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).
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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
Over half of confidently identified peptides in complex mixtures have S/N ratios below 10 on both FT-ICR and Orbitrap instruments
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Comparing cellular proteomes by mass spectrometry.
PMID 19886975 · PMC2784314 · Genome biology · 2009 · 8 claims · 6 setups
MS-based proteomics combined with cryo-electron tomography (CET) enables determination of absolute and relative protein abundances and localization
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iTRAQ proteomic identification of pVHL-dependent and -independent targets of Egln1 prolyl hydroxylase knockdown in renal carcinoma cells.
PMID 19159641 · PMC2716563 · Advances in enzyme regulation · 2009 · 7 claims · 4 setups
Egln1 knockdown induces P1465 hydroxylation and Ser5 phosphorylation of Rpb1 only in VHL(+) cells, not VHL(-) cells
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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
PeptideProphet's fixed LDA coefficients for combining search scores (Xcorr', ΔCn, SpRank) may not be optimal under all search/instrument conditions.
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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
CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling
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Has reproduction · 64
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
The LWS opsin gene was identified in 13 species of caecilians spanning 8 of 10 recognized families
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Has reproduction · 63
Comparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.
PMID 35038924 · PMC8764539 · mBio · 2022 · 7 claims · 8 setups
Of 42 isolates flagged as MRSA by screening agar, only 9 were PBP2a- and mecA-positive true MRSA, while the remaining 33 were mecA-negative and largely met criteria for BORSA
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Has reproduction · 90
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.
PMID 37012480 · PMC10172113 · Nature methods · 2023 · 8 claims · 5 setups
pSCoPE (prioritized precursor selection via MaxQuant.Live) increases sensitivity, data completeness, and proteome coverage more than twofold over shotgun single-cell proteomics
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A rational approach for discovering and validating cancer markers in very small samples using mass spectrometry and ELISA microarrays.
PMID 15502246 · PMC3839270 · Disease markers · 2004 · 8 claims · 4 setups
A two-stage strategy combining MS proteomics for discovery and ELISA microarrays for validation can identify and characterize cancer markers in very small samples
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Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.
PMID 17166507 · PMC7094463 · Journal of chromatography. A · 2007 · 8 claims · 8 setups
Standardizing sample preparation procedures for serum/plasma profiling is critical for obtaining reliable biomarkers, since slight procedural changes can produce very different protein profiles.
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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
Plasma is well suited to proteomic biomarker discovery because it is easily obtained, routinely used diagnostically, and has a rich proteome.
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Proteomic analysis of nipple aspirate fluid from women with early-stage breast cancer using isotope-coded affinity tags and tandem mass spectrometry reveals differential expression of vitamin D binding protein.
PMID 16542425 · PMC1431555 · BMC cancer · 2006 · 8 claims · 5 setups
ICAT tandem MS can identify and quantify differences in specific protein expression between NAF from tumor-bearing and disease-free breasts
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Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.
PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups
HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162
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Isoforms of U1-70k control subunit dynamics in the human spliceosomal U1 snRNP.
PMID 19784376 · PMC2747018 · PloS one · 2009 · 8 claims · 8 setups
Native human U1 snRNP shows differential incorporation of four protein isoforms (U1-70k isoforms 1/2, Sm-B/B')
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Proteomic and phototoxic characterization of melanolipofuscin: correlation to disease and model for its origin.
PMID 17392682 · PMC2642915 · Molecular vision · 2007 · 8 claims · 8 setups
MLF accumulation more closely reflects the onset of AMD than LF accumulation