  The physical-chemical property of molecular collision cross section (CCS) is
increasingly used to assist in small molecule identification; however,
questions remain regarding the extent of its true utility in contributing to
such identifications, especially given its correlation with mass. To
investigate the contribution of CCS to uniqueness within a given library, we
measured its discriminatory capacity as a function of error in CCS values (from
measurement or prediction), CCS variance, parent mass, mass error, and/or
reference database size using a multi-directional grid search. While
experimental CCS databases exist, they are currently small; thus, we used a CCS
prediction tool, DarkChem, to provide theoretical CCS values for use in this
study. These predicted CCS values were then modified to mirror experimental
variance. By augmenting our search within a library based on mass alone with
CCS at a variety of accuracies, we found that, (i) the use of multiple adducts
(i.e. alternative ionized forms of the same parent compound) for the same
molecule, compared to using a single adduct, greatly improves specificity and
(ii) even a single CCS leads to a significant specificity boost when low CCS
error (e.g. 1% composite error) can be achieved. Based on these results, we
recommend using multiple adducts to build up evidence of presence, as each
adduct supplies additional information per dimension. Additionally, the utility
of ion mobility spectrometry when coupled with mass spectrometry should still
be considered, regardless of whether CCS is considered as an identification
metric, due to advantages such as increased peak resolution, sensitivity (e.g.
from reducing load on the detector at any given time), improvements in
data-independent MS/MS spectra acquisition, and cleaner tandem mass spectral
fragmentation patterns.
