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 15

System / cell line: ph+ ✕ Assay: mass ✕ Clear

Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

PMID 17124346 · PMC3862287 · Disease markers · 2006 · 8 claims · 5 setups

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SELDI-TOF MS serum profiling can discriminate MM patients with vs without skeletal (bone lesion) involvement using peak biomarkers

serum seldi seldi-tof serum univariate
Glycoprotein structural genomics: solving the glycosylation problem.

PMID 17355862 · PMC1885966 · Structure (London, England : 1993) · 2007 · 8 claims · 5 setups

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Transiently expressing glycoproteins in HEK293T cells with kifunensine or swainsonine allows correct folding while retaining endo H sensitivity, solving the glycosylation problem for structural genomics

s19a srptpμ hek293t maldi-tof endoglycosidase x-ray
An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.

PMID 15005801 · PMC341449 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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An XML schema called Annotated Gel Markup Language (AGML) is proposed to manage, analyze, and disseminate annotated 2D gel electrophoresis and MS results.

biological 2de agml gel mass visualization
Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.

coli sds-page glutathione pepck-gst sds-page maldi-tof native
Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.

PMID 18416831 · PMC2377273 · BMC cancer · 2008 · 6 claims · 4 setups

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Three protein spots were significantly altered in abundance between metastase-positive and metastase-negative breast cancer patient groups

excised formalin-fixed log-normalized two-dimensional liquid immunohistochemistry
Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

PMID 36457147 · PMC9721438 · RNA biology · 2022 · 8 claims · 7 setups

Has reproduction · 93

Long-read RNA-seq detected 53,863 transcript isoforms from 10,426 genes in HUVECs, of which 22,195 were novel

huvecs huvec long-read bottom-up offline
Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.

PMID 17166507 · PMC7094463 · Journal of chromatography. A · 2007 · 8 claims · 8 setups

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Standardizing sample preparation procedures for serum/plasma profiling is critical for obtaining reliable biomarkers, since slight procedural changes can produce very different protein profiles.

serum aqueous maldi-tof seldi-tof peak
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

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HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162

monocyte-derived mdm mdms western p24 seldi-tof sds-page
Biochemical and functional characterization of the membrane association and membrane permeabilizing activity of the severe acute respiratory syndrome coronavirus envelope protein.

PMID 16507314 · PMC7111751 · Virology · 2006 · 7 claims · 8 setups

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Expression of SARS-CoV E protein in mammalian cells alters membrane permeability

hela sf9 hygromycin site-directed subcellular
Placental proteomics: a shortcut to biological insight.

PMID 19070895 · PMC3532024 · Placenta · 2009 · 7 claims · 5 setups

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Developed a novel small cationic colloidal silica (smCCS) method to uniformly enrich the apical plasma membrane of the syncytiotrophoblast (STB) for proteomics analysis

placenta smccs-coated electron 2-dimensional immunoblot
Tubulin proteomics: towards breaking the code.

PMID 18840397 · PMC4039029 · Analytical biochemistry · 2009 · 8 claims · 8 setups

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Tubulin isotype and posttranslational-modification diversity constitutes a 'tubulin code' that is read by microtubule-associated proteins and translates into specific in vivo functions

bovine mda-mb-231 cancer a549 maldi-tof tandem sds-page
Microbial genomics: from sequence to function.

PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

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Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.

yeast bacteria microbial high-throughput microarray ribosomal
'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.

PMID 20001958 · PMC3022307 · The Biochemical journal · 2009 · 8 claims · 8 setups

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Comparative genomics is the single most effective strategy for predicting functions of unknown proteins and finding genes for orphan enzymes

lactococcus lactis arabidopsis coli gene recombinant enzyme
Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.

PMID 28789673 · PMC5549432 · BMC research notes · 2017 · 7 claims · 7 setups

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Gene and transcript abundances of bacterial type III secretion system (T3SS) genes are positively correlated with methane yield in sheep

rumen reassembled succinivibrio dextrinosolvens metagenomic metatranscriptomic 16s
Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions.

PMID 36560952 · PMC9763275 · Frontiers in microbiology · 2022 · 8 claims · 8 setups

Has reproduction · 54

Inoculation with SAICEUPSM^T significantly reduces the oxidative stress enzymatic response (CAT, APX, SOD, GR) in Lupinus albus grown under mercury stress

lupinus saiceupsm^t greenhouse enzymatic mercury

Experiments

Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

Glycoprotein structural genomics: solving the glycosylation problem.

An XML standard for the dissemination of annotated 2D gel electrophoresis data complemented with mass spectrometry results.

Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.

Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.

Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

Biochemical and functional characterization of the membrane association and membrane permeabilizing activity of the severe acute respiratory syndrome coronavirus envelope protein.

Placental proteomics: a shortcut to biological insight.

Tubulin proteomics: towards breaking the code.

Microbial genomics: from sequence to function.

'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.

Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep.

Oxidative stress protection and growth promotion activity of Pseudomonas mercuritolerans sp. nov., in forage plants under mercury abiotic stress conditions.