ICBM-OCEAN: Processing Ultrahigh-Resolution Mass Spectrometry Data of Complex Molecular Mixtures

Abstract

Untargeted molecular analyses of complex mixtures are relevant for many fields of research, including geochemistry, pharmacology, and medicine. Ultrahigh-resolution mass spectrometry is one of the most powerful tools in this context. The availability of open scripts and online tools for specific data processing steps such as noise removal or molecular formula assignment is growing, but an integrative tool where all crucial steps are reproducibly evaluated and documented is lacking. We developed a novel, server-based tool (ICBM-OCEAN, Institute for Chemistry and Biology of the Marine Environment, Oldenburg−complex molecular mixtures, evaluation & analysis) that integrates published and novel approaches for standardized processing of ultrahigh-resolution mass spectrometry data of complex molecular mixtures. Different from published approaches, we offer diagnostic and validation tools for all relevant steps. Among other features, we included objective and reproducible reduction of noise and systematic errors, spectra recalibration and alignment, and identification of likeliest molecular formulas. With 15 chemical elements, the tool offers high flexibility in formula attribution. Alignment of mass spectra among different samples prior to molecular formula assignment improves mass error and facilitates molecular formula confirmation with the help of isotopologues. The online tool and the detailed instruction manual are freely accessible at www.icbm.de/icbm-ocean.

Organic Matter Composition at Ocean Station Papa Affects Its Bioavailability, Bacterioplankton Growth Efficiency and the Responding Taxa

“…Approximately 1,831 unique molecular features that had an MS/MS spectrum assigned were identified (that were not present in either the processing or instrument blanks) by LC-MS/MS in the PPL-extracted samples. Peaks for all samples were aligned using MZmine (Supplementary Text 1), thereby reducing mass error and improving confirmation of spectral information (Merder et al, 2020). Based on a comparison of fragmentation patterns from aligned spectra in the EXPORTS dataset to that of publicly available MS repositories, 151 unique features matched compounds to an MS library within <0.01 Da mass offset, and an additional 244 library analogs were detected with a mass difference of <50 Da (Supplementary Table 2).…”

“…High-resolution mass spectrometry approaches to studying marine OM continue to evolve with technological developments (Moran et al, 2016), where the use of LC-MS/MS has recently emerged as a potential non-targeted approach to identifying putative library matches of specific molecular compounds (Longnecker et al, 2015). When aligned spectra (Merder et al, 2020) are used with molecular networking approaches (Aron et al, 2020), hundreds of unique molecular features can be classified at the compound level (Longnecker and Kujawinski, 2017;Petras et al, 2017). Samples analyzed by LC-MS/MS presented here suggest that putative amino acid-like and other compound classes were modified by bacterioplankton in most OM remineralization experiments (Figure 3B), consistent with the mol% GABA + B-Ala trends from the more quantitative HPLC-based amino acid analysis ( Figure 2C).…”

Antioxidant Activity and Phenolic Content of Marine Dissolved Organic Matter and Their Relation to Molecular Composition

“…Method detection limit (MDL), mass alignment of different spectra and molecular formula attribution was done with the software ICBM-OCEAN (Merder et al, 2020). The MDL method (MDL level 2.5) was used to eliminate instrumental noise.…”

“…Despite of the limited knowledge of molecular structures in the DOM pool, non-targeted ultrahigh resolution mass spectrometry via Fourier transform Ion Cyclotron Resonance mass spectrometry (FT-ICRMS) provides information of individual molecular formulas, thus allowing DOM molecular characterization with an unprecedent detail. To facilitate the analysis of the complex data obtained by FT-ICR MS, molecular classification of detected molecular formulas into different molecular families is commonly performed (Merder et al, 2020). Among the molecular groups, polyphenols, highly unsaturated or unsaturated alyphatics have been described (Merder et al, 2020).…”

“…To facilitate the analysis of the complex data obtained by FT-ICR MS, molecular classification of detected molecular formulas into different molecular families is commonly performed (Merder et al, 2020). Among the molecular groups, polyphenols, highly unsaturated or unsaturated alyphatics have been described (Merder et al, 2020). Lignins, tannins, and humic acids are examples found in the group of polyphenols (Klavins et al, 1999;Nebioso and Piccolo, 2013).…”