Thermally assisted infrared multiphoton photodissociation (TA-IRMPD) provides an effective means to dissociate ions in the quadrupole ion trap mass spectrometer (QITMS) without detrimentally affecting the performance of the instrument. IRMPD can offer advantages over collision-induced dissociation (CID). However, collisions with the QITMS bath gas at the standard pressure and ambient temperature cause IR-irradiated ions to lose energy faster than photons can be absorbed to induce dissociation. The low pressure required for IRMPD (< or = 10(-5) Torr) is not that required for optimal performance of the QITMS (10(-3) Torr), and sensitivity and resolution suffer. TA-IRMPD is performed with the bath gas at an elevated temperature. The higher temperature of the bath gas results in less energy lost in collisions of the IR-excited ions with the bath gas. Thermal assistance allows IRMPD to be used at or near optimal pressures, which results in an approximately 1 order of magnitude increase in signal intensity. Unlike CID, IRMPD allows small product ions, those less than about one-third the m/z of the parent ion, to be observed. IRMPD should also be more easily paired with fluctuating ion sources, as the corresponding fluctuations in resonant frequencies do not affect IRMPD. Finally, while IR irradiation nonselectively causes dissociation of all ions, TA-IRMPD can be made selective by using axial expansion to move ions away from the path of the laser beam.

Dissociation pathways of alkali-cationized peptides have been studied using multiple stages of mass spectrometry (MSx) with a quadrupole ion trap mass spectrometer. Over 100 peptide ions ranging from 2 to 10 residues in length and containing each of the 20 common amino acids have been examined. The formation of the [b(n-1) + Na + OH]+ product ion is the predominant dissociation pathway for the majority of the common amino acids. This product corresponds to a sodium-cationized peptide one residue shorter in length than the original peptide. In a few cases, product ions such as [b(n-1) + Na - H]+ and those formed by loss, or partial loss, of a sidechain are observed. Both [b(n-1) + Na + OH]+ and [b(n-1) + Na - H]+ product ions can be selected as parent ions for a subsequent stage of tandem mass spectrometry (MS/MS). It is shown that these dissociation patterns provide opportunities for peptide sequencing by successive dissociation from the C-terminus of alkali-cationized peptides. Up to seven stages of MS/MS have been performed on a series of [b + Na + OH]+ ions to provide sequence information from the C-terminus. This method is analogous to Edman degradation except that the cleavage occurs from the C-terminus instead of the N-terminus, making it more attractive for N-terminal blocked peptides. The isomers leucine and isoleucine cannot be differentiated by this method but the isobars lysine and glutamine can.

Collisional cooling rates of infrared excited ions are measured in a quadrupole ion trap (QIT) mass spectrometer at different combinations of temperature and pressure. Measurements are carried out by monitoring fragmentation efficiency of leucine enkephalin as a function of irradiation time by an infrared laser after a short excitation and incrementally increasing cooling periods. Cooling rates are observed to be directly related to bath gas pressure and inversely related to bath gas temperature. The cooling rate at typical ion trap operating pressure (1 mTorr) and temperature (room T) is faster than can be measured. At elevated temperature and the lowest pressure used for the studies, the rate of collisional cooling becomes negligible compared to the rate of radiative cooling. or many years, collisional cooling has been used to damp the kinetic energies of trapped ions to improve the performance of the quadrupole ion trap mass spectrometer [1][2][3]. After formation in, or injection into, the quadrupole ion trap, ions undergo collisions with the bath gas, causing their trajectory to shrink to the center of the ion trap. This more compact cloud of ions increases sensitivity and resolution when using mass-selective instability [2] or resonance ejection [4] for mass analysis. A bath gas pressure of 1 mTorr is the commonly used operating pressure, and all commercial ion traps operate at ambient temperature.Although collisional cooling of the ion's kinetic energy is helpful for ion trap performance, cooling of the ion's internal energy also occurs; this may or may not be desired. This internal cooling can reduce fragmentation efficiency and thus be a detriment when trying to dissociate ions using "slow heating" techniques [5] such as infrared multiphoton photodissociation (IRMPD). IRMPD has been successfully implemented in a quadrupole ion trap [6 -15]. IRMPD works by increasing the internal energy of an ion by multiple photon absorption. When a bath gas pressure of 1 mTorr is used, the transfer of the ion's internal energy to the bath gas via collisions may occur at a faster rate than the rate of energy-transfer to the ions by photon absorption. The ratio of the rate of energy loss via collisional cooling to energy gain via photon absorption depends on the ion's absorption cross-section, the power of the laser, trapping volume temperature, and pressure. If the rate of energy loss by collisions is greater than the rate of energy gained by photon absorption, the ions irradiated will not dissociate. It is due to this reason that IRMPD is not practical for peptide dissociation in a quadrupole ion trap at the typical operating pressure and roomtemperature [6,15]. Most of the examples of IRMPD in the quadrupole ion trap have been accomplished by lowering the bath gas pressure. At decreased pressures, however, the performance of the QIT is adversely affected. Sensitivity is decreased by approximately an order of magnitude [6], and resolution is also decreased.An alternate approach to overcome the problem of collisional c...

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Thermally assisted collision-induced dissociation (TA-CID) provides increased dissociation in comparison with CID performed at ambient temperature in a quadrupole ion trap mass spectrometer. Heating the bath/collision gas during CID increases the initial internal energy of the ions and reduces the collisional cooling rate. Thus, using the same CID parameters, the parent ion can be activated to higher levels of internal energy, increasing the efficiency of dissociation and the number of dissociation pathways. The increase in the number of dissociation pathways can provide additional structural information. A consequence of the increase in initial internal energy is the ability to use less power to effect collisional activation. This allows lower q(z) values to be used and, thus, a greater mass range of product ions to be observed. TA-CID alleviates the problems associated with traditional CID and results in more available information than traditional CID.