Label-Based and Label-Free Strategies for Protein Quantitation

Methods Mol Biol. 2017:1549:31-43. doi: 10.1007/978-1-4939-6740-7_4.


The precise quantification of changes between various physiological states in a biological system is highly complex in nature. Over the past few years, in combination with classical methods, mass spectrometry based approaches have become an indispensable tool in deciphering exact abundance of proteins in composite mixtures. The technique is now well established and employs both label-based and label-free quantitation strategies. Label-based quantitation methods utilize stable isotope labels which are incorporated within the peptides, introducing an expectable mass difference within the two or more experimental conditions. In contrast, label-free proteomics quantitates both relative and absolute protein quantity by utilizing signal intensity and spectral counting of peptides. This chapter focuses on the commonly used quantitative mass spectrometry methods for high-throughput proteomic analysis.

Keywords: Label-free quantitation; Mass spectrometry; Quantitative proteomics; Stable isotope labeling.

MeSH terms

  • Area Under Curve
  • Computational Biology / methods
  • Isotope Labeling
  • Mass Spectrometry / methods
  • Proteins* / chemistry
  • Proteins* / metabolism
  • Proteome*
  • Proteomics / methods*
  • Software
  • Workflow


  • Proteins
  • Proteome