Why is Automating the Determination of Molecular Ions Using Automated Approaches so Hard and How Might it be Used?

Molecular ion identification is the corner stone of all LC/MS1 data analyses. Manual identification can often require significant amounts of time for data processing across all disciplines of mass spectrometry. A number of highly accomplished algorithms using chemometric approaches to reduce or remove low frequency noise from LC/MS datasets are reported in the literature, and, in some cases, are available in commercial formats. Examples include CODA (1) and MEND (2). These algorithms may be loosely classified as extremely sensitive peak extraction algorithms, because the output requires a scientist to analyze the contributing ions as a function of retention time and solve the remaining spectra for molecular weight and other contributing ions. We present here the results of research aimed at developing a sensitive and rugged approach to the automated determination of molecular weight with the minimum of user intervention in optimizing critical parameters. Additionally, we also aimed to reduce the number of false positive results that are obtained in automated determinations of compound presence or absence using targeted ion extraction. It has been found that the output of this research is generic and directly applicable to mass spectrometric determinations of compound and purity, metabolism, impurity and degradants, and metabonomics