UltraMassExplorer: a browser-based application for the evaluation of high-resolution mass spectrometric data.

RATIONALE: High-resolution mass spectrometry (HRMS) with high sample throughput has become an important analytical tool for the analysis of highly complex samples and data processing has become a major challenge for the user community. Evaluating direct-infusion HRMS data without automated tools for batch processing can be a time-consuming step in the analytical pipeline. Therefore, we developed a new browser-based software tool for processing HRMS data. METHODS: The software, named UltraMassExplorer (UME), was written in the R programming language using the shiny library to build the graphical user interface. The performance of the integrated formula library search algorithm was tested using HRMS data derived from analyses of up to 50 extracts of marine dissolved organic matter. RESULTS: The software supports the processing of lists of calibrated masses of neutral, protonated or deprotonated molecules, with masses of up to 700 Da and a mass accuracy <3 ppm. In the performance test, the number of assigned peaks per second increased with the number of submitted peaks and reached a maximum rate of 4745 assigned peaks per second. CONCLUSIONS: UME offers a complete data evaluation pipeline comprising a fast molecular formula assignment algorithm allowing for the swift reanalysis of complete datasets, advanced filter functions and the export of data, metadata and publication-quality graphics. Unique to UME is a fast and interactive connection between data and their visual representation. UME provides a new platform enabling an increased transparency, customization, documentation and comparability of datasets.

Spectral characterization of ten cyclic lipids using time-of-flight secondary ion mass spectrometry.

RATIONALE: Over the last decade, the high lateral resolution and imaging capabilities of time-of-flight secondary ion mass spectrometry (ToF-SIMS) have increasingly stimulated interest in studying organic molecules in complex environmental materials. However, unlike with the established mass spectrometric techniques, the use of ToF-SIMS in the biogeosciences is still hampered by a lack of reference spectra of the relevant biomarker compounds. Here we present and interpret ToF-SIMS reference spectra of ten different cyclic lipids that are frequently used as biological tracers in ecological, organic geochemical and geobiological studies. METHODS: Standard compounds of α,ß,ß-(20R,24S)-24-methylcholestane, (22E)-ergosta-5,7,22-trien-3ß-ol, 17α(H),21ß-(H)-30-norhopane, hope-17(21)-ene, hop-22(29)-ene, 17ß(H),21ß(H)-bacteriohopane-32,33,34,35-tetrol, 17ß(H),21ß(H)-35-aminobacteriohopane-32,33,34-triol, α-tocopherol, ß,ß-carotene, chlorophyll a, and cryosections of microbial mats and a fungus were analyzed using a ToF-SIMS instrument equipped with a Bi(3)(+) cluster ion source. RESULTS: The spectra obtained from the standard compounds showed peaks in the molecular weight range (molecular ions, protonated and deprotonated molecules, adduct ions) and diagnostic fragment ion peaks in both, positive and negative ion modes. For the cyclic hydrocarbons, however, the positive ion mode spectra typically showed more and stronger characteristic peaks than the negative ion mode spectra. Using real world samples the capability of ToF-SIMS to detect and image selected compounds in complex organic matrices was tested. 17ß(H),21ß(H)-35-Aminobacteriohopane-32,33,34-triol, carotene and chlorophyll a were successfully identified in cryosections of microbial mats, and the distribution of ergosterol was mapped at µm resolution in a cryosection of a fungus (Tuber uncinatum). CONCLUSIONS: This study further highlights the utility of ToF-SIMS for the identification and localization of lipids within environmental samples and as a technique for biomarker-related research in organic geochemistry and geobiology.

Spectral characterisation of eight glycerolipids and their detection in natural samples using time-of-flight secondary ion mass spectrometry.

In recent years, time-of-flight secondary ion mass spectrometry (ToF-SIMS) with cluster ion sources has opened new perspectives for the analysis of lipid biomarkers in geobiology and organic geochemistry. However, published ToF-SIMS reference spectra of relevant compounds are still sparse, and the influence of the chemical environment (matrix) on the ionisation of molecules and their fragmentation is still not well explored. This study presents ToF-SIMS spectra of eight glycerolipids as common target compounds in biomarker studies, namely ester- and ether-bound phosphatidylethanolamine, ester- and ether-bound phosphatidylcholine, ester-bound phosphatidylglycerol, ester- and ether-bound diglycerides and archaeol, obtained with a Bi(3) (+) cluster ion source. For all of these compounds, the spectra obtained in positive and negative analytical modes showed characteristic fragments that could clearly be assigned to e.g. molecular ions, functional groups and alkyl chains. By comparison with the reference spectra, it was possible to track some of these lipids in a pre-characterised organic extract and in cryosections of microbial mats. The results highlight the potential of ToF-SIMS for the laterally resolved analysis of organic biomarkers in environmental materials. The identification of the target compounds, however, may be hampered by matrix effects (e.g. adduct formation) and often require careful consideration of all spectral features and taking advantage of the molecular imaging capability of ToF-SIMS.