GdClean: removal of Gadolinium contamination in mass cytometry data.

MOTIVATION: Mass cytometry (Cytometry by Time-Of-Flight, CyTOF) is a single-cell technology that is able to quantify multiplex biomarker expressions and is commonly used in basic life science and translational research. However, the widely used Gadolinium (Gd)-based contrast agents (GBCAs) in magnetic resonance imaging (MRI) scanning in clinical practice can lead to signal contamination on the Gd channels in the CyTOF analysis. This Gd contamination greatly affects the characterization of the real signal from Gd-isotope-conjugated antibodies, severely impairing the CyTOF data quality and ruining downstream single-cell data interpretation. RESULTS: We first in-depth characterized the signals of Gd isotopes from a control sample that was not stained with Gd-labeled antibodies but was contaminated by Gd isotopes from GBCAs, and revealed the collinear intensity relationship across Gd contamination signals. We also found that the intensity ratios of detected Gd contamination signals to the reference Gd signal were highly correlated with the natural abundance ratios of corresponding Gd isotopes. We then developed a computational method named by GdClean to remove the Gd contamination signal at the single-cell level in the CyTOF data. We further demonstrated that the GdClean effectively cleaned up the Gd contamination signal while preserving the real Gd-labeled antibodies signal in Gd channels. All of these shed lights on the promising applications of the GdClean method in preprocessing CyTOF datasets for revealing the true single-cell information. AVAILABILITY AND IMPLEMENTATION: The R package GdClean is available on GitHub at https://github.com/JunweiLiu0208/GdClean. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Evaluation of Optimized Procedures for High-Precision Lead Isotope Analyses of Seawater by Multiple Collector Inductively Coupled Plasma Mass Spectrometry.

The application of Pb isotopes to marine geochemistry is currently hindered by challenges associated with the analysis of Pb isotopes in seawater. The current study evaluates the performance of multiple collector inductively coupled plasma mass spectrometry (MC-ICP-MS) measurements of seawater Pb isotope compositions following Pb separation by either solid-phase extraction with Nobias Chelate PA-1 resin or coprecipitation with Mg(OH)2 and using either a Pb double spike or external normalization to Tl for mass bias correction. The four analytical combinations achieve results of similar quality when measuring 1-7 ng of seawater Pb, with reproducibilities (two standard deviations, 2SD) of 100-1200 ppm for 206Pb/207Pb and 208Pb/207Pb and 300-1700 ppm for ratios involving the minor 204Pb isotope. All four procedures enable significantly improved sample throughput compared to an established thermal ionization mass spectrometry (TIMS) double-spike method and produce unbiased seawater Pb isotope compositions with similar or improved precision. Nobias extraction is preferable to coprecipitation due to its greater analytical throughput and suitability for analyses of large seawater samples with high Si(OH)4 contents. The most accurate Pb isotope data are produced following Nobias extraction and double-spike correction as such analyses are least susceptible to matrix effects. However, Nobias extraction with Tl normalization constitutes an attractive alternative as, unlike the double-spike procedure, only a single mass spectrometric measurement is required, which improves analytical throughput and optimizes Pb consumption for analysis. Despite the advantages of solid-phase extraction, coprecipitation represents a useful Pb separation technique for samples with low to moderate Si contents as it is inexpensive, simple to implement, and the data are only marginally less accurate, especially when combined with a Pb double spike for mass bias correction.

Cellular and sub-cellular Cu isotope fractionation in the human neuroblastoma SH-SY5Y cell line: proliferating versus neuron-like cells.

Cu isotope fractionation was investigated in the human neuroblastoma SH-SY5Y cell line, in a proliferating/tumor phase (undifferentiated cells), and in a differentiated state (neuron-like cells), induced using retinoic acid (RA). The SH-SY5Y cell line displays genetic aberrations due to its cancerous origin, but differentiation drives the cell line towards phenotypes suitable for the research of neurological diseases (e.g., Alzheimer's disease or Parkinson's disease). Cellular Cu distribution was first explored by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) imaging and, subsequently, Cu isotopic analysis was performed at cellular and sub-cellular levels via multi-collector inductively coupled plasma-mass spectrometry (MC-ICP-MS). The SH-SY5Y cells showed a re-distribution of intracellular Cu upon RA differentiation. Both undifferentiated and differentiated cells became systematically enriched in the light 63Cu isotope with increasing intracellular Cu content. Differentiated neuron-like SH-SY5Y cells showed a heavier Cu isotopic composition (+ 0.3‰) than did the undifferentiated proliferating cells when exposed to Cu for 24 h. However, after a longer exposure time (72 h), no difference was observed between both cellular phenotypes. Mitochondrial fractions were enriched in the light 63Cu isotope, compared to whole cells, for both undifferentiated and differentiated cells (no significant difference). The Cu isotopic composition of the remaining cell lysates was heavier than that of the whole cells and + 0.2‰ heavier in the differentiated cells than in the undifferentiated cells. These results indicate that neuronal differentiation affects the Cu isotope fractionation accompanying Cu uptake in the cells, but this effect does not seem to be associated with the mitochondrial Cu pathway. Cu isotope fractionation can be an interesting tool for studying Cu metabolism at a (sub)-cellular level in functional neurons. Graphical abstract.

