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).

• Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

  PMID 18490959 · PMC2386506 · Molecular vision · 2008 · 7 claims · 6 setups

  Full-text index only

  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

• Structural proteomics of the SARS coronavirus: a model response to emerging infectious diseases.

  PMID 17680348 · PMC7088133 · Journal of structural and functional genomics · 2007 · 8 claims · 8 setups

  Full-text index only

  Structures of 16 SARS-CoV proteins or functional domains have been determined, and 8 of these have novel folds

  sars-cov x-ray gst emsa

• Proteomics of the human malaria parasite Plasmodium falciparum.

  PMID 16445353 · PMC2721975 · Expert review of proteomics · 2006 · 8 claims · 8 setups

  Full-text index only

  Completion of the P. falciparum genome sequence together with advances in mass spectrometry has enabled large-scale proteomic analysis of the parasite that was previously limited by inability to identify proteins from 2D gels

  falciparum berghei falciparum-infected mudpit lc-ms co-immunoprecipitation

• Cellular proteins in influenza virus particles.

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

  Full-text index only

  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

• Proteomics and genomics: perspectives on drug and target discovery.

  PMID 18302945 · PMC2386992 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Protein kinases account for approximately 25% of research and development projects in biotechnology and pharma

  proteins blood carbohydrate medicinal x-ray microarrays glycan

• High-throughput crystallography for structural genomics.

  PMID 19765976 · PMC2764548 · Current opinion in structural biology · 2009 · 8 claims · 8 setups

  Full-text index only

  SG programs use genomic sequence data to select structurally novel protein targets, avoiding proteins with known structural homologues

  recombinant recalcitrant hundred family hydrogen situ site-directed

• Protein structure and function by the sea.

  PMID 11983051 · PMC139342 · Genome biology · 2002 · 8 claims · 8 setups

  Full-text index only

  High-throughput structural genomics (X-ray crystallography and NMR) can rapidly expand the number of solved protein structures far beyond what is currently in the Protein Data Bank.

  proteins membrane proteasome bacterial high-throughput electron x-ray

• Improved methods for the enrichment and analysis of glycated peptides.

  PMID 18989935 · PMC2752342 · Analytical chemistry · 2008 · 7 claims · 4 setups

  Full-text index only

  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

• 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

  Full-text index only

  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

• Analysis of nucleolar protein dynamics reveals the nuclear degradation of ribosomal proteins.

  PMID 17446074 · PMC1885954 · Current biology : CB · 2007 · 8 claims · 8 setups

  Full-text index only

  Newly synthesized ribosomal proteins accumulate in nucleoli more quickly than other nucleolar proteins

  hela post-mitotic pulsed fluorescence selective

• Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

  PMID 15502245 · PMC3839274 · Disease markers · 2004 · 7 claims · 3 setups

  Full-text index only

  Standardization of specimen collection, handling, storage, and choice of serum vs. plasma/anticoagulant is essential for comparable proteomic biomarker discovery.

  plasma ppp reference identification quantitative specimen

• SNAP: predict effect of non-synonymous polymorphisms on function.

  PMID 17526529 · PMC1920242 · Nucleic acids research · 2007 · 7 claims · 8 setups

  Full-text index only

  SNAP, a neural network-based method using sequence-derived information, predicts whether a non-synonymous SNP is neutral or non-neutral for protein function

  combined escherichia bacteriophage hiv-1 neural benchmark comparative

• Band 3 Courcouronnes (Ser667Phe): a trafficking mutant differentially rescued by wild-type band 3 and glycophorin A.

  PMID 18174378 · PMC2605348 · Blood · 2008 · 7 claims · 8 setups

  Full-text index only

  Homozygous SLC4A1 Ser667Phe mutation causes both hereditary spherocytosis and incomplete distal renal tubular acidosis in the proband

  erythrocyte genomic erythrocytes xenopus sds-page sscp dids

• Proteomics technologies and challenges.

  PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

  Full-text index only

  The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.

  serum myeloid formalin-fixed general maldi-tof phage maldi

• A catalog of human cDNA expression clones and its application to structural genomics.

  PMID 15345055 · PMC522878 · Genome biology · 2004 · 8 claims · 7 setups

  Full-text index only

  A high-throughput screening approach can identify human cDNA clones from the hEx1 library that express soluble protein in E. coli

  hex1 ensembl coli recombinant small-scale tag-sequencing blastp

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

  Full-text index only

  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand

• Defining the proteome.

  PMID 16356278 · PMC1414090 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  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

• Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

  PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

  Full-text index only

  P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

  falciparum coli native falciparum-infected rt-pcr recombinant peptide