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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Shotgun proteomic analysis of cerebrospinal fluid using off-gel electrophoresis as the first-dimension separation.
PMID 18778093 · PMC4582942 · Journal of proteome research · 2008 · 6 claims · 4 setups
OGE first-dimension fractionation enabled identification of 156 unique CSF proteins compared to 115 identified using SCX fractionation on the same CSF pool
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Prediction of missed cleavage sites in tryptic peptides aids protein identification in proteomics.
PMID 17203985 · PMC2664920 · Journal of proteome research · 2007 · 8 claims · 4 setups
An information-theoretic log-likelihood scoring method can predict experimentally observed missed cleavage sites from amino acid sequence alone with up to 90% accuracy.
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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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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
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.
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A pilot study of proteomic profiles of human hepatocellular carcinoma in the United States.
PMID 19535095 · PMC2859432 · The Journal of surgical research · 2009 · 8 claims · 3 setups
19 protein spots showed significant (>2-fold, P<0.01) abundance differences between HCC tumor and nonmalignant liver tissue
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A mouse plasma peptide atlas as a resource for disease proteomics.
PMID 18522751 · PMC2481425 · Genome biology · 2008 · 8 claims · 6 setups
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.
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In vivo pharmaco-proteomic analysis of hydroxyurea induced changes in the sickle red blood cell membrane proteome.
PMID 19914412 · PMC2818491 · Journal of proteomics · 2010 · 8 claims · 4 setups
2D-DIGE combined with tandem mass spectrometry identified 32 distinct sickle RBC membrane proteins that significantly changed in abundance after in vivo HU therapy
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Proteomics data repositories.
PMID 19795424 · PMC2908408 · Proteomics · 2009 · 5 claims · 5 setups
The YRC Public Data Repository (YRC PDR) provides a single unified interface disseminating multi-technology proteomics data (mass spectrometry, yeast two-hybrid, fluorescence microscopy, structure prediction) linked to protein annotations from many source databases.
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Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.
PMID 15642101 · PMC549070 · Genome biology · 2005 · 8 claims · 4 setups
PeptideAtlas, a public database integrating MS/MS-derived peptide identifications with the human genome, was built as an expandable resource for proteomic data.
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MAZIE: a mass and charge inference engine to enhance database searching of tandem mass spectra.
PMID 19850495 · PMC2818324 · Journal of the American Society for Mass Spectrometry · 2010 · 7 claims · 4 setups
MAZIE is a post-acquisition Perl algorithm that determines precursor ion monoisotopic mass and charge (+1 to +4) from MS1 zoom scan isotopic distributions on a Thermo LTQ-XL
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A surrogate-based approach for post-genomic partner identification.
PMID 11602024 · PMC57814 · BMC biotechnology · 2001 · 8 claims · 5 setups
Peptide surrogates derived from random phage display libraries contain amino acid sequence information that identifies the natural biological partner of the panned target via database searching.
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Novel gene and gene model detection using a whole genome open reading frame analysis in proteomics.
PMID 16646984 · PMC1557991 · Genome biology · 2006 · 8 claims · 4 setups
A six-frame genomic ORF translation used as an MS search database can detect novel peptides absent from standard protein databases, revealing incomplete genome annotation.
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An SVM-based system for predicting protein subnuclear localizations.
PMID 16336650 · PMC1325059 · BMC bioinformatics · 2005 · 7 claims · 3 setups
New kernels defined on k-peptide vectors mapped by BLOSUM62-based high-scored pair matrices (D1, D2, D3) improve SVM discrimination of protein subnuclear localization compared to conventional k-peptide encodings.
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Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.
PMID 16403238 · PMC1351203 · BMC bioinformatics · 2006 · 8 claims · 4 setups
No NPC proteome database existed prior to this work despite availability of other cancer proteome databases
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The Proteomic Code: a molecular recognition code for proteins.
PMID 17999762 · PMC2206014 · Theoretical biology & medical modelling · 2007 · 8 claims · 8 setups
The Proteomic Code is a set of rules by which genetic information is transferred into the physico-chemical properties of amino acids, determining protein-protein interactions and folding; it is part of the redundant Genetic Code.
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A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.
PMID 17521420 · PMC1929158 · Genome biology · 2007 · 7 claims · 6 setups
mtcPTM is a hierarchically organized database of human and mouse phosphosites that preserves experimental context, enabling comparison of phosphorylation patterns across conditions
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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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Toward proteome-scale identification and quantification of isoaspartyl residues in biological samples.
PMID 19663459 · PMC2756321 · Journal of proteome research · 2009 · 8 claims · 4 setups
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
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Protein structure quality assessment based on the distance profiles of consecutive backbone Cα atoms.
PMID 24555103 · PMC3892923 · F1000Research · 2013 · 8 claims · 8 setups
The distance between consecutive backbone Cα atoms in high-quality structures is normally distributed with mean 3.8 Å and standard deviation 0.04 Å, justifying a reference state in which all consecutive Cα atoms are 3.8 Å apart.
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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
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.