Liquid Chromatography, in Combination with a Quadrupole Time-of-Flight Instrument (LC QTOF), with Sequential Window Acquisition of All Theoretical Fragment-Ion Spectra (SWATH) Acquisition: Systematic Studies on Its Use for Screenings in Clinical and Forensic Toxicology and Comparison with Information-Dependent Acquisition (IDA)

Forensic and clinical toxicological screening procedures are employing liquid chromatography-tandem mass spectrometry (LC-MS/MS) techniques with information-dependent acquisition (IDA) approaches more and more often. It is known that the complexity of a sample and the IDA settings might prevent important compounds from being triggered. Therefore, data-independent acquisition (DIA) methods should be more suitable for systematic toxicological analysis (STA). The DIA method sequential window acquisition of all theoretical fragment-ion spectra (SWATH), which uses Q1 windows of 20-35 Da for data-independent fragmentation, was systematically investigated for its suitability for STA. Quality of SWATH-generated mass spectra were evaluated with regard to mass error, relative abundance of the fragments, and library hits. With the Q1 window set to 20-25 Da, several precursors pass Q1 at the same time and are fragmented, thus impairing the library search algorithms to a different extent: forward fit was less affected than reverse fit and purity fit. Mass error was not affected. The relative abundance of the fragments was concentration dependent for some analytes and was influenced by cofragmentation, especially of deuterated analogues. Also, the detection rate of IDA compared to SWATH was investigated in a forced coelution experiment (up to 20 analytes coeluting). Even using several different IDA settings, it was observed that IDA failed to trigger relevant compounds. Screening results of 382 authentic forensic cases revealed that SWATHs detection rate was superior to IDA, which failed to trigger similar to 10% of the analytes.