University of Utah              The JOHN A. MORAN EYE CENTER

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CYTOSOMICS, METABOLOMICS and COMPUTATIONAL MOLECULAR PHENOTYPING

Micromolecules: definitions & links	Cellular domains: Genome, preoteome & metabolome
Metabolic diversity: Scale, dynamics, & phyletics	Phenotyping strategies: proteomics vs metabolomics
CMP Platforms: Platforms and workflow overview	CMP Probes: The probe library
CMP Substrates: Molecular trapping & detection	CMP Datasets: Data arrays for multichannel imaging
CMP Analysis: pattern recognition theory and tools	CMP Exploration: N-space visualization tools
CMP Annotation: browsing & annotating data

Micromolecules

Links and Tools

Unique cell classes can be distinguished by their small molecule or micromolecular signatures. Micromolecules include elements and their molecular forms (e.g. O2), ions, inorganic compounds, organic species formed by group transfer and oligomers formed by ligation reactions (e.g. glutathione). Signatures are partial representations of formal metabolic phenotypes, track physiologic and pathologic metabolic transformations, and can identify novel cell classes. Computational signature visualization in complex heterocellular tissues of all eukaryotic Kingdoms (Plantae, Fungae, and Animalia) reveals unexpectedly diverse metabolic phenotypes across cell classes. Metabolic phenotypes are challenging to interpret, as they arise from genetic and epigenetic demands: maintaining group transfer potentials for molecular synthesis, vectorial molecular transport processes, osmoregulation, redox and reactive oxygen species control, energetics regulation, intercellular signaling and coupling, cell and tissue growth, and protein synthesis. Though no coherent theory of metabolic differentiation predicts these phenotypes, once visualized, micromolecular phenotypes inform models and constrain modes of pharmacologic intervention. Visualizing signatures, tracking phenotype dynamics, and screening molecular interventions all require quantitative micromolecular profiling across cell classes. These measures can be uniquely acquired via Computational Molecular Phenotyping (CMP) with anti-hapten IgG libraries.

Metabolism KEGG PUMA2 Roche Appl Biosci Pathways via ExPASy European Bioinformatics Inst (EBI) BRENDA HMDA Molecules KLOTHO LIGAND Ligands-EBI U West Indies Mona Tools RasMol Chime iMol for OS X Gepasi: metabolic simulation

CMP Targets for Metabolomics Technology Development

Aliphatics

3-phospho-serine phospho-ethanolamine Ethanolamine Putrescine Ac Putrescine Spermine N-Ac Spermine Spermidine N-Ac Spermidine cadaverine carnitine dimethylglycine betaine N-Ac glutamate N-Ac asp-glutamate N-Ac lysine N-carbamoyl asp 5-aminovalerate oxo-5-aminovalerate L-arginine-phosphate L-arginosuccinate carbamate carbamoyl phosphate carbamoyl sarcosine sarcosine trimethyllysine 2-aminoadipate

Aromatics

epinephrine histamine kynurenine melatonin tyramine monoiodotyrosine diiodotyrosine T2 triiodotyrosine T3 tetraiodotyrosineT4

ROS Molecules

glutathione (red) glutathione (ox) cysteinylglycine gamma-glutamylcysteine

Nucleics

Adenine Adenosine dAdenosine AMP dAMP dADP dATP S-AM Cytidine Cytosine dCytosine CMP CDP CTP dCMP dCDP dCTP Guanine Guanosine GMP GDP GTP dGMP dGDP dGTP GDP-mannose GDP-fucose Uracil Uridine UMP UDP UTP dUMP dUDP dUTP UDP-glucose Thymine dThymidine dTMP dTDP dTTP NAD / NADH NADP / NADPH aminoacylAMP allantoin allantoate Urate

Carboxylates

Pyruvic acid 3-phosphoglycerate 2-phosphoglycerate glycerate succinate oxalacetate malate fumarate

Metabolite analogues

D-alanine D-asparagine D-cysteine D-serine canavanine 1-amino-2-oxo-guanidopropane aminoisobutyrate isoguvacine

Sugars

D-glucose D-glucuronate D-6-phospholuconate myo-inositol inositol-1-PP, inositol-1,4-PP, inositol-1,4,5-PP,

Cofactors

CoASH Acetyl CoA Succinyl CoA Folate Tetrahydrofolate Formyl THF Methylenyl THF THF polyglu THB DHB Thiamine Thiamine-PP FAD FMN Pyridoxamine Cobalamin Pantothenate Biotin Quinolinate Ascorbate

Steroids / Precursors

Mevalonate Mevalonate 5P,PP Testosterone Estradiol Estrogen Progesterone Cortisol Dihdroxycalciferol

Bilins, Bile Acids

Porphobilinogen Uroporphyrins Heme Cytochromes Urobilins Stercobilins Bilirubin Bilirubin glucuronides Glycocholate Cholate Taurocholate

Eicosanoids

Arachidonate Prostaglandins Leukotrienes Leukotriene C4

Polyketides / peptides

Penicillins Cephalosporin Streptomycin Oxytetracycline creatine creatine-P

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