A new anion exchange purification method for Cu stable isotopes in blood samples.

The isotopic composition of iron, zinc, copper, and cadmium (δ56Fe, δ66Zn, δ65Cu, and δ114Cd) are novel and promising tools to study the metabolism and homeostasis of trace metals in the human body. Serum δ65Cu has been proposed as a potential tool for diagnosis of cancer in liquid biopsy, and other metals may have similar utility. However, accurate analysis of trace metal isotopes is challenging because of the difficulties in purifying the metals from biological samples. Here we developed a simple and rapid method for sequential purification of Cu, Fe, Zn, and Cd from a single blood plasma sample. By using a combination of 11 M acetic acid and 4 M HCl in the first steps of column chemistry on AG-MP1 resin, we dramatically improve the separation of Cu from matrix elements compared to previous methods which use concentrated HCl alone. Our new method achieves full recovery of Cu, Fe, Zn, and Cd to prevent column-induced isotope fractionation effects, and effectively separates analytes from the matrix in order to reduce polyatomic interferences during isotope analysis. Our methods were verified by the analysis of isotope standards, a whole blood reference material, and a preliminary sample set including five plasma samples from healthy individuals and five plasma samples from cancer patients. This new method simplifies preparation of blood samples for metal isotope analysis, accelerating multi-isotope approaches to medical studies and contributing to our understanding of the cycling of Fe, Zn, Cu, and Cd in the human body. Graphical abstract ᅟ.

Possible Mechanisms of Biological Effects Observed in Living Systems during 2H/1H Isotope Fractionation and Deuterium Interactions with Other Biogenic Isotopes.

This article presents the original descriptions of some recent physics mechanisms (based on the thermodynamic, kinetic, and quantum tunnel effects) providing stable 2H/1H isotope fractionation, leading to the accumulation of particular isotopic forms in intra- or intercellular space, including the molecular effects of deuterium interaction with 18O/17O/16O, 15N/14N, 13C/12C, and other stable biogenic isotopes. These effects were observed mainly at the organelle (mitochondria) and cell levels. A new hypothesis for heavy nonradioactive isotope fractionation in living systems via neutron effect realization is discussed. The comparative analysis of some experimental studies results revealed the following observation: "Isotopic shock" is highly probable and is observed mostly when chemical bonds form between atoms with a summary odd number of neutrons (i.e., bonds with a non-compensated neutron, which correspond to the following equation: Nn - Np = 2k + 1, where k ϵ Z, k is the integer, Z is the set of non-negative integers, Nn is number of neutrons, and Np is number of protons of each individual atom, or in pair of isotopes with a chemical bond). Data on the efficacy and metabolic pathways of the therapy also considered 2H-modified drinking and diet for some diseases, such as Alzheimer's disease, Friedreich's ataxia, mitochondrial disorders, diabetes, cerebral hypoxia, Parkinson's disease, and brain cancer.

Quantitative Evaluation of Algorithms for Isotopic Envelope Extraction via Extracted Ion Chromatogram Clustering.

LC-MS precursor (MS1) data are used increasingly often in conjunction with MS/MS data for the quantification, validation, and other computational mass spectrometry tasks. The efficacy of MS1 data on downstream tasks is dependent on the coverage and accuracy of the MS1 isotopic envelope extraction algorithms that delineate them from the dense backgrounds common in complex samples. Although several algorithms for extracted ion chromatogram (XIC) clustering exist, their performance has not yet been quantified, in part due to the difficulty of obtaining, isolating, and running some algorithms and in part due to the lack of quantitative MS1 ground truth. Using a newly available manually annotated ground truth data set, we measure the performance of several popular XIC clustering algorithms in time, coverage, and accuracy of resulting isotopic envelopes. We intend this work to provide a benchmark against which future algorithms can be scored.

In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides.

Cross-linking/mass spectrometry has undergone a maturation process akin to standard proteomics by adapting key methods such as false discovery rate control and quantification. A poorly evaluated search setting in proteomics is the consideration of multiple (lighter) alternative values for the monoisotopic precursor mass to compensate for possible misassignments of the monoisotopic peak. Here, we show that monoisotopic peak assignment is a major weakness of current data handling approaches in cross-linking. Cross-linked peptides often have high precursor masses, which reduces the presence of the monoisotopic peak in the isotope envelope. Paired with generally low peak intensity, this generates a challenge that may not be completely solvable by precursor mass assignment routines. We therefore took an alternative route by '"in-search assignment of the monoisotopic peak" in the cross-link database search tool Xi (Xi-MPA), which considers multiple precursor masses during database search. We compare and evaluate the performance of established preprocessing workflows that partly correct the monoisotopic peak and Xi-MPA on three publicly available data sets. Xi-MPA always delivered the highest number of identifications with ∼2 to 4-fold increase of PSMs without compromising identification accuracy as determined by FDR estimation and comparison to crystallographic models.

