The rapidly expanding data sets derived from genomic and transcriptomic analyses have allowed greater understanding of structural and functional network patterns within the genome resulting in a realignment of thinking within a systems biologic framework of cancer. However, insofar as spatially and temporally dynamic differential gene expression at the protein level is the mediate effector of cellular behavior and, in view of extensive post translational modiﬁcation (PTM), the need for sensitive, quantitative, and high throughput proteomic analytic techniques has emerged. To circumvent the problems of tissue sample heterogeneity, laser capture microdissection (LCM) allows for the acquisition of homogeneous cell populations. Using different ﬂ uorescent dyes to label protein samples prior to gel electrophoresis, 2-D DIGE (two- dimensional differential in-gel electrophoresis) can, with reasonable sensitivity, process three protein samples on the same gel allowing for intragel relative quantiﬁcation. MudPIT (multidimensional protein identiﬁcation technology) is a non-gel approach exploiting the unique physical properties of charge and hydrophobicity which allows the separation of peptide mixtures as well as direct MS (mass spectrometry) and database searching. The introduction of iTRAQ (isobaric tags for relative and absolute quantiﬁcation) achieves labeling of all peptides by employing an 8-plex set of amine reactive tags to derivatize peptides at the N-terminus and lysine side chains allowing for absolute quantiﬁcation and assessment of PTM. These and other new laboratory technologies, along with improved bioinformatics tools, have started to make signiﬁ cant contributions in cancer diagnostics and treatments.
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