Proteomics Platform

Proteomics Platform

  • Proteomics of whole organisms, organs, organelles, tissues, cell pellets, pulldowns, complex or single protein mixes from solutions or gels
  • Quantification by label-free or multiplexed labeling (e.g., TMT-10/16plex) techniques with microscale sub-fractionation to increase coverage
  • High resolution/high mass accuracy data for intact mass protein analysis
  • Phosphoproteomics using TiO2 phosphopeptide enrichment
  • Technological platforms supported by bioinformatics tools to process data and report results

  • Post-translational modification characterization

     

 
Thermo Orbitrap Eclipse Tribrid with FAIMS and ETD coupled to a Dionex U3000 RSLCnano
Laboratory scene showing a researcher wearing a lab coat and gloves operating a Thermo Scientific Orbitrap Eclipse Tribrid mass spectrometer. The tall instrument includes stacked analytical modules, tubing, and illuminated panels enclosed behind a glass front. The researcher adjusts controls on the instrument, indicating active operation of high‑resolution mass spectrometry equipment used for advanced proteomics and metabolomics analysis.
Thermo Orbitrap Eclipse Tribrid with FAIMS and ETD coupled to a Dionex U3000 RSLCnano
  • Resolving power up to 500,000 FWHM
  • MS acquisition rate up to 40 Hz
  • Flow rate of the nanopump: 20 nL/min to 1.5 µL/min
  • Pressure to 800 bar (11,600 psi)

 

Thermo Q-Exactive – High Field (QE-HF) coupled to Thermo Vanquish H binary UPLC
  • High Resolution/Accurate Mass (HR/AM) instrument
  • Resolving power up to 240,000 at 200 m/z
  • Sub ppm mass accuracy
  • Scan speed of 18 Hz at 15,000 resolution
  • Flow rate of the nanopump: 20 nL/min to 1.5 µL/min
  • Pressure to 800 bar (11,600 psi)
Laboratory bench setup featuring a Thermo Scientific Q‑Exactive mass spectrometer connected to liquid chromatography components. The image shows stacked analytical modules with solvent bottles on top and a mass spectrometer unit to the right. In the foreground, gloved hands hold a sample tray being loaded into the instrument. Cabinets, tubing, and a computer monitor are visible, showing an active high‑resolution mass spectrometry used for proteomics or metabolomics analysis.
Thermo Q-Exactive

 

❖ Mascot 2.6.1 (Matrix Science Ltd) for protein identification from MS/MS spectra

❖ Proteome Discoverer 2.4 Search Engine (Thermo) for metabolic, isotope labeling and label free quantitative proteomics

❖ Scaffold 4.8.9 (Proteome Software) for protein identification, reporting and label-free quantitative proteomics

❖ PEAKS 8 (Bioinformatics Solutions Inc) for de novo sequencing and PTM characterization

PROTEOMICS AND METABOLOMICS