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).

• An initial characterization of the serum phosphoproteome.

  PMID 19824718 · PMC2789176 · Journal of proteome research · 2009 · 8 claims · 8 setups

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  A TiO2-based phosphopeptide enrichment method coupled with LC-MS/MS (LTQ-Orbitrap CID and LTQ-ETD) was developed and applied to characterize the serum phosphoproteome

  u266 serum lc-ms immunoprecipitation sensitivity

• 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

• The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.

  PMID 18798661 · PMC2746028 · Journal of proteome research · 2008 · 8 claims · 7 setups

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  Over half of confidently identified peptides in complex mixtures have S/N ratios below 10 on both FT-ICR and Orbitrap instruments

  jurkat silac-based sds-page database

• Shotgun proteomics and biomarker discovery.

  PMID 12364816 · PMC3851423 · Disease markers · 2002 · 8 claims · 7 setups

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  Shotgun (LC/LC-MS/MS, e.g. MudPIT) proteomic approaches show advantages over gel-based techniques in speed, sensitivity, scope of analysis, and dynamic range.

  urine yeast cysteine-containing hemoglobin 2d-ge lc-ms imac

• Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells.

  PMID 17949499 · PMC2148065 · BMC genomics · 2007 · 8 claims · 8 setups

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  ECM-stimulated hMSC and OS-media-stimulated hMSC represent two distinct intermediate/transitional phenotypes en route to becoming osteoblasts

  naive hmsc osteoblasts proteomic lc-ms gene computational

• Versatile online-offline engine for automated acquisition of high-resolution tandem mass spectra.

  PMID 18841935 · PMC2716176 · Analytical chemistry · 2008 · 7 claims · 6 setups

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  An integrated hardware/software online-offline platform (TriVersa NanoMate + 12T LTQ FT Ultra + AUTOMATION WAREHOUSE) automates collection of high-resolution MS/MS data for polypeptides >3 kDa that cannot be acquired online on a chromatographic timescale

  acid-extracted hela online offline

• 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

• 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

• 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

• A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage.

  PMID 20026476 · PMC2849709 · Molecular & cellular proteomics : MCP · 2010 · 6 claims · 5 setups

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  A SILAC-based 'spatial proteomics' method can quantitatively measure the relative subcellular distribution of thousands of proteins across cytoplasm, nucleus, and nucleolus.

  hct116 silac silac-based immunofluorescence

• Toward proteome-scale identification and quantification of isoaspartyl residues in biological samples.

  PMID 19663459 · PMC2756321 · Journal of proteome research · 2009 · 8 claims · 4 setups

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  In ECD MS/MS, isoaspartyl (but not aspartyl) residues produce specific fragments c_n•+58.0054 (C2H2O2) and z_(l-n)-56.9976 (C2HO2), which serve as markers for Asp isomerization

  a431 brain ecd cad label-free

• Mass spectrometry for proteomics.

  PMID 18718552 · PMC2642903 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups

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  New instrumentation (Orbitrap) and new fragmentation methods (ETD) have enabled exciting new areas of proteomic application

  digested intact yeast large shotgun top-down quantitative

• Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production.

  PMID 37223250 · PMC10117727 · microLife · 2021 · 8 claims · 9 setups

  Has reproduction · 50

  Grad-seq resolves in-gradient sedimentation profiles for ~87-88% of annotated C. difficile transcripts and ~50% of annotated proteins, providing a comprehensive RNA-protein complexome resource

  difficile grad-seq rna-seq lc-ms

• 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

• Tags for labeling protein N-termini with subtiligase for proteomics.

  PMID 18762420 · PMC2590642 · Bioorganic & medicinal chemistry letters · 2008 · 6 claims · 4 setups

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  Arginine-rich peptide esters (3, 4, 5) are markedly more soluble than the original TEVest2 ester (1) and give significantly higher N-terminal tagging of proteins by subtiligase at higher concentrations.

  jurkat neutravidin-coated synthetic proteomic sds-page sandwich aqueous

• A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed.

  PMID 19828875 · PMC2816009 · Molecular & cellular proteomics : MCP · 2009 · 7 claims · 6 setups

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  A stacked-ring ion guide (S-lens) increases ion transmission from the source into the instrument roughly 10-fold in MS/MS mode and 3-5-fold in full scan mode

  intact bsa hela model top-down nanoflow ion

• Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

  PMID 36457147 · PMC9721438 · RNA biology · 2022 · 8 claims · 7 setups

  Has reproduction · 93

  Long-read RNA-seq detected 53,863 transcript isoforms from 10,426 genes in HUVECs, of which 22,195 were novel

  huvecs huvec long-read bottom-up offline

• 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