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 6

System / cell line: same ✕ 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
Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors.

PMID 16901338 · PMC1779605 · Genome biology · 2006 · 8 claims · 4 setups

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491 proteins were identified in human tear fluid using in-gel digestion and LC-MS/MS/MS3 on LTQ-FT and LTQ-Orbitrap instruments

closed-eye tear analysis sds-page in-solution gene
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
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.

Identification of 491 proteins in the tear fluid proteome reveals a large number of proteases and protease inhibitors.

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.

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.