Lasertram: A Python library for time resolved analysis of laser ablation inductively coupled plasma mass spectrometry data

A time series approach for clustering mass spectrometry data

Sector field inductively coupled plasma mass spectrometry (SF-ICPMS) has been used with analysis of solution samples and laser ablation (LA) of electrodeposited alpha sources to characterize plutonium activities and atom ratios prevalent in the western USA. A large set of surface soils and attic dusts were previously collected from many locations in the states of Nevada, Utah, Arizona, and Colorado; specific samples were analyzed herein to characterize the relative contributions of stratospheric fallout vs. Nevada Test Site (NTS) plutonium. This study illustrates two different ICPMS-based analytical strategies that are successful in fingerprinting Pu in environmental soils and dusts. Two specific datasets have been generated: (1) soils are leached with HNO3-HCl, converted into electrodeposited alpha sources, counted by alpha spectrometry, then re-analyzed using laser ablation SF-ICPMS; (2) samples are completely dissolved by treatment with HNO3-HF-H3BO3, Pu fractions are prepared by extraction chromatography, and analyzed by SF-ICPMS. Optimal laser ablation and ICPMS conditions were determined for the re-analysis of archived alpha spectrometry "planchette" sources. The best ablation results were obtained using a large spot size (200 microm), a defocused beam, full repetition rate (20 Hz) and scan rate (200 microm s(-1)); LA-ICPMS data were collected with a rapid electrostatic sector scanning experiment. Less than 10% of the electroplated surface area is consumed in the LA-ICPMS analysis, which would allow for multiple re-analyses. Excellent agreement was found between (239+240)Pu activities determined by LA-ICPMS vs. activity results obtained by alpha spectrometry for the same samples ten years earlier. LA-ICPMS atom ratios for 240Pu/239Pu and 241Pu/239Pu range from 0.038-0.132 and 0.00034-0.00168, respectively, and plot along a two-component mixing line (241Pu/239Pu = 0.013 [240Pu/239Pu] - 0.0001; r2 = 0.971) with NTS and global fallout end-members. A rapid total dissolution procedure, followed by extraction chromatography and SF-ICPMS solution Pu analysis, generates excellent agreement with certified (239+240)Pu activities for standard reference materials NIST 4350b, NIST 4353, NIST 4357, and IAEA 385. (239+240)Pu activities and atom ratios determined by total dissolution reveal isotopic information in agreement with the LA-ICPMS dataset regarding the ubiquitous mixing of NTS and stratospheric fallout Pu sources in the regional environment. For several specific samples, the total dissolution method reveals that Pu is incompletely recovered by simpler HNO3-HCl leaching procedures, since some of the Pu originating from the NTS is contained in refractory siliceous particles.

Mass spectrometry (MS) is widely used for isotopic studies of metabolism and other (bio)chemical processes. Quantitative applications in systems and synthetic biology require to correct the raw MS data for the contribution of naturally occurring isotopes. Several tools are available to correct low-resolution MS data, and recent developments made substantial improvements by introducing resolution-dependent correction methods, hence opening the way to the correction of high-resolution MS (HRMS) data. Nevertheless, current HRMS correction methods partly fail to determine which isotopic species are resolved from the tracer isotopologues and should thus be corrected. We present an updated version of our isotope correction software (IsoCor) with a novel correction algorithm which ensures to accurately exploit any chemical species with any isotopic tracer, at any MS resolution. IsoCor v2 also includes a novel graphical user interface for intuitive use by end-users and a command-line interface to streamline integration into existing pipelines. IsoCor v2 is implemented in Python 3 and was tested on Windows, Unix and MacOS platforms. The source code and the documentation are freely distributed under GPL3 license at https://github.com/MetaSys-LISBP/IsoCor/ and https://isocor.readthedocs.io/.

