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Omics Facility Core

The OFC provides quantitation of toxicant exposures, and the subsequent effects on the proteome and genome, enabling investigators to determine how and where toxicants act.

Determining the exposure to, and effects of, environmental toxicants and the sites and modes of toxicant actions requires a multimethod approach. Combined with data obtained by the Cellular Imaging Facility Core, biochemical assays, and analysis provided by the Translational Research Support Core (TRSC), the OFC aims to advance Center member research. The OFC encompasses a wide range of techniques from routine sample preparation to state-of-the-art chromatography separation, mass spectrometry, and sequencing technologies. The OFC Co-Directors are here to guide and assist Center members with grant proposals, experimental design, sample and data acquisition, data analysis, and dissemination through methods of figure generation using equipment and expertise beyond the scope of their individual Center member laboratories. The OFC also provides more in-depth services including assay development, statistical analysis through the TRSC, and access to self-service instrumentation.

The Omics Facility Core is composed of three labs to support Center members Omics research needs:

  1. An exposomic lab providing services to quantitate toxicants of relevance to the Southwest including inorganics such as metals (arsenic, lead, and mercury), and organics such as polyfluoroalkyl (PFAS) compounds, and industrial chemicals (trichloroethylene) from diverse matrices such as water, air, dust, bodily tissues, and plants;
  2. The Quantitative Proteomics Laboratory provides comprehensive mass spectrometry-based proteomics services including peptide and protein identification, quantitative proteomics (whole proteome, subcellular fraction, and translational proteomics), spatial proteomics to define changes in protein localization, quantitative interactomics, post-translational modification (PTM) identification and quantification, targeted proteomics using parallel reaction monitoring (PRM), and quantitative phosphoproteomics to characterize signaling networks and disease-associated molecular mechanisms.;
  3. A genomics lab providing next-gen DNA sequencing (NGS) of whole genomes, exomes, and transcriptomes (RNA-seq), real time RT-PCR, genotyping, fragment analysis, and Sanger sequencing. Finally, epigenomic and metabolomic services including analysis of histone protein modifications, DNA methylation, and quantitation of toxicant metabolites (e.g., methylarsonic acid) are distributed across the three Omics laboratories based on the analyte and expertise required.

The OFC provides state-of-the-art mass spectrometry, sequencing, and fragment analysis instrumentation to generate exposomic, metabolomic, proteomic, genomic and epigenomic data. The OFC Co-Directors seek to apply their 60 years of collective expertise to provide multimethod approaches that drive research forward through overlapping analyses between the three Omics labs. Serving Center members goes beyond simply analyzing samples and returning raw data. The OFC Co-Directors seek to expand members’ vision of future research ambitions through expert consultation on analytic approaches of which members may not be aware. In addition, the Co-Directors provide advice on study design in consultation with the Translational Research Support Core, consult on logistics, perform initial pilot tests, and advise on budget management before studies begin. Lastly, through their respective experience and expertise, the Co-Directors consult with individual Members after experiments are complete and throughout the dissemination process to ensure quality control of samples and results, perform data analysis and generate figures, and provide interpretation of results. Contact one of the Co-Directors below to get started with achieving your research goals.

Utilizing the Arizona Laboratory for Emerging Contaminants

Exposomic analysis is provided in a laboratory to analytical chemistry of a variety of compounds and chemicals. Those relevant to environmental research within the SWEHSC include:

  • Metals. Trace: (Be, Al, Mn, Ni, Cu, Zn, Mo, Ag, Cd, Sn, Sb, Ba, Pb); Toxic: (As, Pb, Hg, Cd, Al)
  • Inorganic Measurements. Major anions: (Fl-, Cl-, NO2-, Br-, NO3-, PO43-, SO42- ); Major cations: (K+, Ca2+, Na+, Mg2+).
  • Organic Measurements. Pesticides: Atrazine, simazine, prometon, carbaryl, chloropyrifos, DEET; Surfactants: Nonylphenol; PFAS, Perfluorinated compounds (PFAS/PFAC): PFOS, PFOA, PFBS, PFNA, PFHxS, GenX; Pharmaceuticals: Antibiotics, hormones, Industrial chemicals, TMAH, NMP, azoles.
  • Complex Matrices. Water: groundwater, effluent/influent, industrial discharge; Biological: blood, serum, tissues; Environmental: soils, plant matter, biochars, biosolids, and mine tailings.
  • Elemental Measurements. Carbon: Total carbon, organic/inorganic carbon; Nitrogen: Total nitrogen, liquid and solid samples; Sulfur: Total sulfur, solid samples.
  • Water Quality: pH, Conductivity, Metals, Nutrients.

