Quantitative Proteomics

Label Free Expression


  • Can accommodate complex experimental designs, ideal for clinical samples and provide increased proteome coverage
  • Easy transition to a 'bottom up' validation analysis (increased proteome coverage)
  • Amendable to low sample concentration (600 ng for LC-MS/MS)
  • High reproducible chromatography and accurate mass accuracy
  • Suited to pre-fractioning strategies
    • Not limited in comparisons because isotope labels are not used


  • Difficulty quantifying post translational modifications
  • High degree sample of complexity for the mass spectrometer


Label Free Expression Proteomics


Label Free Expression Review

Wenhong Zhu, et al. Mass Spectrometry-Based Label-Free Quantitative Proteomics,. Journal of Biomedicine and Biotechnology. 2010;1-6. Article ID 840518, doi:10.1155/2010/840518

Center Paper

Schlatzer DM, et al. Human biomarker discovery and predictive models for disease progression for idiopathic pneumonia syndrome following allogeneic stem cell transplantation. Mol Cell Proteomics. 2012;11(6): doi: 10.1074/mcp.M111.015479.

Global Phospho-Label Free Proteomics

The core provides global quantification of Post-Translational Modifications (PTMs) to provide key information on the functional status of the proteome. PTM-specific enrichments prior to quantitative profiling provide unique information and deep proteome mining. Selective enrichment for phosphorylation is conducted using titanium dioxide resin (TiO2).

global phospho expression proteomics

Selected publications

McClinch K, et al. Small-Molecule Activators of Protein Phosphatase 2A for the Treatment of Castration-Resistant Prostate Cancer. Cancer Res 2018, 78(8):2065-2080.

Najm FJ, et al. Drug-based modulation of endogenous stem cells promotes functional remyelination in vivo. Nature 2015, 522(7555):216-220.

Sangodkar J, et al. Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth. J Clin Invest 2017, 127(6):2081-2090.

Wiredja DD, et al. Phosphoproteomics Profiling of Nonsmall Cell Lung Cancer Cells Treated with a Novel Phosphatase Activator. Proteomics 2017, 17(22).

Interaction Proteomics

The Core uses Affinity Purification-Mass Spectrometry (AP-MS) platform to study protein interactions and complexes. AP-MS combines the specificity of antibody based protein purification with the sensitivity of mass spectrometry to identify and quantify putative interacting proteins. Either native antibody or an epitope-tagging approach may be used to purify protein complexes. In the epitope-tagging approach, a recombinant epitope-tagged bait protein of interest is expressed in cultured cells, and then the bait protein and associated proteins are then retrieved using an antibody against the epitope, followed by identification of prey proteins using mass-spectrometry. The mass-spectrometry data quantified by spectral counting (Scaffold) and scoring metrics are applied to identify those proteins that are specific to the bait of interest.

Interaction Proteomics AP-Mass Spectrometry

Contact Person

Daniela Schlatzer