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 11

System / cell line: spectra ✕ Assay: trypsin ✕ Clear

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

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PeptideProphet's fixed LDA coefficients for combining search scores (Xcorr', ΔCn, SpRank) may not be optimal under all search/instrument conditions.

trypsin-digested mix serum same shotgun sequest lc-ms
Large-scale and high-confidence proteomic analysis of human seminal plasma.

PMID 16709260 · PMC1779515 · Genome biology · 2006 · 8 claims · 6 setups

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923 proteins were identified with high confidence in seminal plasma from a single individual, combining results from three ejaculate samples

seminal same list combined sds-page database decoy
Comparative cytochrome P450 proteomics in the livers of immunodeficient mice using 18O stable isotope labeling.

PMID 17296599 · PMC2315784 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 5 setups

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SDS-PAGE combined with post-digest 18O/16O labeling and LC-MS/MS enables relative quantification of multiple P450 proteins from liver microsomes, including highly homologous isoforms

liver recombinant tryptic sds-page western mascot
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
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
The synovial proteome: analysis of fibroblast-like synoviocytes.

PMID 15059280 · PMC400437 · Arthritis research & therapy · 2004 · 7 claims · 5 setups

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2D-PAGE combined with MALDI mass spectrometry can characterize the FLS cellular proteome with high confidence

fibroblast-like excised fls computational 2d-page in-gel maldi
In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

PMID 19764811 · PMC2783959 · Journal of proteome research · 2009 · 8 claims · 6 setups

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This is the first large-scale in vivo phosphoproteomic study of human skeletal muscle

vastus skeletal spectra identified phosphopeptide in-solution strong
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

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OGE first-dimension fractionation enabled identification of 156 unique CSF proteins compared to 115 identified using SCX fractionation on the same CSF pool

pooled csf spectra shotgun trypsin peptide
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

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Over half of confidently identified peptides in complex mixtures have S/N ratios below 10 on both FT-ICR and Orbitrap instruments

jurkat silac-based sds-page database
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
Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.

PMID 18510725 · PMC2481497 · Breast cancer research : BCR · 2008 · 7 claims · 7 setups

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Unsupervised hierarchical clustering of 130 SELDI-TOF peaks yielded six peak clusters and five distinct groups of breast cancer patients.

lysates breast microarrays imac-preseparated seldi-tof pilot immunohistochemistry

Experiments

Adaptive discriminant function analysis and reranking of MS/MS database search results for improved peptide identification in shotgun proteomics.

Large-scale and high-confidence proteomic analysis of human seminal plasma.

Comparative cytochrome P450 proteomics in the livers of immunodeficient mice using 18O stable isotope labeling.

Improved methods for the enrichment and analysis of glycated peptides.

Investigation of the human tear film proteome using multiple proteomic approaches.

The synovial proteome: analysis of fibroblast-like synoviocytes.

In vivo phosphoproteome of human skeletal muscle revealed by phosphopeptide enrichment and HPLC-ESI-MS/MS.

Shotgun proteomic analysis of cerebrospinal fluid using off-gel electrophoresis as the first-dimension separation.

The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.

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.

Surface-enhanced laser desorption/ionization time-of-flight proteomic profiling of breast carcinomas identifies clinicopathologically relevant groups of patients similar to previously defined clusters from cDNA expression.