Systems and methods for determination of oligonucleotide sequence by tandem mass spectrometry

A mass spectrometer system for complex mass spectrometry experiments and measurements using ion trap type resonant collision induced dissociation (CID), the system comprising:

• an ion source;
• a dissociation cell;
• a detector;
• and
• a memory storing non-transitory computer readable instructions that, when executed on the one or more processors cause the processors to cause the mass spectrometer system to perform a method for ion trap type resonant CID on labile compounds to drive selective dissociation along desired dissociation pathways, the method comprising:
• injecting, from the ion source, a population of ions into a confinement volume of the dissociation cell, wherein (i) the population of ions comprises ions of a labile compound with multiple dissociation pathways that produce different types of bond cleavages and different types of product ions, and (ii) the dissociation cell provides a substantially quadrupolar radio frequency (RF) electrostatic confinement potential in the confinement volume of the dissociation cell during kinetic activation of selected precursor ions in the population of ions;
• and
• kinetically activating the precursor ions in one or more dimensions of the substantially quadrupolar confinement potential such that the precursor ions undergo collisions with a buffer gas present in the confinement volume of the dissociation cell, wherein the collisions cause (i) the precursor ions to selectively dissociate without being ejected from the confinement region, and (ii) at least some resulting product ions from the selective dissociation to remain confined in the dissociation cell.