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Supervised Non-negative Matrix Factorization Methods for MALDI Imaging Applications
摘要： Motivation: Non-negative matrix factorization (NMF) is a common tool for obtaining low-rank approximations of non-negative data matrices and has been widely used in machine learning, e.g., for supporting feature extraction in high-dimensional classification tasks. In its classical form NMF is an unsupervised method, i.e. the class labels of the training data are not used when computing the NMF. However, incorporating the classification labels into the NMF algorithms allows to specifically guide them towards the extraction of data patterns relevant for discriminating the respective classes. This approach is particularly suited for the analysis of mass spectrometry imaging (MSI) data in clinical applications, such as tumor typing and classification, which are amongst the most challenging tasks in pathology. Thus, we investigate algorithms for extracting tumor specific spectral patterns from MSI data by NMF methods. Results: In this paper, we incorporate a priori class labels into the NMF cost functional by adding appropriate supervised penalty terms. Numerical experiments on a MALDI imaging dataset confirm that the novel supervised NMF methods lead to significantly better classification accuracy and stability as compared to other standard approaches.
关键词： MALDI imaging,tumor typing,Non-negative matrix factorization,mass spectrometry imaging,supervised learning
更新于2025-09-23 15:21:01
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Modeling of surface spectra with and without dust from Martian infrared data: new aspects
摘要： Purpose – This paper aims to characterize the mineral composition of Martian surfaces based on Thermal Emission Spectrometer (TES; Mars Global Surveyor) as measured in the infrared thermal range. It presents modeling and interpreting of TES spectral data from selected Martian regions from which the atmospheric influences had been removed using radiative transfer algorithm and deconvolution algorithm. The spectra from the dark area of Cimmeria Terra and the bright Isidis Planitia were developed in Philip Christensen’s and Joshua Bandfield’s publications, where these spectra were subjected to spectral deconvolution to estimate the mineral composition of the Martian surface. The results of the analyses of these spectra were used for the modeling of dusty and non-dusty surface of Mars. As an additional source, the mineral compositions of Polish basalts and mafic rocks were used for these surfaces as well as for modeling Martian meteorites Shergottites, Nakhlites and Chassignites. Finally, the spectra for the modeling of the Hellas region were obtained from the Planetary Fourier Spectrometer (PFS) – (Mars Express) and the mineralogical compositions of basalts from the southern part of Poland were used for this purpose. The Hellas region was modeled also using simulated Martian soil samples Phyllosilicatic Mars Regolith Simulant and Sulfatic Mars Regolith Simulant, showing as a result that the composition of this selected area has a high content of sulfates. Linear spectral combination was chosen as the best modeling method. The modeling was performed using PFSLook software written in the Space Research Centre of the Polish Academy of Sciences. Additional measurements were made with an infrared spectrometer in thermal infrared spectroscopy, for comparison with the measurements of PFS and TES. The research uses a kind of modeling that successfully matches mineralogical composition to the measured spectrum from the surface of Mars, which is the main goal of the publication. This method is used for areas where sample collection is not yet possible. The areas have been chosen based on public availability of the data.
关键词： Spectra modelling,Infrared spectrometry,Linear spectral addition,Mars
更新于2025-09-23 15:21:01
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Combination of sequential cloud point extraction and hydride generation atomic fluorescence spectrometry for preconcentration and determination of inorganic and methyl mercury in water samples
摘要： A sequential cloud point extraction method was established for the determination of trace mercury species in water samples by hydride generation atomic fluorescence spectrometry (HGAFS). The proposed extraction system consisted of two chief steps: isolation of inorganic mercury (Hg2+) by chelating with potassium?iodide and methyl green, and then isolation of methyl mercury (CH3Hg+) by chelating with ammonium pyrrolidinedithiocarbamate. The nonionic surfactant Triton X?114 was chosen as the extractant, while the brominating agent was applied to convert extracted CH3Hg+ into Hg2+. Before HGAFS detection, the two surfactant?rich phases obtained in the sequential process were separately diluted to 3 mL with 5% (v/v) HCl after the addition of antifoam (0.4 mL). The effects of experimental conditions, including pH and concentration of surfactant and chelating agents, on cloud point extraction were optimized. Under the optimum conditions, the limits of detection for Hg2+ and CH3Hg+ were 0.007 and 0.018 μg/L with the enrichment factors of 15.1 and 11.2, respectively. The proposed method was successfully used for the determination of trace Hg2+ and CH3Hg+ in water samples with satisfactory recoveries of 95?104%.
关键词： Hydride generation atomic fluorescence spectrometry,Non?chromatographic mercury speciation,Cloud point extraction
更新于2025-09-23 15:21:01
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Detectors on the Basis of High-Purity Epitaxial GaAs Layers for Spectrometry of X and Gamma Rays
摘要： The characteristics of detectors of soft-X and γ rays based on high-purity epitaxial GaAs layers are discussed. The characteristics of detectors with different rectifying contacts are compared, that is, those with a Schottky barrier and a p–n junction. The spectral characteristics of the manufactured detectors that were obtained under the irradiation by 57Co and 241Am sources at different bias voltages and in a photovoltaic mode and the simulation results using the Geant 3.21 software package are presented.