Plasma biomarkers of abdominal aortic aneurysm

Chapter 6 - Centrifugal partition chromatography isolation of glaucolides sesquiterpenes and LC-ESIMS/MS technique for differentiation the mass spectrometry behavior of hirsutinolide and glaucolide skeletons

Despite being information rich, the vast majority of untargeted mass spectrometry data are underutilized; most analytes are not used for downstream interpretation or reanalysis after publication. The inability to dive into these rich raw mass spectrometry datasets is due to the limited flexibility and scalability of existing software tools. Here we introduce a new language, the Mass Spectrometry Query Language (MassQL), and an accompanying software ecosystem that addresses these issues by enabling the community to directly query mass spectrometry data with an expressive set of user-defined mass spectrometry patterns. Illustrated by real-world examples, MassQL provides a data-driven definition of chemical diversity by enabling the reanalysis of all public untargeted metabolomics data, empowering scientists across many disciplines to make new discoveries. MassQL has been widely implemented in multiple open-source and commercial mass spectrometry analysis tools, which enhances the ability, interoperability and reproducibility of mining of mass spectrometry data for the research community.

A novel remote deep ultraviolet laser ablation inlet connected to a dual electrospray ionization-atmospheric pressure chemical ionization (rDUVLAESCI) source is presented. This system allows for the simultaneous and spatial acquisition of mass spectrometry (MS) data for organic molecules with diverse polarities and molecular weights. Deep 193 nm UV laser ablation was used to sample analytes from dried spots for molecular MS analysis precisely. Furthermore, molecular MS imaging (MSI) with a variable laser spot size down to 3 μm was demonstrated. The complementary ionization modes generated mass spectra with sufficient analyte signals, detecting a broad range of molecules from polar compounds like caffeine and PEG 600, to nonpolar analytes, such as anthracene and wax esters, all within a single analytical run. Detection limits were found in the tens of attomoles per ablated/desorbed pixel. The powerful capabilities of the fully automated rDUVLAESCI dual source were demonstrated by visualizing the spatial distribution of new psychoactive substances on latent fingerprints. MSI for both sebum components and psychoactive substances revealed a connection between the chemical evidence and biometrical information. The rDUVLAESCI-MSI enabled the unambiguous identification of individuals, even using partially overlapped latent fingerprints. This unique rDUVLAESCI approach, with its remote laser ablation unit, improved spatial resolution and analyte coverage, particularly for nonpolar compounds.

Tile-based Fisher ratio (F-ratio) analysis of comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC × GC-TOFMS) data is a powerful, supervised discovery methodology for pinpointing sample class-distinguishing analytes between two or more sample classes. Herein, we extend this analytical methodology to focus upon specific chemical groups in kerosene-based aerospace fuel using solid-phase extraction (SPE). Treating samples with SPE removes specific compounds depending on the SPE stationary phase (i.e., silica), creating an altered "pass" sample, identical to the original "neat" sample except for the extracted compounds. Application of F-ratio analysis to the neat samples against the pass samples provides global discovery with a numerically sorted hit list of all analytes affected by the SPE procedure. Sections of GC × GC-TOFMS data from the top analyte hits are reconstructed to form a "stitch" chromatogram to visualize the sample class-distinguishing compounds, revealing excellent agreement with the extract chromatogram. Additionally, utilizing the four-grid tiling scheme developed for tile-based F-ratio analysis, we demonstrate a tile-based pairwise analysis method, referred to as 1v1 analysis, to discover analytes that differ in concentration between two fuel chromatograms. Application of 1v1 analysis is highly efficient since replicates do not necessarily need to be run on the GC × GC-TOFMS instrument, which is beneficial for sample-limited applications. The 1v1 analyses discovered most of the same features as F-ratio analysis, ranging from 69 to 81% of the features discovered by F-ratio analysis while requiring one-sixth the data. Lastly, the overall methodology is applied to three candidate rocket fuels to better understand the compound class-distinguishing differences. The separate hit lists produced for high-concentration bulk hydrocarbon differences and low-concentration level polar compound differences provided valuable insight into these candidate rocket fuels.

