Single Analyzer Neutral Loss Scans in a Linear Quadrupole Ion Trap Using Orthogonal Double Resonance Excitation

In this follow-up paper to our previous work on single analyzer precursor ion scans in a linear quadrupole ion trap (Snyder, D. T.; Cooks, R. G. Single analyzer precursor ion scans in a linear quadrupole ion trap using orthogonal double resonance excitation. J. Am. Soc. Mass Spectrom. 2017, DOI: 10.1007/s13361-017-1707-y), we now report the development of single analyzer neutral loss scans in a linear quadrupole ion trap using orthogonal double resonance excitation. Methodologically, there are three key differences between single analyzer precursor ion scans and neutral loss scans under constant radiofrequency (rf) conditions: (1) in the latter experiment, both excitation and ejection frequencies must be scanned, whereas in the former the ejection frequency is fixed, (2) the need to maintain a constant neutral loss while incrementing both precursor and product ion masses, complicated by the complex relationship between secular frequency and mass, requires use of two simultaneous frequency scans, both linear in mass, and (3) because the ejection frequency is scanned, a third ac signal occurring between the ac excitation and ac ejection frequency scans must also be applied and scanned in order to reject artifact peaks caused by ejection of unfragmented precursor ions. Using this methodology, we demonstrate neutral loss scans on a commercial linear ion trap using mixtures of illicit drugs and acylcarnitines. We also demonstrate neutral loss scanning on a Populus deltoides leaf and on a lignin sample, both significantly more complex mixtures.