关键词： photovoltaic mode,Geant 3.21,Schottky barrier,high-purity epitaxial GaAs layers,spectrometry,X and Gamma Rays,p–n junction
更新于2025-09-23 15:21:01
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Insights into the Synthesis Mechanism of Ag <sub/>29</sub> Nanoclusters
摘要： The current understanding of the synthesis mechanisms of noble metal clusters is limited, in particular for Ag clusters. Here, we present a detailed investigation into the synthesis process of atomically monodisperse Ag29 clusters, prepared via reduction of AgNO3 in the presence of dithiolate ligands. Using optical spectroscopy, mass spectrometry and X-ray spectroscopy, it was determined that the synthesis involves a rapid nucleation and growth to species with up to a few hundred Ag atoms. From these larger species, Ag29 clusters are formed and their concentration increases steadily over time. Oxygen plays an important role in the etching of large particles to Ag29. No other stable Ag cluster species are observed at any point during the synthesis.
关键词： synthesis mechanism,Ag29 nanoclusters,optical spectroscopy,X-ray spectroscopy,mass spectrometry
更新于2025-09-23 15:21:01
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MALDI MS Imaging at Acquisition Rates Exceeding 100 Pixels per Second
摘要： The practicality of matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) applied to molecular imaging of biological tissues is limited by the analysis speed. Typically, a relatively low speed of stop-and-go micromotion of XY stages is considered as a factor substantially reducing the rate with which fresh sample material can be supplied to the laser spot. The sample scan rate in our laboratory-built high-throughput imaging TOF mass spectrometer was significantly improved through the use of a galvanometer-based optical scanner performing fast laser spot repositioning on a target plate. The optical system incorporated into the ion source of our MALDI TOF mass spectrometer allowed focusing the laser beam via a modified grid into a 10-μm round spot. This permitted the acquisition of high-resolution MS images with a well-defined pixel size at acquisition rates exceeding 100 pixel/s. The influence of selected parameters on the total MS imaging time is discussed. The new scanning technique was employed to display the distribution of an antitumor agent in 3D colorectal adenocarcinoma cell aggregates; a single MS image comprising 100 × 100 pixels with 10-μm lateral resolution was recorded in approximately 70 s.
关键词： MSI,TOF,Mass spectrometry imaging,High throughput,Laser beam scanning,Colorectal adenocarcinoma,3D cell aggregates,Spheroids,Grid ion source,MALDI
更新于2025-09-23 15:21:01
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Unique Distribution of Diacyl-, Alkylacyl-, and Alkenylacyl-Phosphatidylcholine Species Visualized in Pork Chop Tissues by Matrix-Assisted Laser Desorption/Ionizationa??Mass Spectrometry Imaging
摘要： Phosphatidylcholine (PC) is the major phospholipid in meat and in?uences meat qualities, such as healthiness. PC is classi?ed into three groups based on the bond at the sn-1 position: Diacyl, alkylacyl, and alkenylacyl. To investigate their composition and distribution in pork tissues, including longissimus thoracis et lumborum (loin) spinalis muscles, intermuscular fat, and transparent tissues, we performed matrix-assisted laser desorption/ionization–mass spectrometry imaging (MALDI–MSI). Eleven diacyl-, seven alkylacyl-, and six alkenylacyl-PCs were identi?ed using liquid chromatography (LC)-tandem MS (MS/MS) analysis. Despite many alkylacyl- and alkenylacyl-PC species sharing identical m/z values, we were able to visualize these PC species using MALDI–MSI. Diacyl- and alkylacyl- and/or alkenylacyl-PC species showed unique distribution patterns in the tissues, suggesting that their distribution patterns were dependent on their fatty acid compositions. PCs are a major dietary source of choline in meat, and the amount was signi?cantly higher in the muscle tissues. Consumption of choline mitigates age-related memory decline and neurodegenerative diseases; therefore, the consumption of pork muscle tissues could help to mitigate these diseases. These results support the use of MALDI–MSI analysis for assessing the association between PC species and the quality parameters of meat.
关键词： mass spectrometry imaging (MSI),lipid distribution,phosphatidylcholines,liquid chromatography-tandem mass spectrometry (LC-MS/MS),pork,matrix-assisted laser desorption/ionization (MALDI)
更新于2025-09-23 15:19:57
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Convenient Construction of Orthogonal Dual Aptamer-Based Plasmonic Immunosandwich Assay for Probing Protein Disease Markers in Complex Samples and Living Animals
摘要： Aptamers, due to their outstanding merits including simple synthesis and easy modification, have been widely used as antibody alternatives to construct novel immunosandwich assays. Dual aptamer-based sandwich assays exhibit multiple advantages over conventional immunosandwich assays and single aptamer-based sandwich assays. However, their construction is hampered by the limited knowledge of binding orthogonality of aptamers reported in literature. Herein we present a new strategy for conveniently constructing an orthogonal dual aptamer-based plasmonic immunosandwich assay (odA-PISA) for probing proteins in complex samples and living animals. An orthogonal aptamer pair was first efficiently selected from aptamers reported in literature by affinity capillary electrophoresis (ACE). Then, a target protein-capturing gold thin layer-coated probe and silver nanoparticle-based Raman labeling nanotags were conveniently prepared with the selected aptamers and used to construct the assay. The double aptamers used ensured the specificity while the plasmonic coupling effect between the target-capturing probe and Raman nanotags generated significantly enhanced Raman signal intensity, providing high sensitivity. As a proof of principle, alkaline phosphatase (ALP) was used as the target. The constructed odA-PISA exhibited high specificity and high sensitivity toward ALP, giving cross-reactivity ≤ 4.2% and limit of detection (LOD) of 3.8 pM (S/N = 4). Quantitative determination of ALP in human serum and probing ALP in tumor-bearing mice were achieved, showing the great application potential of the method. This strategy is widely applicable to other protein disease markers. Therefore, it opened a new access to the construction of sensitive dual aptamer-based sandwich assays for real-world applications particularly disease diagnosis.
