Characterizing lignins from various sources and treatment processes after optimized sample preparation techniques and analysis via ESI-HRMS and custom mass defect software tools

Sample preparation of complex, natural mixtures such as lignin prior to mass spectrometry analysis, however minimal, is a critical step in ensuring accurate and interference-free results. Modern shotgun-MS techniques, where samples are directly injected into a high-resolution mass spectrometer (HRMS) with no prior separation, usually still require basic sample pretreatment such as filtration and appropriate solvents for full dissolution and compatibility with atmospheric pressure ionization interfaces. In this study, sample preparation protocols have been established for a unique sample set consisting of a wide variety of degraded lignin samples from numerous sources and treatment processes. The samples were analyzed via electrospray (ESI)-HRMS in negative and positive ionization modes. The resulting information-rich HRMS datasets were then transformed into the mass defect space with custom R scripts as well as the open-source Constellation software as an effective way to visualize changes between the samples due to the sample preparation and ionization conditions as well as a starting point for comprehensive characterization of these varied sample sets. Optimized conditions for the four investigated lignins are proposed for ESI-HRMS analysis for the first time, giving an excellent starting point for future studies seeking to better characterize and understand these complex mixtures.

New algorithms demonstrate untargeted detection of chemically meaningful changing units and formula assignment for HRMS data of polymeric mixtures in the open-source constellation web application

The field of high-resolution mass spectrometry (HRMS) and ancillary hyphenated techniques comprise a rapidly expanding and evolving area. As popularity of HRMS instruments grows, there is a concurrent need for tools and solutions to simplify and automate the processing of the large and complex datasets that result from these analyses. Constellation is one such of these tools, developed by our group over the last two years to perform unsupervised trend detection for repeating, polymeric units in HRMS data of complex mixtures such as natural organic matter, oil, or lignin. In this work, we develop two new unsupervised algorithms for finding chemically-meaningful changing units in HRMS data, and incorporate a molecular-formula-finding algorithm from the open-source CoreMS software package, both demonstrated here in the Constellation software environment. These algorithms are evaluated on a collection of open-source HRMS datasets containing polymeric analytes (PEG 400 and NIST standard reference material 1950, both metabolites in human plasma, as well as a swab extract containing polymers), and are able to successfully identify all known changing units in the data, including assigning the correct formulas. Through these new developments, we are excited to add to a growing body of open-source software specialized in extracting useful information from complex datasets without the high costs, technical knowledge, and processor-demand typically associated with such tools.

Mass spectrometry-based methods for the advanced characterization and structural analysis of lignin: A review

Lignin is currently one of the most promising biologically derived resources, due to its abundance and application in biofuels, materials and conversion to value aromatic chemicals. The need to better characterize and understand this complex biopolymer has led to the development of many different analytical approaches, several of which involve mass spectrometry and subsequent data analysis. This review surveys the most important analytical methods for lignin involving mass spectrometry, first looking at methods involving gas chromatography, liquid chromatography and then continuing with more contemporary methods such as matrix assisted laser desorption ionization and time-of-flight-secondary ion mass spectrometry. Following that will be techniques that directly ionize lignin mixtures-without chromatographic separation-using softer atmospheric ionization techniques that leave the lignin oligomers intact. Finally, ultra-high resolution mass analyzers such as FT-ICR have enabled lignin analysis without major sample preparation and chromatography steps. Concurrent with an increase in the resolution of mass spectrometers, there have been a wealth of complementary data analyses and visualization methods that have allowed researchers to probe deeper into the "lignome" than ever before. These approaches extract trends such as compound series and even important analytical information about lignin substructures without performing lignin degradation either chemically or during MS analysis. These innovative methods are paving the way for a more comprehensive understanding of this important biopolymer, as we seek more sustainable solutions for our human species' energy and materials needs.

Constellation: An Open-Source Web Application for Unsupervised Systematic Trend Detection in High-Resolution Mass Spectrometry Data

The increasing popularity of high-resolution mass spectrometry has led to many custom software solutions to process, interpret, and reveal information from high-resolution mass spectra. Although there are numerous software packages for peak-picking, calibration, and formula-finding, there are additional layers of information available when it comes to detecting repeated motifs from polymers or molecules with repeating structures or products of chemical or biochemical transformations that exhibit systematic, serial chemical changes of mass. Constellation is an open-source, Python-based web application that allows the user first to expand their high-resolution mass data into the mass defect space, after which a trend finding algorithm is used for supervised or unsupervised detection of repeating motifs. Many adjustable parameters allow the user to tailor their trend-search to target particular chemical moieties or repeating units, or search for all potential motifs within certain limits. The algorithm has a built-in optimization routine to provide a good starting point for the main trend finding parameters before user customization. Visualization tools allow interrogation of the data and any trends/patterns to a highly specific degree and save publication-quality images directly from the interface. As Constellation is deployed as a web application, it is easily used by anyone with a web browser; no software download or high-powered computer is required, as computations are performed on a remote high-powered data server run by our group.

A semi-quantitative approach for the rapid screening and mass profiling of naphthenic acids directly in contaminated aqueous samples

We report the use of a direct sampling, online analytical approach for the determination of acid extractable naphthenic acids in complex aqueous samples, known as condensed phase membrane introduction mass spectrometry (CP-MIMS). The technique employs a capillary hollow fibre semi-permeable membrane probe configured for immersion into a pH adjusted sample. A continuously flowing methanol acceptor phase transfers naphthenic acids to an electrospray ionization source, operated in negative ion mode, whereupon they are analysed by mass spectrometry as [M-H](-) ions. High-resolution mass spectrometry is used to characterize the influence of sample pH on membrane transport of multiple components of complex naphthenic acid mixtures. We demonstrate the use of CP-MIMS for semi-quantitative analysis of real-world samples using selected ion monitoring and full scan mass spectra at unit mass resolution. The technique has also been employed to continuously monitor the temporal evolution in the mass profile and concentrations of individual naphthenic acid isomer classes in heterogeneous solutions during adsorption processes. Copyright © 2015 John Wiley & Sons, Ltd.

Photosensitized degradation kinetics of trace halogenated contaminants in natural waters using membrane introduction mass spectrometry as an in situ reaction monitor

On-line membrane introduction mass spectrometry used to directly measure the photosensitized reductive dehalogenation kinetics of trace aqueous halocarbons in the presence of naturally occurring dissolved organic matter.

Structure and composition of the cell wall of Choanephora cucurbitarum

Mechanically isolated, cytoplasm-free cell walls of Choanephora cucurbitarum were analyzed qualitatively and quantitatively by use of microchemical methods, infrared spectrophotometry, and X-ray diffraction. Chemical analysis of cell wall revealed the presence of chitin (17%), chitosan (28.4%), neutral sugars (7.2%), uronic acid (2.4%), proteins (8.2%), and lipids (13.8%). The structure of hyphal wall, investigated by electron microscopy of shadowed replicas before and after alkali-acid hydrolysis, showed two distinct regions: microfibrillar and amorphous. The microfibrils, which were composed of mainly chitin, were organized into two distinct layers; an outer, thicker layer of randomly oriented microfibrils, and an inner, thin layer of parallel microfibrils. In its structure and chemical composition the cell wall of C. cucurbitarum resembles those of other zygomycetous fungi.