, combined with an FTLD-U comparator cohort, can be used to identify AD-specific changes in the detergent-insoluble brain subproteome.

  pooled postmortem individual detergent-insoluble lc-ms sequential sds-page

• Mouse-specific tandem IgY7-SuperMix immunoaffinity separations for improved LC-MS/MS coverage of the plasma proteome.

  PMID 19722698 · PMC2783519 · Journal of proteome research · 2009 · 7 claims · 6 setups

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  Tandem IgY7-SuperMix separation nearly doubles overall proteome coverage compared to IgY7 flow-through alone (523 vs 263 confidently identified proteins)

  plasma identified lc-ms sds-page spike-in