Mass spectrometry is commonly used in the identification of species present in microbial samples, but the high similarity in the peptide composition between strains of a single species has made ...analysis at the subspecies level challenging. Prior research in this area has employed methods such as Principal Component Analysis (PCA), the k-Nearest Neighbors’ (kNN) algorithm, and Pearson correlation. Previously, 1D cross-correlation of mass spectra has been shown to be useful in the classification of small molecule compounds as well as in the identification of peptide sequences via the SEQUEST algorithm and its variants. While direct application of cross-correlation to mass spectral data has been shown to aid in the identification of many other types of compounds, this type of analysis has not been demonstrated in the literature for the purpose of LC-MS based identification of microbial strains. A method of identifying microbial strains is presented here that applies the principle of 2D cross-correlation to LC-MS data. For a set of N = 30 yeast isolate samples representing 5 yeast strains (K-97, S-33, T-58, US-05, WB-06), high-resolution LC-MS-Orbitrap data were collected. Reference spectra were then generated for each strain from the combined data of each sample of that strain. Sample strains were then predicted by computing the 2D cross-correlation of each sample against the reference spectra, followed by application of correction factors measuring the asymmetry of the 2D correlation functions.
Digital learning tools and laboratory simulations have been an area of great interest not only due to the advancements of at-home learning but also by allowing students and institutions access to ...experiences they would not have otherwise due to the high cost of commercial instrumentation. The need for online learning tools became especially relevant during the COVID-19 pandemic, when students and educators were forced to embrace new ways to construct a learning environment. A time-of-flight mass spectrometer virtual instrument named TOFSim, written in National Instrument’s LabVIEW graphical programming language, is presented here as a means for teaching the principles of time-of-flight mass spectrometry through first-hand experience and guided exercises. TOFSim is capable of generating realistic data that allows the user to explore and optimize their virtual instrument outside of a traditional laboratory environment.
A method is developed to determine the position of ion formation along the flight axis of a MALDI TOFMS instrument using the image of the laser on the sample surface. Previous work (JASMS 2018, 29, ...422–434) showed that misalignment of the sample stage in a Bruker Autoflex III MALDI TOFMS as well as multiple insertions/mountings of the target plate and differences in target plate shape itself produced reproducible changes in the measured ion time-of-flight which could be attributed to changes in the position of ion formation along the instrument flight axis. Here, a small but reproducible change in the position of the laser in the sample-viewing camera image was observed, with the movement depending on both the sample position and target plate used. Using the change in coordinates of the laser position in the camera image and the known angle of incidence of the laser on the sample surface, the initial
z
-axis position of the ion at different locations on the plate can be calculated, exactly defining changes in the ion flight path length and the distance between the sample plate and first extraction plate/grid with sample position on the target plate. A correction method is developed to correct the time-of-flight values collected from different locations on the sample plate using the laser images, with the relative standard deviation (RSD) being reduced from 23 ppm to below 6 ppm. The laser images, along with the measured target plate heights, are also used to calculate the misalignment of the sample stage.
Graphical Abstract
Matrix-assisted laser desorption ionization (MALDI) time-of-flight mass spectrometry (TOF MS) is now accepted as a quick, easy-to-use, cost-effective, and accurate technique for the identification of ...microorganisms. However, the successful identification of microorganisms is dependent upon careful attention to factors such as growth conditions, extraction methods, mass spectral data collection, and data analysis procedures. Currently, most microorganism identification has been limited to the species level, and only a limited number of publications have been successful in achieving strain-level identification. In this work, a “cell-free” approach is introduced where peptide analytes secreted by several
Saccharomyces cerevisiae
strains during their growth period are analyzed. The analysis of the cell supernatant generates mass spectral patterns that are specific to each strain. The patterns generated in combination with a robust data analysis workflow using the open-source programs MALDIquant and Mass-Up allows for strain-level identification of
S. cerevisiae
. The cell-free approach using the yeast supernatant to accurately identify yeast strains is presented here as a proof of concept.
Graphical Abstract
Current literature shows a gap for methods which can identify yeast sub-species (strains or serovars) in samples where there are no viable cells remaining. Presented here is a technique for the ...analysis of yeast supernatant, including solid phase extraction, data-dependent acquisition liquid chromatography/mass spectrometry (LC-MS), and two chemometric methods to identify and classify yeast strains. Five strains of
Saccharomyces cerevisiae
were successfully identified in various stages of growth. In addition, peptide/protein identification was performed, without the need for additional data acquisition.
