Unraveling the different proteomic platforms

Irene Messana, Tiziana Cabras, Federica Iavarone, Federica Vincenzoni, Andrea Urbani, Massimo Castagnola

Research output: Contribution to journalArticlepeer-review


This review is addressed to scientists working outside the field of proteomics and wishes to shed a light on the possibility offered by the latest proteomics strategies. Bottom-up and top-down platforms are critically examined outlining advantages and limitations of their application to qualitative and quantitative investigations. Discovery, directed and targeted proteomics as different options for the management of the MS instrument are defined emphasizing their integration in the experimental plan to accomplish meaningful results. The issue of data validation is analyzed and discussed. The most common qualitative proteomic platforms are described, with a particular emphasis on enrichment methods to elucidate PTMs codes (i.e. ubiquitin and histone codes). Label-free and labeled methods for relative and absolute quantification are critically compared. The possible contribution of proteomics platforms to the transition from structural proteomics to functional proteomics (study of the functional connections between different proteins) and to the challenging system biology (integrated study of all the functional cellular functions) is also briefly discussed.

Original languageEnglish
Pages (from-to)128-139
Number of pages12
JournalJournal of Separation Science
Issue number1
Publication statusPublished - Jan 2013


  • Bottom up
  • Directed
  • Discovery
  • Targeted
  • Top down

ASJC Scopus subject areas

  • Analytical Chemistry
  • Filtration and Separation


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