Confidence in a compound identification for a screening assay is greatly increased by making use of MS/MS data. It can be used for library searching or measuring fragment ion ratios. However, obtaining an MS/MS for every compound in a run can be a challenge. SWATH® Acquisition can acquire MS/MS that represents every precursor mass of interest at every time point. However, the deconvolution of MS/MS requires that each fragment ion have a different chromatographic profile or elution time. Information dependent acquisition (IDA) will consistently trigger on the most abundant compounds but can occasionally miss some candidates. Combining SWATH acquisition with IDA improves the identification of compounds in screening assays. SWATH acquisition uses precursor isolation windows that typically range from 5-50 Da or wider. Even when two or more compounds fall within a SWATH acquisition precursor isolation window, and have similar elution times, deconvolution of the MS/MS is usually possible using a PCA/PCVG based technique1. This MS/MS is used for library searching and subsequent compound identification. A method is demonstrated combining SWATH acquisition and IDA methods run separately on tea and orange samples spiked with pesticides and comparing it to combining SWATH + IDA in one acquisition method and measuring its impact on confidence in identification using targeted screening.

KC Hyland is the Global Technical Marketing chemist with SCIEX in the area of Food and Environmental applications. Particular areas of interest include cannabis product analysis, perfluorinated surfactants in the environment, food authenticity analyses, and development of methods and workflows using high resolution mass spectrometry to advance the current state of food and environmental sciences. KC received her PhD in 2014 from the Colorado School of Mines in Environmental Science and Engineering, and has been with SCIEX for the four years since earning that degree. For KC, the most enjoyable part of her job at SCIEX is interacting with researchers, scientists, and the many other incredibly knowledgeable people in these highly impactful fields.



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