The Exposomic lab instrumentation relevant to SWEHSC research needs includes:

  • Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS): consists of a Quattro Premier XE tandem mass spectrometer from Waters-Micromass and an Acquity Ultra performance (UP) LC.
  • Liquid Chromatography Tandem Mass Spectrometry (LC[QToF]MSMS): The LCMSMS TripleTOF 5600 (quadrupole-Time of flight) tandem mass spectrometer from ABSciex is attached to an Agilent 1260 Infinity HPLC; together they are configured for ESI-LC-MSMS.
  • Gas Chromatography Tandem Mass Spectrometer (GC-MS/MS): is provided by a Quattro micro tandem mass spectrometer 7890A gas chromatograph with a 7683 automatic liquid sampler.
  • UV-Vis/Fluorescence Spectrophotometry: Aqualog Benchtop Fluorometer capable of simultaneously measuring both absorbance spectra and fluorescence Excitation-Emission Matrices.
  • Size Exclusion Chromatography/Asymmetric Field Flow Fractionation-Multi-angle Light Scattering (SEC/AFFF-MALS): This instrument uses liquid chromatographic separation for characterization of mobile particulates in the sub-micrometer range.
  • Ion Chromatography: Thermo Scientific Dionex ICS-6000 HPIC system for the analysis of inorganic anions in environmental samples as it can determine multiple anions in a single analysis.
  • Sample extraction: AT SPE Workstations which can process up to six large volume liquid samples in parallel for further analysis by LCMSMS, GCMSMS, ion chromatography, ICPMS or other techniques.

This resource leverages ALEC, an existing core analytical facility at UA, which is dedicated to providing the analytical capabilities and technical expertise required to detect and quantify small contaminant molecules (organic and inorganic) in complex matrices including biological fluids, tissue, water, air, soil, sediment, and biomass.

Laboratory instrumentation in ALEC is maintained by a combination of funding sources including NSF, NIH, DoE, and the State of Arizona. Principal methods involve off-line or on-line separations followed by mass spectrometric detection. Instruments found in ALEC include:

  • Inductively Coupled Plasma Mass Spectrometers (ICP-MS)
  • Liquid Chromatography Tandem Mass Spectrometers (LC-MS/MS)
  • Gas Chromatography Tandem Mass Spectrometer (GC-MS/MS)
  • UV-Vis/Fluorescence Spectrophotometer
  • Size Exclusion Chromatography/Asymmetric Field Flow Fractionation-Multi-angle Light Scattering (SEC/AFFF-MALS)
  • X-ray Fluorescence (XRF) Spectrometry
  • CNS Analyzer
  • Ion Chromatography
  • Carbon/Nitrogen Analyzer
  • Sample prep equipment - Solid Phase Extraction Workstation, Microwave Digestion

For additional information about ALEC, see the lab website at https://www.alec.arizona.edu/

Consultation:

Complex chemical analysis is best begun with a conversation about the researcher's specific needs. This allows our expertise to consider the intricacies of the project and to suggest the most appropriate steps. Working with us before submitting your samples ensures the best possible research outcomes.

For a consultation, please contact the ALEC Director, Jon Chorover, PhD, by calling (520) 626-5635 or click here to send him an email

Personnel

The ALEC Resource is Directed by Jon Chorover, PhD, and includes two full-time research scientists dedicated to assisting SWEHSC researchers to access the full range of analytical capabilities. Leif Abrell, PhD, oversees organic mass spectrometric analyses (LC-MS/MS, GC-MS/MS, LC-QToF-MS), whereas Mary Kay Amistadi, MS, is in charge of inorganic mass spectrometry (ICP-MS, LC-ICP-MS). These individuals train frequent users or perform analyses on a cost-recovery basis.

The Quantitative Proteomics Laboratory supports the mission of the Southwest Environmental Health Sciences Center by providing advanced mass spectrometry-based proteomics technologies for systems-level investigation of how environmental factors influence biological systems and human health. Through comprehensive analysis of protein abundance, localization, interaction networks, and post-translational modifications, the facility enables investigators to define molecular mechanisms linking environmental exposures to disease susceptibility, toxicity, and therapeutic response.

Proteomics Capabilities

Peptide and Protein Identification

  • Identification of proteins from gel bands, purified proteins, immunoprecipitations, affinity enrichments, and complex biological samples. 
  • Characterization of protein composition in tissues, cells, biofluids, and environmental samples. 

Quantitative Proteomics

  • Label-free and targeted quantitative proteomics. 
  • Whole proteome profiling to identify global protein abundance changes. 
  • Subcellular fraction proteomics to characterize compartment-specific protein regulation. 
  • Translational proteomics to investigate disease mechanisms, therapeutic responses, and biomarker discovery. 

Spatial & Subcellular Proteomics

  • Quantitative assessment of protein localization and redistribution between cellular compartments. 
  • Characterization of protein trafficking, organelle remodeling, and changes in subcellular protein networks. 

Quantitative Interactomics

  • Analysis of protein-protein interaction networks using affinity purification and immunoprecipitation-based workflows. 
  • Identification and quantification of dynamic changes in protein complexes and signaling assemblies. 