The abundance of platinum group alloy (PGA) grains available from some alluvial deposits combined with their great chemical resistance to conventional acid attack generates the need for an alternative method of obtaining routine, rapid yet precise Os isotopic data. Laser ablation multi-collector ICP-MS (LA-MC-ICP-MS) is ideally suited for this purpose and has been applied, in a relatively limited extent, to Os-rich samples by previous workers (e.g., Hirata, T., Michinari Hattori, M., and Tsuyoshi Tanaka, T., 1998. In-situ osmium isotope ratio analyses of iridosmines by laser ablation-multiple collector-inductively coupled plasma mass spectrometry. Chem Geol., 144, 269–280.; Malitch, K.N., 2004. Osmium isotope constraints on contrasting sources and prolonged melting in the Proterozoic upper mantle: evidence from ophiolitic Ru–Os sulfides and Ru–Os–Ir alloys. Chem Geol. 208. 157–173.; Walker, R.J., Brandon, A.D., Bird, J.M., Piccolia, P.M., McDonougha, W.F., R.D., Asha, R.D., 2005. 187Os– 186Os systematics of Os–Ir–Ru alloy grains from southwestern Oregon. Earth Planet. Sci. Lett. 230, 211–226.). The wide variety of PGA minerals yield a broad spectrum of Pt, Re and Os contents which translate into a wide spread in parent–daughter ratios that is an attractive proposition for geochronology using the Re–Os and Pt–Os decay schemes. Here we show that single PGA grains, can contain sufficient internal Re, Pt and Os elemental variability and coupled variations in parent/daughter and daughter isotope compositions that they present an opportunity to obtain ‘isochron’ ages from two different isotope decay systems. We present a rapid (40 s acquisition time), precise and accurate LA-MC-ICP-MS methodology suitable for applying Pt–Os and Re–Os geochronology approaches to single PGA grains, for use in dating chromitite deposits and identifying and dating multiple sources in alluvial PGA deposits. Because of isobaric interferences from Pt, PGA analyses by LA-MC-ICP-MS are best corrected for instrumental mass fractionation using the 189Os/ 188Os ratio. We demonstrate that, within our analytical uncertainties, mass bias effects for Os isotope ratios during LA-MC-ICP-MS are similar in nature and magnitude to mass bias variations observed during normal solution-mode analysis. While robust elemental interference corrections can be applied for Re and W on the Os mass spectrum during solution analyses (Nowell, G.M., Luguet, A., Pearson, D.A., Horstwood, M.S.A., 2008-this volume. Precise and accurate 186Os/ 188Os and 187Os/ 188Os measurements by Multi-Collector Plasma Ionisation Mass Spectrometry (MC-ICP-MS) part I: solution analyses. Chem Geol.) we show that the accurate correction for the Re interference on Os during laser ablation is problematic at 187Re/ 188Os ratios > ∼ 0.5 which means that Re-corrected 187Os/ 188Os ratios for some PGAs and high Re/Os sulfides must be regarded as problematic. Our interfering element correction approach can also be used for the correction for Os on 190Pt for obtaining 190Pt/ 188Os ratios, removing the need for an independent Pt monitor isotope. Accurate and precise geochronology by LA-MC-ICP-MS can be further limited by poorly quantified fractionation of the parent/daughter elemental ratio during ablation. Although additional work is required to understand the nature and exact extent of inter-element fractionation of the Pt/Os and Re/Os ratios during laser ablation analysis of Pt- and Re-rich PGA grains, our best estimate is that fractionation of the Pt/Os during laser ablation is around 5% or less. We present multi-grain isochrons and single-grain internal ‘isochrons’ for the Re–Os and Pt–Os isotope systems in PGA grains from Lapland. In all cases, the Pt–Os isotope system gives significantly more precise ‘isochrons’ than the Re–Os system. We interpret this discordance between the two systems as being most likely due to problems inherent with Re interference corrections at elevated Re/Os ratios. We show that a suite of Pt-rich PGA grains from the Central Lapland greenstone belt yields a spectrum of internal Pt–Os isochron ages that coincides well with pulses of formation of chromitite-bearing ophiolitic material within this magmatic terrane and we take this to indicate the record of chromitite formation in different magmatic units. The single-grain Pt–Os and Re–Os geochronology technique shows great promise in the dating of chromitite deposits in ophiolites and in the discrimination of multiple source regions within alluvial PGA deposits.

