Quadrupole ion traps are widely used for bottom-up proteomics analyses. The sensitivity, MS/MS efficiency, and speed of analysis of ion traps for characterization of peptides make them very attractive for the bottom-up approach. An alternative approach in proteomics is top-down, in which intact proteins are introduced directly into the mass spectrometer. Little work has been done with intact proteins in quadrupole ion traps, in part because collision induced dissociation is not as efficient for these larger ions. An alternative dissociation approach that can be implemented on ion trapping instruments is infrared multiphoton photodissociation (IRMPD). IRMPD has a number of advantages versus CID, most importantly not being affected by the trapping parameters (e.g. qz values). Proteins up to 64 kDa have been successfully dissociated via IRMPD. Different charge states show different dissociation patterns, providing complementary information. Because the ion activation with IRMPD is not mass dependent, multiple charge states may readily be dissociated simultaneously. This provides all the information available from the different charge states in one experiment rather than sequential experiments (one for each charge state) as is common for CID.
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