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J Biomol Tech. 2007 February; 18(1): 88.
PMCID: PMC2291920

EP1 Top-Down Proteomics


In the past several years, there have been a growing number of researchers working together to push forward the field of top-down proteomics. In its most basic form, top down (TD) involves observing intact proteins and incorporating the intact masses derived either from mass spectra or gels in the reported description of the proteins. In most applications, intact mass information alone is not enough to unambiguously identify a protein, and so tandem mass spectrometry must be performed. The most complete incarnation of TD involves observing a native (i.e., unchanged from its in vivo state) protein/peptide in a mass spectrometer, followed by its isolation and fragmentation. From the precursor and fragment ion masses, one can then make an unambiguous determination of not just the protein identity, but also its native post-translational state. This includes all post-translational modifications, proteolytic cleavages (e.g., signal peptide cleavages), amino acid changes from non-synonymous coding single nucleotide polymorphisms, and primary structure changes due to alternative splice variants. In this educational session, we will discuss some of the basic questions surrounding top-down proteomics. What is it? Why do it? How is it done? Do you really need a $700,000 instrument to do it? We will also include some recent results from some of the top labs that are using TD technology to explore both targeted and proteome-wide problems. We hope to pique your interest in this growing field and engender lively discussion.

Articles from Journal of Biomolecular Techniques : JBT are provided here courtesy of The Association of Biomolecular Resource Facilities