Quadrupole ion trap mass spectrometry.

A number of other features of ITMS systems that will enhance their ability to analyze biological macromolecules are worth mentioning. As has already been demonstrated for ESI/quadrupole, ESI/magnetic sector, and ESI/FTICR systems, the capability of inducing fragmentation of the ESI-generated multiply charged ions of biological macromolecules in the capillary/skimmer region of the ESI source and subsequently selectively analyzing fragments can also be carried out with the QITMS, as we have demonstrated using bovine serum albumin (data not shown). The ability to carry out chemical reactions on biological macromolecules inside the QITMS has been demonstrated by McCluckey et al. by showing that the introduction of a pulse of volatile base, such as diethylamine, can result in proton removal from multiply charged protein ions, resulting in species with lower charge states. The application of the technique of deuterium exchange of active hydrogens on peptides to simplify the interpretation of MS/MS sequencing experiments can be implemented for ESI/QITMS. Carrying out such exchange inside the ITMS may also be possible, with resulting analytical advantages. Reports of a hybrid QITMS-TOF system, which was operated with either ESI or MALDI methodology, and which demonstrated low femtomolar sensitivity with higher resolution of the TOF analyzer because of ion injection of essentially monoenergetic ions from the QITMS into the TOF, illustrate additional uses of the QITMS. The reverse combination (e.g., ESI/TOF/QITMS or MALDI/TOF/QITMS) could afford preselection of ions for even higher performance in the QITMS, because space charging (loss of performance such as resolution because of too much charge in close proximity in the ion trap) would be minimized. Opportunities for the application of QITMS technology for the analysis of biological macromolecules abound, including ultrahigh-sensitivity protein sequencing using specifically derivatized amino acids released by Edman chemistry; rapid sequencing of MHC-associated antigenic peptides of variable length (approximately nonamers for the MHC I complexes to > dodecamers for the MHC II complexes), which are available in only very low amounts (femtomole/attomole) and in very complex mixtures (5000-10,000 species) of closely related peptide structures; ultrahigh-sensitivity analysis of peptides and proteins directly in vivo using microelectrospray; direct analysis of metal ion binding to peptides and proteins and analysis of noncovalent interactions, including conformation; and possible analysis of plasmid DNA, as has been suggested by ESI ionization of a 2-MDa DNA species. In summary, the ability of the QITMS to interface to key separations systems such as HPLC and HPCE through the critical ionization techniques of ESI and MALDI, coupled with the high mass range, high mass resolution, high sensitivity, high-efficiency CID, and MS capabilities of this device, will provide an astonishing array of cost-effective capabilities for the qualitative and quantitative analysis of biological macromolecules.