Differential, functional and mapping proteomic analyses of complex biological mixtures suffers from a severe problem associated with component resolution. Numerous attempts have been made to alleviate this resolution issue with limited success. In part this is due to levels of complexity that challenge the resolution and identification of mixture components. Here we describe a promising new approach, ion mobility-mass spectrometry (IMS-MS). This gas-phase, ion dispersion method provides more than an order of magnitude enhancement in component resolution. Additionally, the mobility separation often removes high-abundance species from spectral regions containing lowabundance species, effectively increasing measurement dynamic range.

The high speed relative to liquid phase separations and increased separation capacity allows proteomics analyses to be performed in a higher throughput fashion. Finally, collision-induced dissociation of all ions can be recorded in a single experimental sequence while conventional MS methods sequentially select precursors. Advantages of IMS-MS methods are demonstrated in a single, relatively rapid analysis of a plasma digest where protein database searches have yielded 6167 peptide assignments for 3856 proteins of diverse plasma concentration (108 to 109 range). Results have been compiled into an initial, analytical proteome map of higher dimension than those obtained with conventional MS techniques. IMS-MS technology is presented here as an emerging analytical tool for differential, functional, and mapping proteomic analyses and a major thrust in the pursuit of individual plasma profiling.

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