Capabilities of the Proteomics Core

• Identity proteins and measure their abundance in a sample
• Measure post-translational modifications (PTM) of proteins (phosphorylation, ubiquitination)
• Identify
  • Interaction partners of proteins
  • proteins in specific spatial locations (proximity biotinylation-Apex or BioID)
  • HLA associated peptides-immunopeptidomics
  • Targets of compounds
• Investigate protein structure by cross-linking mass spectrometry

Quantitation approaches

• SILAC
• TMT (Tandem Mass Tag) chemical labeling (10-11 plex, 16 plex, 18 plex)
• Label free quantification data-independent acquisition (LFQ-DIA)

Types of Samples that can be processed

• in vitro (cell pellets, purified protein complexes, etc)
• in vivo (i.e. animal tissues, etc)
• cell secretome
• human tissues/biopsies (frozen, FFPE)
• human body fluids (plasma/serum, CSF, synovial fluid, etc)