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).

Publications 1.3k Datasets 392.5k Experiments 34

System / cell line: peptides ✕ Assay: comparison ✕ Clear

Bcipep: a database of B-cell epitopes.

PMID 15921533 · PMC1173103 · BMC genomics · 2005 · 8 claims · 2 setups

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Bcipep is a comprehensive database of experimentally determined linear B-cell epitopes compiled from literature and other public databases

synthetic antigenic anti-peptide sequence
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

PMID 18053132 · PMC2254445 · BMC bioinformatics · 2007 · 6 claims · 5 setups

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The paired oligo-border kernel (POBK) combined with SVMs predicts peptide adsorption/elution in SAX-SPE and retention time in IP-RP-HPLC more accurately than existing methods.

peptides peptide sax-spe ip-rp-hplc cross-run
Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

PMID 15626334 · PMC5172349 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 5 setups

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Well-resolved, reproducible 2-DE profiles of human lung squamous carcinoma and normal bronchial epithelial tissues were obtained under optimized conditions (0.75-mg protein load, TCA precipitation)

lung scanned excised peptide 2-d 2-de maldi-tof-ms
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

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mtcPTM is a hierarchically organized database of human and mouse phosphosites that preserves experimental context, enabling comparison of phosphorylation patterns across conditions

nonredundant database high-throughput homology
Improved methods for the enrichment and analysis of glycated peptides.

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

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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
Developmental and genetic regulation of human surfactant protein B in vivo.

PMID 18776725 · PMC2765709 · Neonatology · 2009 · 8 claims · 7 setups

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Pro-SP-B peptides are more common in developmentally less mature humans (amniotic fluid, neonatal tracheal aspirates) than in adults

amniotic tracheal bronchoalveolar simultaneous immunoblotting reducing gene
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
Applying proteomics to the diagnosis and treatment of ALS and related diseases.

PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups

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Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use

csf spinal biofluid muscle 2d-dige antibody luminex
Characterization of the 3a protein of SARS-associated coronavirus in infected vero E6 cells and SARS patients.

PMID 15312778 · PMC7127270 · Journal of molecular biology · 2004 · 8 claims · 7 setups

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ORF3a of SARS-CoV encodes an actual 31 kDa, 274-residue protein detected in infected cells and virions

vero crude sera sars-cov 2d-lc-ms sds-page western
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
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.

PMID 37012480 · PMC10172113 · Nature methods · 2023 · 8 claims · 5 setups

Has reproduction · 90

pSCoPE (prioritized precursor selection via MaxQuant.Live) increases sensitivity, data completeness, and proteome coverage more than twofold over shotgun single-cell proteomics

bulk hek293 single-cell bone prioritized single-cell spike-in
Proteomics in alcohol research.

PMID 12875051 · PMC6683837 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2002 · 7 claims · 8 setups

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The proteome is larger and more complex than the genome due to differential splicing, post-translational modifications (PTMs), and protein-protein interactions.

mixtures tryptic liver plasma two-dimensional liquid maldi-tof
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
Serum S100A6 concentration predicts peritoneal tumor burden in mice with epithelial ovarian cancer and is associated with advanced stage in patients.

PMID 19888321 · PMC2765613 · PloS one · 2009 · 8 claims · 8 setups

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Serum S100A6 concentration correlates with peritoneal tumor burden in a mouse OVCA xenograft model, based on inverse regression calibration against bioluminescent imaging data.

serum skov-3 pooled ovca lc-ms antigen whole-animal
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
MEROPS: the peptidase database.

PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

archaean holotype c-x-c proteins comparative domain substrate
Comparing cellular proteomes by mass spectrometry.

PMID 19886975 · PMC2784314 · Genome biology · 2009 · 8 claims · 6 setups

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MS-based proteomics combined with cryo-electron tomography (CET) enables determination of absolute and relative protein abundances and localization

leptospira saccharomyces specified shotgun selected cryo-electron
Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery.

PMID 19856998 · PMC2924679 · Journal of proteome research · 2009 · 7 claims · 4 setups

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RCL2/CS100-fixed tissues yield peptide and protein identifications by nanoRPLC-MS/MS comparable to matched fresh-frozen tissues, with proteome coverage not obviously compromised by fixation.

colonic rcl2 colon nanorplc-ms extraction laser
A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.

PMID 19813771 · PMC2789208 · Journal of proteome research · 2009 · 7 claims · 7 setups

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Coupling DRC (hexapeptide libraries) with 3D peptide fractionation (IEF + SCX + µLC-MS/MS) substantially increases the number of proteins identified in whole saliva

saliva offgel-fractionated identified sds-page trypsin strong
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

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ICAT tandem MS can identify and quantify differences in specific protein expression between NAF from tumor-bearing and disease-free breasts

paired icat-labeled spectra naf icat sds-page liquid

Experiments

Bcipep: a database of B-cell epitopes.

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

Proteomic comparison of two-dimensional gel electrophoresis profiles from human lung squamous carcinoma and normal bronchial epithelial tissues.

A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

Improved methods for the enrichment and analysis of glycated peptides.

Developmental and genetic regulation of human surfactant protein B in vivo.

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

Applying proteomics to the diagnosis and treatment of ALS and related diseases.

Characterization of the 3a protein of SARS-associated coronavirus in infected vero E6 cells and SARS patients.

IDEAL-Q, an automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation.

Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.

Proteomics in alcohol research.

The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

Serum S100A6 concentration predicts peritoneal tumor burden in mice with epithelial ovarian cancer and is associated with advanced stage in patients.

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

MEROPS: the peptidase database.

Comparing cellular proteomes by mass spectrometry.

Liquid chromatography-tandem and MALDI imaging mass spectrometry analyses of RCL2/CS100-fixed, paraffin-embedded tissues: proteomics evaluation of an alternate fixative for biomarker discovery.

A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.

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.