Negative nucleotide ions as sensitive probes for energy
specificity in collision‐induced fragmentation in mass
Michael W. Linscheid
Department of Chemistry, Humboldt‐
Universitaet zu Berlin, Brook‐Taylor‐Str. 2,
12489 Berlin, Germany
Bundesanstalt für Materialforschung und
‐pruefung, Richard‐Willstaetter‐Str. 11, 12489
J. Riedel, Bundesanstalt für Materialforschung
und ‐pruefung, Richard‐Willstaetter‐Str. 11,
12489 Berlin, Germany.
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.
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.
The differences are represented in heat‐maps, which allow for a direct visual inspection
of large amounts of data. In these false colour representations the, sometimes subtle, changes in the
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.
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.
The technical evolution of mass spectrometry is a perpetual success
story in which a pronounced cross‐pollination between supply
(instrumentation) and demand (application) can be observed.
analytical demands fueled the technical inventions, while at the same
time ever‐increasing technological achievements pushed the
expectations of the users. This evolution was catalyzed by the broad
and profound knowledge of the pioneers in this field.
example for this is the invention of tandem mass spectrometry
(MS/MS). While the large abundance of fragments in electron
ionization mass spectra was merely accepted by most users, some felt
challenged to conduct more thorough studies which finally resulted in
a broad knowledge of characteristic fragmentation mechanisms.
Applying the underlying rules, an experienced user can readily derive
both, the molecular mass and the chemical structure, from a MS
spectrum with a distinctive fragment pattern.
The concept of a characteristic dissociation led to another
instrumental breakthrough, tandem mass spectrometry (MS/MS).
Here the structure elucidating fragmentation was not an undesired
side reaction anymore but the desired goal. While in the beginning
MS/MS was intended to fully establish the relation between the
dissociation mechanism and the geometry of the precursor ion, it soon
became a standard tool for structural identification. This additional
dimensionality in the insights an MS study can provide was powered
by the commercialization of MS/MS devices. All early MS/MS setups
consisted of two individual mass separation units which are spatially
intersected by a fragmentation cell,
a geometry that would later lead
to the term tandem‐in‐space.
The fragmentation is usually achieved
by an electrostatic acceleration of the preselected ions into a collision
cell filled with neutral gas collision partners.
The advent of ion trap mass spectrometers led to a new approach
Since the ions are trapped in a confined space
and usually ion trap MS allows for a much higher total pressure, the
Received: 1 June 2017 Revised: 3 January 2018 Accepted: 4 January 2018
Rapid Commun Mass Spectrom. 2018;32:597–603. Copyright © 2018 John Wiley & Sons, Ltd.wileyonlinelibrary.com/journal/rcm 597