Abstract: Coupling large-scale sequencing projects with the amino acid
sequence information that can be gleaned from tandem mass spectrometry (MS/MS)
has made it much easier to analyze complex mixtures of proteins. The limits of
this "shotgun" approach, in which the protein mixture is proteolytically
digested before separation, can be further expanded by separating the resulting
mixture of peptides prior to MS/MS analysis. Both single dimensional high
pressure liquid chromatography (LC) and multidimensional LC (LC/LC) can be
directly interfaced with the mass spectrometer to allow for automated
collection of tremendous quantities of data. While there is no single technique
that addresses all proteomic challenges, the shotgun approaches, especially
LC/LC-MS/MS-based techniques such as MudPIT (multidimensional protein
identification technology), show advantages over gel-based techniques in speed,
sensitivity, scope of analysis, and dynamic range. Advances in the ability to
quantitate differences between samples and to detect for an array of
post-translational modifications allow for the discovery of classes of protein
biomarkers that were previously unassailable.
Keywords: proteomics, proteome, biomarker, MudPIT, mass spectrometry, multidimensional chromatography