Background Substance abuse poses an escalating health risk in the United States. While acute drug exposure can be tracked using drugs and their metabolites as biomarkers in clinical settings, there is a notable absence of biomarkers for chronic drug exposure or addiction. The development and availability of such biomarkers could significantly enhance clinicians’ ability to identify patients at high risk of addiction, and more accurately predict disease progression and treatment responses. Methods Our study aimed to discover novel biomarkers associated with substance abuse by analyzing raw mass spectrometry (MS) data from urine comprehensive drug screening (UCDS) conducted at the University of Pittsburgh Medical Center (UPMC). The MS data, acquired through untargeted data collection using LC-qToF-MS at the UPMC Clinical Toxicology Laboratory, was initially preprocessed (including peak identification, alignment, and putative annotation) using MS-DIAL to generate a data matrix. This matrix, consisting of objects (cases) and features (m/z and retention time), was further normalized and analyzed using MetaboAnalyst. A combination of statistical methods, including point biserial correlation analysis, volcano plot, significance analysis of microarrays and metabolites (SAM), empirical Bayesian analysis of microarrays and metabolites (EBAM), partial least squares discriminant analysis (PLS-DA), and random forest (RF), were employed to select features significantly associated with the EIA-results. These features were subsequently evaluated for analyte identification using MS-FINDER. Results Our analysis identified nine significant features associated with 6MAM-EIA for heroin abuse, including 6-monoacetylmorphine itself and norfentanyl. For features associated with cocaine metabolite-EIA, 37 significant features were selected, including multiple cocaine metabolites, nicotine metabolites, and norfentanyl. Some of these selected features are likely products of in-source fragmentation or endogenous metabolites. Conclusions Our study has identified a set of potential biomarker candidates for illicit drug exposure. Notably, norfentanyl was found to be significantly associated with both 6MAM-EIA and cocaine metabolite-EIA, reflecting current trends in illicit drug use. Further chemical identification of these biomarkers is planned for future work.

The interpretation of mass spectrometry (MS) data is a crucial step in proteomics analysis, and the identification of post-translational modifications (PTMs) is vital for the understanding of the regulation mechanism of the living system. Among various PTMs, glycosylation is one of the most diverse ones. Though many search engines have been developed to decipher proteomic data, some of them are difficult to operate and have poor performance on glycoproteomic datasets compared to advanced glycoproteomic software. To simplify the analysis of proteomic datasets, especially O-glycoproteomic datasets, here, we present a user-friendly proteomic database search platform, MS-Decipher, for the identification of peptides from MS data. Two scoring schemes can be chosen for peptide-spectra matching. It was found that MS-Decipher had the same sensitivity and confidence in peptide identification compared to traditional database searching software. In addition, a special search mode, O-Search, is integrated into MS-Decipher to identify O-glycopeptides for O-glycoproteomic analysis. Compared with Mascot, MetaMorpheus and MSFragger, MS-Decipher can obtain about 139.9%, 48.8% and 6.9% more O-glycopeptide-spectrum matches. A useful tool is provided in MS-Decipher for the visualization of O-glycopeptide-spectra matches. MS-Decipher has a user-friendly graphical user interface, making it easier to operate. Several file formats are available in the searching and validation steps. MS-Decipher is implemented with Java, and can be used cross-platform. MS-Decipher is freely available at https://github.com/DICP-1809/MS-Decipher for academic use. For detailed implementation steps, please see the user guide. Supplementary data are available at Bioinformatics online.

