Open‐source feature detection for non‐target LC–MS analytics

Abstract

Funding informationBundesministerium für Bildung und Forschung, Grant/Award Number: 02WRM1367C Rationale: Non-target screening techniques using high-resolution mass spectrometers become more and more important for environmental sciences. Highly reliable and sophisticated software solutions are required to deal with the large amount of data obtained from such analyses. Methods: Processing of high-resolution LC-HRMS data was performed upon conversion into an open, XML-based data format followed by an automated assignment of chromatographic peaks using the open-source programming language R. Raw data from three different LC-HRMS systems were processed as a proof of principle. Results: We present a simple and straightforward algorithm to extract chromatographic peaks from previously m/z-centroided data based on the opensource programming language R and C++. The working principle and processing parameters are explained in detail. A ready-to-use script is provided in the supporting information. Conclusions: The developed algorithm enables a comprehensible automated peak picking of non-target LC-MS data. Application to three completely different HRMS raw data files showed reasonable False Positives and False Negatives detection and moderate calculation times.

Communication Breakdown: Into the Molecular Mechanism of Biofilm Inhibition by CeO2 Nanocrystal Enzyme Mimics and How It Can Be Exploited

“…A reduction of approximately 20% of the bromide concentration (Figure S6) indicates that oxidative bromination may occur also in bacterial media. This supports the hypothesis that hypobromous acid was formed and reacted with QS molecules and that this affected the subsequent QQ process. , …”

“…This is crucial to elucidate the reason for the apparent reduction of the bromide concentration (Figure S6, vide supra ). Non-target measurements with LC-ESI-QToF of the extracts were evaluated by an approach , enabling the identification of halogenated compounds by their isotope patterns. Hence, a list of potential transformation products was generated.…”

“…For high-resolution measurements, the same LC method as for the LC-ESI-MS/MS measurements was used. However, the eluents were adapted from ref to obtain a more general LC method. Briefly, 100% Milli-Q water for Eluent A and 100% acetonitrile for Eluent B (both with 0.1% formic acid) were used.…”

Ozonation of Sitagliptin: Removal Kinetics and Elucidation of Oxidative Transformation Products

“…Data evaluation for STG and TFA was done by isolating their mass traces and integrating peaks using MultiQuant 3.0.2 software (Sciex). For the TP search, a nontarget approach was used by peak picking using the Software R (see Section ).…”

“…Determination of potential TPs was performed with the time series samples of the kinetic experiments, which were analysed by LC-ESI-QTOF. Changes in the intensity of detected masses over time were observed by peak picking and alignment of the results in the software R. 26 Potential TPs were isolated for further investigation if they appeared in at least three samples of a time series as well as in replicates of the experiments and if MS 2 spectra were recorded. Structure elucidation was based on assigning neutral losses and identification of characteristic fragments in the MS 2 spectra of the TPs.…”