Comparison of Software Tools for Liquid Chromatography–High-Resolution Mass Spectrometry Data Processing in Nontarget Screening of Environmental Samples

Abstract

The field of high-resolution mass spectrometry has undergone a rapid progress in the last years due to instrumental improvements leading to a higher sensitivity and selectivity of instruments. A variety of qualitative screening approaches, summarized as nontarget screening, have been introduced and have successfully extended the environmental monitoring of organic micropollutants. Several automated data processing workflows have been developed to handle the immense amount of data that are recorded in short time frames by these methods. Most data processing workflows include similar steps, but underlying algorithms and implementation of different processing steps vary. In this study the consistency of data processing with different software tools was investigated. For this purpose, the same raw data files were processed with the software packages MZmine2, enviMass, Compound Discoverer, and XCMS online and resulting feature lists were compared. Results show a low coherence between different processing tools, as overlap of features between all four programs was around 10%, and for each software between 40% and 55% of features did not match with any other program. The implementation of replicate and blank filter was identified as one of the sources of observed divergences. However, there is a need for a better understanding and user instructions on the influence of different algorithms and settings on feature extraction and following filtering steps. In future studies it would be of interest to investigate how final data interpretation is influenced by different processing software. With this work we want to encourage more awareness on data processing as a crucial step in the workflow of nontarget screening.

New software tools, databases, and resources in metabolomics: updates from 2020

“…Though, there are decade old popular preprocessing tools available to the community in the form of xcms (Tautenhahn et al 2008 ), MZmine 2 (MZmine Development Team 2015 ), MS-DIAL (Tsugawa et al 2015 ) there is a consistent effort to improve the workflows- from reducing computational time, to developing graphical user interfaces (GUIs) for users to render them user friendly to addressing challenges associated with interpretation of data from advanced platforms such as HRMS data or those from IMS, MSI etc. In fact, a recent comparative effort (among software tools such as software packages MZmine 2, enviMass, Compound Discoverer™, and XCMS Online) demonstrated a low coherence between the four processing tools, as overlap of features between all four programs was only about 10%, and for each software between 40 and 55% of features did not match with any other program (Hohrenk et al 2020 ). Moreover, quality control (QC) tools are important to take care of systematic and random variations/ errors induced during experimental and analytical workflows.…”

Molecular Networking: A Useful Tool for the Identification of New Psychoactive Substances in Seizures by LC–HRMS

“…HRMS has, then, become essential in forensic toxicology for the detection of unknown substances; however, the complexity of the data generated from the analysis of a sample is high and annotation is still a bottleneck, often limiting the use of the collected data. A number of proprietary or open software and platforms exist for the analysis of complex raw data from untargeted LC-HRMS analysis; they only allow the annotation of known compounds, through library searches (Hohrenk et al, 2020).…”

Patroon: Open Source Software Platform for Environmental Mass Spectrometry Based Non-target Screening

“…Commercial software tools such as MetaboScape [26] [30,31] and summarized in Table 1). While many tools were originally developed to process metabolomics and proteomics data, approaches such as XCMS [32] and MZmine [33] have also been applied to environmental NTA studies [6,34].…”