CID fragment annotation from data-independent experiments in non-target organic aerosol analysis: presenting an easy-to-use tool.

The open-source tool presented in this work provides a simple, reliable, and comprehensive method for analyzing and annotating CID fragments of precursor ions in data-independent full MS/AIF experiments in non-targeted HPLC-UHRMS analyses (NTA). The method provides similar results to established data-dependent fragmentation experiments while simultaneously increasing the informational value of the resulting raw data file, giving a more unbiased view of the sample, which is crucial for NTA, and improving the limit of detection for fragment ions. Using the tool to analyze a mixture of 28 standard compounds has shown that fragment identification and annotation were equal to or better for 71% of the measured compounds - compared to manual analysis - while being completely automated and not requiring input from the experimenter. Formula prediction performed better, with the tool being able to correctly identify 96% of the standard compounds. The purpose of this paper is to provide an easy-to-use tool to facilitate the usage of full MS/AIF measurements for non-targeted analysis, automating the process of fragment annotation and identification for structural analysis of precursor ions. The proposed workflow will significantly increase the informational value of each measurement file, allowing for the creation of databases, and ultimately speed up scientific progress. The algorithm presented in this work yields comparable results as would be obtained by manual analysis of isolated MS2 spectra.