Post-Translational Modification (PTM) Analysis

  • Identification and quantification of phosphorylation, acetylation, ubiquitination, glycosylation, and other PTMs. 
  • Comprehensive PTM site mapping and characterization. 
  • Targeted PTM validation using Parallel Reaction Monitoring (PRM) and other targeted mass spectrometry approaches. 

Quantitative Phosphoproteomics

  • Global and targeted phosphoproteomic analyses. 
  • Phosphopeptide enrichment using Immobilized Metal Affinity Chromatography (IMAC) and titanium dioxide (TiO₂)-based workflows. 
  • Quantitative assessment of signaling pathways and kinase-regulated networks. 

Targeted Proteomics and Biomarker Validation

  • High-sensitivity quantitative assays using Parallel Reaction Monitoring (PRM). 
  • Biomarker verification and translational assay development.

Computational Proteomics and Bioinformatics

  • High- Integrated computational workflows support protein identification, quantitative proteomics, phosphoproteomics, targeted proteomics, pathway analysis, and protein network interpretation. The facility provides end-to-end support from experimental design and data acquisition through statistical analysis, biological interpretation, and publication.

The Quantitative Proteomics Laboratory operates two Thermo Scientific Orbitrap Fusion Lumos Tribrid mass spectrometers coupled to Dionex UltiMate 3000 nano-flow liquid chromatography systems and EASY-Spray nano-electrospray ionization sources. These integrated LC-MS/MS platforms provide high-resolution, high-mass-accuracy analyses for peptide and protein identification, quantitative proteomics, phosphoproteomics, interactomics, post-translational modification analysis, and targeted proteomics using Parallel Reaction Monitoring (PRM).

Utilizing the ORP University of Arizona Genetics Core

The OFC Genomics lab provides state-of-the-art genomic analysis resources and services including a CLIA/CAP certified laboratory for high complexity laboratory testing. In addition, the Genomics core provides novel bioinformatics pipelines for clinical and research purposes designed to integrate UA high-throughput computing for use in analyzing large genomic data sets. Genomics services of relevance to SWEHSC research include:

  • RNA-Seq: Whole transcriptome sequencing and expression profiling with sample barcoding, multiplexing, and data analysis. Large RNA-seq projects can be submitted to an Illumina NovaSeq.
  • DNA-Seq: Both de novo and reference genomes with sample processing starting from DNA extraction through library preparation and sequencing including metagenomic analysis of microbiomes. Sample processing includes unique protocols such as CHIPseq, exome sequencing, amplicon enrichment, and custom library types.
  • Real-Time PCR: Training and access, as well as full service, for genotyping, mutation analysis, gene expression, and custom tests such as measuring epigenetic biomarkers.
  • SNP Genotyping: The Agena MassARRAY, the leading technology for SNP genotyping for sub-whole genome study applications, is used for fine mapping and validation studies.
  • TaqMan expression and genotyping: SNP and gene expression analysis pre-validated probe sets in 96-well and 384-well formats.
  • Sanger Sequencing: Single sample and high volume (96-well plate) Sanger sequencing using the Applied Biosystems 3730 DNA Analyzer. Researchers may expect 600- 800 bases of reliable sequence.
  • Authentication/identification genotyping: Human cell line authentication, transgenic mouse genotyping, STR analysis and custom PCR assays for a variety of organisms and study models.
  • DNA Methylation Analysis: Both NGS technologies, real-time PCR, and the Sequenom MassARRAY system are offered to perform epigenomic analysis of DNA methylation.

The Genomics lab instrumentation includes:

  • Illumina NextSeq500, MiSeq, and sample submission to an Illumina NovaSeq for high-throughput sequencing paired with an Opentrons Library Preparation System.
  • Agena MassARRAY system for high-throughput SNP genotyping.
  • NanoString nCounter Analysis System for digital, single molecule analysis of expression and mutation.
  • ABI 3730 DNA analyzers for low and high throughput Sanger sequencing.
  • ABI 7900 Quantitative/Real Time PCR instruments for 96- and 384-well reactions.
  • KingFisher FLEX Magnetic Isolation Platform and Beckman Biomek FX/NX for automated liquid handling in sample preparation, library preparation, and molecular barcoding.
  • Agilent Bioanalyzer, Qubit fluorimeter, and NanoDrop spectrophotometer for sample QA/QC.

Sequencing:

  • Ion Torrent PGM 314: 0.1 Gbase (small panels, bacterial sequencing)
  • Ion Torrent PGM 316: 0.3 Gbase (large panels, multiplexed samples)
  • Ion Torrent PGM 318: 1 Gbase (large panels, multiplexed samples
  • Ion Torrent Proton 1: 10 Gbase (exome, RNA-seq, Chip-seq)

Microarray:

  • Affymetrix GeneChip platform including 7G upgraded 3000 laser scanner, hybridization oven, and two fluidics stations

PCR/RT-PCR:

  • ABI 7500 Sequence Detection System

Sample quality control:

  • Agilent Bioanalyzer 2100 system
  • Nanodrop 2000 Spectrophotometer
  • Qubit 3.0 fluorimeter