- Electron Induced Ion Excitation (and Electron Energy): The electron ionization process imparts up to several electron volts intra-molecular-ion internal vibrational energy that leads into molecular ion dissociation. This added vibrational energy can originate via direct excitation of high lying vibrational states of the lowest electronic state of the molecular ion or via the excitation of additional high lying electronic states of the molecular ion which undergo internal conversion into highly excited vibrational states of the ground electronic state of the molecular ion which leads into dissociation. The use of lower electron energy make these high lying electronic states of the molecular ion inaccessible hence the degree of molecular ion dissociation at low electron energies can be reduced. However, for certain compounds such as those with many heteroatoms high lying electronic states of the molecular ion are not accessible due to unfavorable Frank-Condon factors and for these molecules lowering the electron energies does not affect the mass spectra while it largely reduces the ionization yield. The simplest example is PFTBA that serves as the GC-MS calibration compound in which the molecular ion at m/z 671 cannot be observed at any electron energy.
- Thermal vibrational energy: In standard GC-MS the sample compounds can have up to 3NKT vibrational energy (heat capacity) in which N is the number of atoms, K the Boltzmann constant and T is the ion source temperature in Kelvins. Usually the high temperature heat capacity limit is not achieved and a closer estimate for the sample internal vibrational energy is NKT. For small molecules with up to 15-20 atoms this thermal energy contribution to the molecular ion dissociation is smaller than that of the electron energy. However, for large molecules this contribution is central and it serves as the dominant reasons for molecular ions dissociation. In Cold EI this thermal vibrational energy is practically eliminated and thus the molecular ions are enhanced and the larger the compound the greater is the effect of Cold EI on the enhancement of the molecular ions. You may read further material on this topic in another blog article. We note that while in Cold EI the intra molecular vibrational energy can be eliminated for small and medium molecules via the supersonic expansion, large molecules may require specially shaped nozzle and higher make up gas flow rate for effective full elimination of their internal vibrational energy and in general the skimmer used must be sharp and relatively large to reduce and/or eliminate sample compounds reheating via a reflected shock-wave that can be formed on blunt and/or small skimmers.
- Weaker Molecular Ion Chemical Bonds: Molecular ions by definition have one less electron than the neutral compound hence their weakest chemical bond is typically weaker than the weakest bond of the neutral molecule. Thus, molecular ions can be inherently unstable and sometimes dissociate even without any added intra-ion vibrational energy.
- Collision Induced Dissociation (CID): Once the molecular ion is formed, even if it is stable and not dissociated via the three reasons above it can dissociate in its flight path to the mass analyzer via collisions with the residual carrier gas such as helium that comes from the GC column. It is well known that in GC-MS with internal ionization ion traps such as the Varian Saturn 2000 or Varian 220 the molecular ions of hydrocarbons are often fully missing while they are small yet observed in Quadrupole based GC-MS. In these ion traps the molecular ions undergo CID inside the ion trap prior to its detection. We found in our 1200-SMB GC-MS with Cold EI which is based on a Varian 1200 triple quadrupole MS system, that when we select in the first quadrupole MS the molecular ion m/z=226 of hexadecane (n-C16H34) as a parent ion without adding any Q2 collision gas and CID voltage we observe in the scanning Q3 that about 30% of the hexadecane molecular ion is dissociated despite having double differential pumping in this system. As demonstrated below, CID could be an important residual fragmentation mechanism once the three above reasons are eliminated.
In order to differentiate the relative roles of CID from skimmer induced reheating we explored Soft Cold EI and Cold EI of PFTBA. This compound that serves for MS tune in GC-MS is unique in two aspects: a) Its cooling effect in Cold EI is small and; b) Its m/z=264 fragment ion is relatively stable in MS-MS based CID while its abundant m/z=219 fragment ion is weak and easily dissociates into m/z=131 and 69 daughter ions. In the NIST library the ratio of m/z=264/219 ratio is 17% in the main library MS while in the replica it can be up to 26%. In Cold EI with nozzle-skimmer distance of 16 mm and 84 ml/min helium make up gas flow rate we found that the ratio of m/z=264/219 is 25% while at 7 mm nozzle-skimmer distance it was 28%. Under these conditions the m/z=131/219 ratio increased from 31% to 45%. While such increase in the m/z=131/219 can be explained by both increased CID and skimmer induced heating, the increase in the m/z=264/219 must originate only from CID as skimmer induced heating should slightly reduce this ratio.
- Classical EI mass spectra can be obtained via the simple reduction of the helium make-up gas flow rate to reduce the sample vibrational cooling.
- Cold EI mass spectra are provided as the main and most useful mode of operation, typically with 60 ml/min combined column and helium make up gas flow rate, 70 eV electron energy and 7 mm nozzle-skimmer distance. Cold EI provides the most sensitive, selective and informative EI mass spectra combined with the best NIST library identification probabilities.
- Soft Cold EI mass spectra are provided as a complementary mode of operation, typically with 90 ml/min combined column and helium make up gas flow rate, 18 eV electron energy and 16 mm nozzle-skimmer distance. Soft Cold EI provides the most selective mode of EI mass spectra which is approaching to molecular ion only MS.
- Increased helium make up gas flow rate. This increased cooling gas flow rate is not required for small molecules with molecular weight of 300-400 and even for n-C25H50 it made no observable effect. However, for large molecules and those with highly labile molecular ions such as of squalane it is important and helpful although it may reduce the TIC by a factor of less than 2.
- Reduced electron energy. With hydrocarbons the reduction of the Cold EI electron energy can significantly increase the relative abundance of the molecular ion and suppress the fragments ions while losing about x10 in TIC signal at 18 eV. The effect of reduced electron energy is not easy to predict and in some cases it has no effect. Electron energy reduction below 18 eV has limited further gain in the ratio of molecular ion to fragment ions while the TIC signal can be largely reduced.
- Increased nozzle-skimmer distance. This newly discovered effect of increased nozzle-skimmer distance on further enhanced molecular ion in Cold EI mass spectra seems essential for having Soft Cold EI. It can generate significant gain in the molecular ion while losing less than a factor of 2 in the TIC signal. Since this increased nozzle-skimmer distance requires a mechanical change in the system this change cannot be automated and thus should be implemented mostly for those experiments in which top sensitivity is not needed while enhanced molecular ion is highly desirable such as in complex hydrocarbon mixtures analysis and/or service GC-MS for synthetic organic chemistry. Once the nozzle-skimmer distance is set, the fly-through ion source can serve with automated method based change in all the three modes of Soft Cold EI, Cold EI and classical EI-SMB.