title: Unraveling the different proteomic platforms.
abstract: 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.
authors.affiliation: Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Cagliari, Italy.
authors.forename: Irene
authors.initials: I
authors.lastname: Messana
authors.forename: Tiziana
authors.initials: T
authors.lastname: Cabras
authors.forename: Federica
authors.initials: F
authors.lastname: Iavarone
authors.forename: Federica
authors.initials: F
authors.lastname: Vincenzoni
authors.forename: Andrea
authors.initials: A
authors.lastname: Urbani
authors.forename: Massimo
authors.initials: M
authors.lastname: Castagnola
mesh_terms: D013058:Mass Spectrometry; D011506:Proteins / Q000032:analysis / Q000378:metabolism; D040901:Proteomics; D015203:Reproducibility of Results; D049490:Systems Biology
chemical_list: D011506:Proteins