Nonselective collision-induced dissociation (CID) is a technique for producing fragmentation products for all ions generated in an ion source. It is typical of liquid chromatography/mass spectrometry (LC/MS) analysis of complex samples that matrix-related components may contribute to the resulting product ion spectra and confound the usefulness of this technique for structure interpretation. In this proof-of-principle study, a high-resolution LC/MS-based background subtraction algorithm was used to process the nonselective CID data to obtain clean product ion spectra for metabolites in human plasma samples. With buspirone and clozapine metabolites in human plasma as examples, this approach allowed for not only facile detection of metabolites of interest but also generation of their respective product ion spectra that were clean and free of matrix-related interferences. This was demonstrated with both an MS(E) technique (where E represents collision energy) with a quadrupole time-of-flight (QTOF) instrument and an in-source fragmentation technique with an LTQ Orbitrap instrument. The combined nonselective CID and background subtraction approach should allow for detection and structural interpretation of other types of sample analyses where control samples are obtained.