We demonstrate a pyrometric contactless temperature sensor using a flexible fused silica fiber of 360 μm diameter for endoscopic/laparoscopic surgery equipment. The large bandwidth (up to several kilohertz), and the broad temperature range (from 35°C to 250°C) of the sensor can be instrumental for time-resolved analysis and control of laser ablation and electrothermal surgery procedures. Fused silica fibers, as opposed to dedicated MIR fibers, are non-degrading, low-cost and biocompatible. Through dual-band detection, we also demonstrate a ratiopyrometric measurement scheme, which improves the detection of hot-spots, providing a helpful tool for focused thermal processes observed, for example, in pulsed laser ablation.

A novel solution-based calibration method for quantitative spatial resolved distribution analysis (imaging) of elements in thin biological tissue sections by LA-ICP-MS (laser ablation inductively coupled plasma mass spectrometry) is described. A dual flow of the carrier and nebulizer gas is used to transport the aerosol of the laser ablated solid sample (brain tissue) and that of the nebulized aqueous standard into inductively coupled plasma (ICP) source, respectively. Both aerosols are introduced separately in the injector tube inside a special ICP torch and then mixed in the inductively coupled plasma. Calibration curves were obtained via two different calibration strategies: (i) solution based calibration and (ii) with a set of well characterized homogeneous brain laboratory standards. In the first approach matrix matching is performed by solution nebulization of a series of aqueous standards with defined analyte concentrations and simultaneous laser ablation of brain homogenate followed by nebulization of 2% (v/v) HNO3 and laser ablation of a whole brain slice (line by line). In the second approach of calibration a set of brain homogenates with defined analyte concentrations is analyzed by LA-ICP-MS followed by the imaging of brain tissue under the same experimental conditions (dry plasma). Calibration curves of elements of interest (e.g., Li, Na, Al, K, Ca, Ti, V, Mn, Ni, Co, Cr, Cu, Zn, As, Se, Rb, Sr, Y, Cd, Ba, La, Ce, Nd, Gd, Hg, Pb, Bi and U) were obtained using (i) aqueous standards or (ii) the set of synthetic laboratory standards prepared from a mouse brain homogenate doped with elements at defined concentrations. The ratio of the slope of the calibration curves (obtained by using aqueous standards and solid standards) was applied to correct the differences of sensitivity among ICP-MS and LA-ICP-MS. Quantitative images of Li, Mn, Fe, Cu, Zn and Rb in mouse brain were obtained under wet plasma condition (nebulization of HNO3 solution in parallel with ablation of solid brain sample).

Laser ablation split-stream analysis of the Sm-Nd and U-Pb isotope compositions of monazite, titanite, and apatite – Improvements, potential reference materials, and application to the Archean Saglek Block gneisses

The detection of layer-by-layer self-assembly multilayer films was carried out using low-temperature plasma (LTP) mass spectrometry (MS) under ambient conditions. These multilayer films have been prepared on quartz plates through the alternate assembling of oppositely charged 4-aminothiophenol (4-ATP) capped Au particles and thioglycolic acid (TGA) capped Ag particles. An LTP probe was used for direct desorption and ionization of chemical components on the films. Without the complicated sample preparation, the structure information of 4-ATP and TGA on films was studied by LTP-MS. Characteristic ions of 4-ATP (M) and TGA (F), including [M](+•), [M-NH(2)](+), [M-HCN-H](+), and [F + H](+), [F-H](+), [F-OH](+), [F-COOH](+) were recorded by LTP-MS on the films. However, [M-CS-H](+) and [F-SH](+) could not be observed on the film, which were detected in the neat sample. In addition, the semi-quantitative analysis of chemical components on monolayer film was carried out, and the amounts of 4-ATP and TGA on monolayer surface were 45 ng/mm(2) and 54 ng/mm(2), respectively. This resulted the ionization efficiencies of 72% for 4-ATP and 54% for TGA. In order to evaluate the reliability of present LTP-MS, the correlations between this approach and some traditional methods, such as UV-vis spectroscopy, atomic force microscope and X-ray photoelectron spectroscopy were studied, which resulted the correlation coefficients of higher than 0.9776. The results indicated that this technique can be used for analyzing the films without any pretreatment, which possesses great potential in the studies of self-assembly multilayer films.