Graphical Abstract
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Background, aim and scope
Over 50% of the global population live in urban centres and, therefore, an understanding of the processes acting upon urban systems is a global issue. The nature of ...human-made, often impervious, land surfaces and heavily engineered waterways results in hydrological and sedimentological systems in urbanised basins which contrast significantly to those within more natural (i.e. pristine, forested, agricultural) aquatic systems. In addition, the abundance of contamination sources in urban systems results in chemical pressures often manifested as high pollution concentrations or loadings, which in turn have detrimental impacts on human and ecosystem health. These lead to management and sustainability issues not generally encountered in more natural environments. The purpose of this review is to provide a state-of-the-art assessment of sediment sources, pathways and storage within urban river systems, to consider sediment management within urban systems and river basins, and examine the role of local and global environmental changes on sediment processes and management. Inevitably, much of the sediment that is transported within urbanised basins is contaminated, so this review also considers sediment–contaminant sources and interactions.
Conclusions and recommendations
We reach a number of conclusions and recommendations for future research. There is a need for better sampling and monitoring of sediment and sediment-associated contaminant fluxes and cycling in urban river channels and basins. This should include better techniques and studies to identify sources and transfers of road-deposited sediment (RDS), airborne particulate matter and sediments in the river system. Greater interdisciplinary research, combining sedimentologists, hydrologists, urban planners, urban archaeologists, chemists and biologists, is needed. More attention needs to focus on upscaling and connecting urban areas to the rest of the river basin, both upstream and downstream. Finally, there is a need to balance multiple needs (urban population, water resources) with likely trends in both urban development and global environmental change.
Matrix‐assisted laser desorption/ionization (MALDI) is a soft ionization technique that when used to analyze synthetic polymer analytes often requires the addition of a metal cationization agent ...(herein termed the “salt”). The choice of both the matrix and the cationization agent needs to be taken into account when considering the polymer under study; different polymers have shown different affinities toward different cationization agents, and their selectivity can change as the matrix changes. Salt‐to‐analyte ratio (S/A) plots are used in this work to investigate the effect of the quantity of cationization agent employed in the analysis of a poly (methylmethacrylate) (PMMA) analyte with different MALDI matrices. The point at which analyte signal stops increasing with the added cationization agent is termed the “cation saturation point,” and it was found to occur around a S/A of 1. When the analyte signal after this point remains constant, it is termed an “ideal case.” The “non‐ideal case” occurs when the analyte signal decreases after the cation saturation point. The amount of matrix present (measured as the matrix‐to‐analyte molar ratio, M/A) and the use of different counterions for the salt are also found to affect the intensity of the analyte signal. In non‐ideal cases, changes in the counterion or an increase in the M/A are found to increase the analyte signal, often converting an initially observed non‐ideal case into an ideal case. Several experiments attempting to uncover the reason for observation of the non‐ideal S/A behavior are also described.
In this work an attenuated total reflection Fourier transform infrared (FT-IR) absorption based method is used to measure the solubility of two matrix-assisted laser desorption–ionization (MALDI) ...matrices in a few pure solvents and mixtures of acetonitrile and water using low microliter amounts of solution. Results from a method that averages the values obtained from multiple calibration curves created by manual peak picking are compared to those predicted using a partial least squares (PLS) chemometrics approach. The PLS method provided solubility values that were in good agreement with the manual method with significantly greater ease of analysis. As a test, the solubility of adipic acid in acetone was measured using the two methods of analysis, and the values are in good agreement with solubility values reported in literature. The solubilities of the MALDI matrices α-cyano-4-hydroxy cinnamic acid (CHCA) and sinapinic acid (SA) were measured in a series of mixtures made from acetonitrile (ACN) and water; surprisingly, the results show a highly nonlinear trend. While both CHCA and SA show solubility values of less than 10 mg/mL in the pure solvents, the solubility value for SA increases to 56.3 mg/mL in a 75:25 v/v ACN:water mixture. This can have a significant effect on the matrix-to-analyte ratios in the MALDI experiment when sample protocols call for preparation of a saturated solution of the matrix in the chosen solvent system.
