Label Free Protein Expression

Provides accurate quantitative information about changes in protein expression as a a function of stimulation.


  • 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

Contact Person

Danie Schlatzer (
Senior Research Associate
Case Center for Proteomics and Bioinformatics
Case Western Reserve University
10900 Euclid Avenue, BRB 947 Cleveland, Ohio 44106
phone: 216-368-4014 fax: 216-368-6846

Label Free Protein 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.

Relative Quantification

Absolute Quantification