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 open-source 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.
© 2021 The Authors. Rapid Communications in Mass Spectrometry published by John Wiley & Sons Ltd.