关键词： aptamer,binding orthogonality,Raman spectrometry,plasmonic immunosandwich assay,disease marker
更新于2025-09-23 15:19:57
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Detecting Laser-Volatilized Salts with a Miniature 100-GHz Spectrometer
摘要： Rotational transitions are unique identi?ers of molecular species, including isotopologues. This article describes the rotational detections of two laser-volatilized salts, NaCl and KCl, made with a miniature Fourier transform millimeter-wave (FTmmW) cavity spectrometer that could one day be used to measure solid composition in the ?eld or in space. The two salts are relevant targets for icy moons in the outer solar system, and in principle, other molecular solids could be analyzed with the FTmmW instrument. By coupling the spectrometer to a collisionally cooling laser ablation source, (a) we demonstrate that the FTmmW instrument is sensitive enough to detect ablation products, and (b) we use the small size of the FTmmW cavity to measure ablation product signal along the carrier gas beam. We ?nd that for 532 nm nanosecond pulses, ablated molecules are widely dispersed in the carrier-gas jet. In addition to the miniature spectrometer results, we present several complementary measurements intended to characterize the laser ablation process. For pulse energies between 10 and 30 mJ, the ablation product yield increases linearly, reaching approximately 1012 salt molecules per 30 mJ pulse. Using mass spectrometry, we observe Li+, Na+, and K+ in the plumes of ablated NaCl, KCl, and LiCl, which implies dissociation of the volatilized material. We do not observe salt ions (e.g., NaCl+). However, with 800 nm femtosecond laser pulses, the triatomic ion clusters Li2Cl+, Na2Cl+, and K2Cl+ are produced. Finally, we observe incomplete volatilization with the nanosecond pulses: some of the ejecta are liquid droplets. The insights about ablation plume physics gleaned from these experiments should guide future implementations of the laser-volatilization technique.
关键词： KCl,Fourier transform millimeter-wave,FTmmW,rotational transitions,NaCl,mass spectrometry,outer solar system,icy moons,laser-volatilized salts,laser ablation
更新于2025-09-23 15:19:57
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Determination of the isotopic composition of enriched materials using laser ablation molecular isotopic spectrometry: partial least squares and multivariate curve resolution for the determination of 15N content in enriched urea
摘要： A quantitative analytical method based on laser ablation molecular isotopic spectrometry (LAMIS) and multivariate analysis was developed and evaluated for the determination of the isotopic composition of enriched materials. The method consists preparing a concentrated solution of the enriched material, using small quantities of a sample (125 mg), and ensuring the economic efficiency of the analysis. Standard solutions of known isotopic contents are prepared by employing mixtures of urea highly enriched in 15N and urea of natural isotopic ratio and analyzed by mass spectrometry. A small volume (30 μL) of these solutions is delivered to a filter paper disc (3 cm diameter). After drying, the disc, offering a homogeneously distributed analyte, is presented to a LAMIS equipment to acquire the vibronic emission spectra containing information about the isotopologues of interest. To illustrate the proposed method, the content of 15N is determined in enriched samples of urea. In this case, each spectrum is normalized by the intensity of emission of the CN isotopologues for the electronic (Δν = 0) emission band at 387.1 nm, ensuring better accuracy. Selected regions and single wavelengths of the vibronic emission spectrum (Δν = + 1 or ? 1) related to CN species were employed to construct multivariate partial least squares (PLS) and univariate regression models to predict the isotopic content of new samples. Besides, the LAMIS data set was evaluated by multivariate curve resolution (MCR) algorithm. The best MCR and PLS models presented similar results regarding the accuracy to determine 15N content in enriched urea. MCR is capable of identifying spectral interferences and minimizing its effect. The results show that the proposed method based on LAMIS and PLS or MCR multivariate analysis can determine the 15N content in the range 5–50% with a root mean square error of prediction (RMSEP) respectively equal to 0.5 or 0.7% (m/m) in comparison with reference results obtained by mass spectrometry.
关键词： 15N determination in enriched urea,Laser ablation molecular isotopic spectrometry (LAMIS),Isotopic composition of enriched materials,Partial least squares,Multivariate regression,Multivariate curve resolution (MCR)
更新于2025-09-23 15:19:57