This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. In many cases, the need to do multiple stages of MS/MS is removed by the use of high-energy CAD. With low energy activation methods now in use, one or more additional stages of MS/MS may be required because the low ion internal energy results in the sampling of one fragmentation pathway that is non informative. The laboratory frame energies of multiply charged protein ions are calculated to be the order of 10 KeV or more for our 12-T Bruker FTMS instrument. The broad distribution of internal energies that are produced by high-energy CAD result in the sampling of multiple fragmentation pathways and an information rich product ion spectrum. Except in cases such as the quantitation of a targeted molecule, the use of multiple stages of MS/MS to extract information is costly in terms of time and sample. Recent advances in trap design have incorporated the ideas of compensation to improve the detection peformance. All of these efforts seek to remove the detrimental effects of the trapping electric field on detection performance by reshaping the trapping electric field. One of these detrimental effects is the reduction of detection performance for ions that are distributed at high radius that would result from high-energy CAD. Advances in compensation provide a means to remove this limitation that impedes the use of high-energy CAD in the FTMS experiment.
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