Comparative Omics Core

Advanced Proteomics and Comparative Omics for Aging Research

The Comparative Omics Core provides comprehensive proteomics and comparative omics services specifically tailored for aging research. Our state-of-the-art mass spectrometry platforms and bioinformatics capabilities enable researchers to study changes in protein and regulatory elements across species, tissues, and aging conditions.

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Core Members

Core Instrumentation

Mass Spectrometric Instrumentation

High-resolution mass spectrometers:

  • Orbitrap Astral
  • timsTOF Ultra
  • Q Exactive Plus Hybrid Quadrupole-Orbitrap

Applications: Discovery proteomics, targeted assays, structural biology

Sample Preparation

Automated systems:

  • Robotic liquid handling workstations
  • Automated digestion platforms
  • SPE and solid-phase extraction
  • Ultrasonic sample preparation

Protocols: Species-specific extraction methods, standardized workflows, quality control procedures

Comparative and Integrative Omics

Computational Platforms:

  • High-performance bioinformatic platforms
  • Methods Regulatory element annotation
  • Analysis tools for epigenetic modifications
  • Strategies for multiomics integration

Applications: Data processing and quality control, comparative biology, multiomics integration



Core Services

Proteomics Services

  • Global protein identification and quantification
  • Targeted protein quantification (MRM/PRM)
  • Post-translational modification analysis
  • Protein-protein interaction studies

Comparative Omics Services

  • Data processing and analysis pipelines
  • Statistical analysis and visualization
  • Pathway and network analysis
  • Comparative analysis across species

Multiomics Integration Services

  • Multiomics data integration
  • Aging-related genome elements
  • Genomics, epigenomics and proteomics
  • Database development and maintenance

Training & Education

  • Hands-on training workshops
  • Data analysis tutorials
  • One-on-one consultation
  • Method development support

Supported Sample Types

Biological Samples

Sample formats we can process:

  • Cultured cells and cell lines
  • Fresh and frozen tissues
  • Body fluids (blood, plasma, serum, urine)
  • Subcellular fractions
  • Protein complexes and purified proteins

Species: Mammals, invertebrates, model organisms, non-model species

Sample Requirements

Minimum sample amounts:

  • Proteomics: 10-100 μg protein
  • Targeted assays: Lower amounts possible

Storage: -80°C for frozen samples, specific requirements for different sample types

Quality Control

QC measures:

  • Sample integrity assessment
  • Protein concentration determination
  • Digestion efficiency monitoring
  • Instrument performance tracking
  • Data quality metrics

Specialized Applications for Aging Research

Age-Related Protein Changes

  • Protein aggregation and misfolding
  • Oxidative protein modifications
  • Age-related phosphorylation changes
  • Protein turnover rate measurements

Comparative Biology

  • Cross-species protein evolution
  • Epigenetic regulation
  • Species-specific aging biomarkers
  • Longevity-associated molecular signatures

Data Resources & Databases

Aging Proteome Database

Features:

  • Age-related protein expression data
  • Cross-species comparisons
  • Tissue-specific profiles
  • Interactive visualization tools

Access: Web interface with advanced search and analysis capabilities

Analysis Tools

Software and pipelines:

  • Automated data processing workflows
  • Statistical analysis scripts
  • Visualization and plotting tools
  • Custom analysis applications

Support: Documentation, tutorials, and user support

Project Workflow

Step 1: Consultation

Initial discussion to understand research goals, sample types, and analytical requirements. We'll recommend the most appropriate approaches and protocols.

Step 2: Method Development

Optimize extraction and analysis protocols for your specific samples. Pilot studies may be conducted to validate methods and estimate sample requirements.

Step 3: Sample Analysis

High-quality mass spectrometry analysis using optimized protocols. Quality control measures ensure data reliability and reproducibility.

Step 4: Data Delivery

Processed data with quality metrics, statistical analysis results, and detailed protocols. Ongoing support for data interpretation and publication.

Training & Workshops

Regular Workshops

  • Introduction to Proteomics (Monthly)
  • Mass Spectrometry Fundamentals (Quarterly)
  • Data Analysis Bootcamp (Biannual)
  • Advanced Methods Workshop (Annual)

Specialized Training

  • Aging-specific protocols
  • Cross-species comparative analysis
  • Biomarker discovery methods
  • Custom training for research teams

Contact Information

Get Started

For project consultation:
Sina Ghaemmaghami, Ph.D. (sina.ghaemmaghami@rochester.edu)
Hongbo Liu, Ph.D. (Hongbo_Liu@URMC.Rochester.edu)

For training inquiries:
Contact us about upcoming workshops and custom training opportunities

For data access:
Request access to our proteomics and comparative omics databases