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).

• Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.

  PMID 19121650 · PMC2706936 · Journal of proteomics · 2009 · 7 claims · 5 setups

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  A new MRM worksheet was implemented in The Global Proteome Machine database (GPMDB) that provides all information needed to design MRM transitions based solely on archived observations from previous experiments by other researchers.

  platelet proteins reaction midas mrm

• Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter.

  PMID 17720713 · PMC2034477 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  The native 22-nt c-kit87 sequence occurs only once in the entire human genome.

  genome synthetic c-kit87 c-kit genome-wide circular molecular

• RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

  PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups

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  Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.

  consensus sap query all-against-all blast cross-database

• A mouse plasma peptide atlas as a resource for disease proteomics.

  PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups

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  A publicly available, high-quality mouse plasma peptide/protein repository (mouse PeptideAtlas) was built from 568 LC-MS/MS runs on four reference plasma pools.

  plasma peptides fully tissues lc-ms anion database

• The PeptideAtlas project.

  PMID 16381952 · PMC1347403 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  PeptideAtlas provides an automated repository that identifies peptides by MS/MS, statistically validates identifications, and maps them to eukaryotic genomes to enable data exchange and integration with genomic data.

  plasma drosophila yeast tandem sequence

• 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

• Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

  PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

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  CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

  sputum phage metagenomes inferred metagenomic functional diversity

• Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

  PMID 40990923 · PMC12687342 · Evolution; international journal of organic evolution · 2025 · 8 claims · 5 setups

  Has reproduction · 64

  The LWS opsin gene was identified in 13 species of caecilians spanning 8 of 10 recognized families

  caecilian caecilia archival lws pcr eye histology

• Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

  PMID 16141191 · PMC1197137 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  A novel 'bioluminometric assay coupled with terminator (ddNTP) incorporation' (BATI) platform was developed for multiplex SNP typing in a single reaction chamber.

  pcr-amplified same sequence luciferase bioluminometric bati comparison

• Antibody binding loop insertions as diversity elements.

  PMID 17023486 · PMC1635297 · Nucleic acids research · 2006 · 7 claims · 8 setups

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  A lysozyme-binding VHH CDR3 loop can be grafted into two surface-exposed loops of superfolder GFP, conferring lysozyme-binding activity while the protein remains fluorescent.

  gfp-anti-lysozyme coli full-length gfp-hcdr3 elisa flow surface

• Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

  PMID 17576681 · PMC1934990 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  Cryptic 5'ss are best predicted by computational algorithms that accommodate nucleotide dependencies (e.g., Markov model, maximum entropy, maximum dependence decomposition) rather than by weight-matrix models

  disease mammalian compiled literature minigene computational

• Biomarkers of lupus nephritis determined by serial urine proteomics.

  PMID 18596723 · PMC2614389 · Kidney international · 2008 · 7 claims · 6 setups

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  SELDI-TOF-MS screening of the LMW urine proteome identifies protein ions that are differentially expressed across phases of the lupus nephritis flare cycle (baseline, pre-flare, flare, post-flare)

  low-molecular-weight lmw urine kidney seldi-tof-ms on-chip capillary

• 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

• Proteomic analysis of stage I primary lung adenocarcinoma aimed at individualisation of postoperative therapy.

  PMID 18212748 · PMC2243141 · British journal of cancer · 2008 · 5 claims · 6 setups

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  LC-MS/MS proteomic analysis of stage I lung adenocarcinoma specimens identified myosin IIA and vimentin as candidate biomarker proteins with signal intensities that differed significantly among patient outcome groups

  surgically tryptic set lysates lc-ms mascot immunohistochemistry

• High-throughput genomic technology in research and clinical management of breast cancer. Plasma-based proteomics in early detection and therapy.

  PMID 17184556 · PMC1797031 · Breast cancer research : BCR · 2006 · 8 claims · 8 setups

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  Plasma is well suited to proteomic biomarker discovery because it is easily obtained, routinely used diagnostically, and has a rich proteome.

  plasma serum maldi-tof seldi-tof tandem

• A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

  PMID 19087293 · PMC2636810 · BMC bioinformatics · 2008 · 6 claims · 6 setups

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  A theoretical exon-exon junction protein database accounting for all in-phase (frame-preserving) exon combinations can be built from the Ensembl Core Database using Perl/Bioperl/MySQL/Ensembl API.

  ensembl liver candidate same database tandem decoy

• Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

  PMID 15640441 · PMC546178 · Nucleic acids research · 2005 · 8 claims · 7 setups

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  NCL aggregation of DNA-modified gold nanoparticles shows extraordinary selectivity against terminal mismatches at the free ends of surface-bound duplexes

  probe-modified probe-gnp synthetic four uv-vis ssdna pcr