Partially overlapping sequential window acquisition of all theoretical mass spectra: A methodology to improve the spectra quality of veterinary drugs present at low concentrations in highly complex biological matrices.

Rationale: Residues of veterinary drugs in food matrices have to be detected, identified and confirmed at low concentrations. Data-independent acquisition (DIA) methods such as the sequential window acquisition of all theoretical spectra (SWATH) permit the extraction of relatively clean spectra out of complex matrices. Such spectra can be significantly improved by using a modified SWATH algorithm which provides several times narrower mass isolation windows without affecting the cycle time.

Methods: A quadrupole-time-of-flight mass spectrometer was operated in a partially overlapping SWATH mode. Unlike in conventional SWATH, acquisition sequences are not identically repeated, but each sequence is initiated with a mass intercept (mass shift). Pearson correlation is used to assign HRMS-resolved product ions to the precursor mass of interest. Trace analytes (veterinary drugs) in a complex matrix extract (bovine liver) were investigated.

Results: Utilizing identical cycle times, the partially overlapping SWATH mode produced for the investigated small molecules a significantly higher selectivity than the conventional SWATH acquisition mode. The acquisition strategy enables long ion accumulation times and therefore the required high sensitivity of detection. The study investigates the quality of the obtained product ion spectra and compares it with that in conventional acquisition modes.

Conclusions: The modified SWATH mode permits high duty cycles in combination with narrow virtual mass windows. The technique is a further step toward harvesting a HRMS product ion spectrum out of a data-independent acquisition which moves closer towards the quality of a dedicated precursor unit isolation product ion spectrum.