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- CID (1)
- Collision-induced dissociation (1)
- DNA (1)
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- HCD (1)
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- Mass spectrometry (1)
- Oligonucleotide (1)
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- Tandem-MS (1)
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- 1.9 Chemische und optische Sensorik (2) (entfernen)
Mass spectrometry is applied as a tool for the elucidation of molecular structures. This premises that gas-phase structures reflect the original geometry of the analytes, while it requires a thorough understanding and investigation of the forces controlling and affecting the gas-phase structures. However, only little is known about conformational changes of oligonucleotides in the gas phase. In this study, a series of multiply charged DNA oligonucleotides (n¼15–40) has been subjected to a comprehensive tandem mass spectrometric study to unravel transitions between different ionic gas-phase structures. The nucleobase sequence and the chain length were varied to gain insights into their influence on the geometrical oligonucleotide organization. Altogether, 23 oligonucleotides were analyzed using collision-induced fragmentation. All sequences showed comparable correlation regarding the characteristic collision energy. This value that is also a measure for stability, strongly correlates with the net charge density of the precursor ions. With decreasing charge of the oligonucleotides, an increase in the fragmentation energy was observed. At a distinct charge density, a deviation from linearity was observed for all studied species, indicating a structural reorganization. To corroborate the proposed geometrical change, collisional cross-sections of the oligonucleotides at different charge states were determined using ion mobility-mass spectrometry. The results clearly indicate that an increase in charge density and thus Coulomb repulsion results in the transition from a folded, compact form to elongated structures of the precursor ions. Our data show this structural transition to depend mainly on the charge density, whereas sequence and size do not have an influence.
Rationale: The most commonly used fragmentation methods in tandem mass spectrometry (MS/MS) are collision‐induced dissociation (CID) and higher energy collisional dissociation (HCD). While in CID the preselected ions in the trap are resonantly (and m/z exclusively) excited, in HCD the entire m/z range experiences the dissociative acceleration. The different excitation is reflected in different fragment distributions. Methods: As a test‐bed for particularly pronounced fragmentation specificity, here MS/MS experiments on several 4‐mer oligonucleotides were conducted employing both collision methods and the results were thoroughly compared. Oligonucleotides are shown to be sensitive probes to subtle changes, especially in the negative ion mode. A detailed analysis of these differences reveals insight into the dissociation mechanics. Results: Thedifferencesarerepresentedinheat‐maps,whichallowforadirectvisualinspection oflargeamountsofdata.Inthesefalsecolourrepresentationsthe,sometimessubtle,changesinthe individual dissociation product distributions become distinct. Another advantage of these graphic plots can be found in the formation of systematic patterns. These patterns reflect trends in dissociation specificity which allow for the formulation of general rules in fragmentation behavior. Conclusions: Instruments equipped with two different excitation schemes for MS/MS are today widely available. Nonetheless, direct comparisons between the individual results are scarcely made. Such comparative studies bear a powerful analytical potential to elucidate fragmentation reaction mechanism.