Modern mass spectrometry
techniques produce a wealth of spectral
data, and although this is an advantage in terms of the richness of
the information available, the volume and complexity of data can prevent
a thorough interpretation to reach useful conclusions. Application
of molecular formula prediction (MFP) to produce annotated lists of
ions that have been filtered by their elemental composition and considering
structural double bond equivalence are widely used on high resolving
power mass spectrometry datasets. However, this has not been applied
to secondary ion mass spectrometry data. Here, we apply this data
interpretation approach to 3D OrbiSIMS datasets, testing it for a
series of increasingly complex samples. In an organic on inorganic
sample, we successfully annotated the organic contaminant overlayer
separately from the substrate. In a more challenging purely organic
human serum sample we filtered out both proteins and lipids based
on elemental compositions, 226 different lipids were identified and
validated using existing databases, and we assigned amino acid sequences
of abundant serum proteins including albumin, fibronectin, and transferrin.
Finally, we tested the approach on depth profile data from layered
carbonaceous engine deposits and annotated previously unidentified
lubricating oil species. Application of an unsupervised machine learning
method on filtered ions after performing MFP from this sample uniquely
separated depth profiles of species, which were not observed when
performing the method on the entire dataset. Overall, the chemical
filtering approach using MFP has great potential in enabling full
interpretation of complex 3D OrbiSIMS datasets from a plethora of
material types.