A Model of Isotope Separation in Plants.

A model representing isotope separation during water evaporation in plants was constructed. The model accounts for substance diffusion, convective transfer and evaporation from the surface of the leaves. The dependence of the system's separation and enrichment coefficients on various parameters (liquid velocity, diffusion coefficient, and potential barriers for molecules and their thermal velocities) was determined. A comparison was made between the enrichment coefficients calculated from experimental data from different plants and those based on the model. Qualitative agreement between the experimental and theoretical values was obtained for the case of [Formula: see text], where u is the average velocity of water in the plant, h is the height of the plant, and D is the diffusion coefficient of the substance.

Fast isotopic separation of 10 B and 11 B boric acid by capillary zone electrophoresis.

Fast isotopic separation of 10 B and 11 B boric acid by CZE was demonstrated. The BGE contained 25 mM phenylalanine and 5 mM putrescine (рН 8.95). The running conditions were +25 kV at 20°C with indirect photometric detection at 210 nm. Baseline separation was achieved in less than 9 min. RSD of migration times and corrected peak areas were less than 0.5 and 3%, respectively (n = 5). Linearity was demonstrated in the range 0.2-2 mM for 11 B and 0.2-0.5 mM for 10 B.

Isotopic separation of lithium ions by capillary zone electrophoresis.

Separation of (6)Li and (7)Li isotopes by CZE was demonstrated. The BGE contained 5 mM 4-aminopyridine, 0.9 mM oxalic acid, 0.25 mM CTAB, and 0.25% w/v Tween 20 (рН = 9.2). The running conditions were +25 kV at 30°C with indirect photometric detection at 261 nm. Under optimal experimental conditions, the analysis time was less than 21 min. Separation of Li preparations with mole fraction of (6)Li ranging from 3.44 up to 90.38% was demonstrated.

Carbon, hydrogen and oxygen stable isotope ratios of whole wood, cellulose and lignin methoxyl groups of Picea abies as climate proxies.

RATIONALE: Carbon, hydrogen and oxygen (C, H and O) stable isotope ratios of whole wood and components are commonly used as paleoclimate proxies. In this work we consider eight different proxies in order to discover the most suitable wood component and stable isotope ratio to provide the strongest climate signal in Picea abies in a southeastern Alpine region (Trentino, Italy). METHODS: δ(13)C, δ(18)O and δ(2)H values in whole wood and cellulose, and δ(13)C and δ(2)H values in lignin methoxyl groups were measured. Analysis was performed using an Isotopic Ratio Mass Spectrometer coupled with an Elemental Analyser for measuring (13)C/(12)C and a Pyrolyser for measuring (2)H/(1)H and (18)O/(16)O. The data were evaluated by Principal Component Analysis, and a simple Pearson's correlation between isotope chronologies and climatic features, and multiple linear regression were performed to evaluate the data. RESULTS: Each stable isotope ratio in cellulose and lignin methoxyl differs significantly from the same stable isotope ratio in whole wood, the values begin higher in cellulose and lignin except for the lignin δ(2)H values. Significant correlations were found between the whole wood and the cellulose fractions for each isotope ratio. Overall, the highest correlations with temperature were found with the δ(18)O and δ(2)H values in whole wood, whereas no significant correlations were found between isotope proxies and precipitation. CONCLUSIONS: δ(18)O and δ(2)H values in whole wood provide the best temperature signals in Picea abies in the northern Italian study area. Extraction of cellulose and lignin and analysis of other isotopic ratios do not seem to be necessary.

Use of Cl and C isotopic fractionation to identify degradation and sources of polychlorinated phenols: mechanistic study and field application.

The widespread use of chlorinated phenols (CPs) as a wood preservative has led to numerous contaminated sawmill sites. However, it remains challenging to assess the extent of in situ degradation of CPs. We evaluated the use of compound-specific chlorine and carbon isotope analysis (Cl- and C-CSIA) to assess CP biotransformation. In a laboratory system, we measured isotopic fractionation during oxidative 2,4,6-trichlorophenol dechlorination by representative soil enzymes (C. fumago chloroperoxidase, horseradish peroxidase, and laccase from T. versicolor). Using a mathematical model, the validity of the Rayleigh approach to evaluate apparent kinetic isotope effects (AKIE) was confirmed. A small but significant Cl-AKIE of 1.0022 ± 0.0006 was observed for all three enzymes, consistent with a reaction pathway via a cationic radical species. For carbon, a slight inverse isotope effect was observed (C-AKIE = 0.9945 ± 0.0019). This fractionation behavior is clearly distinguishable from reported reductive dechlorination mechanisms. Based on these results we then assessed degradation and apportioned different types of technical CP mixtures used at two former sawmill sites. To our knowledge, this is the first study that makes use of two-element CSIA to study sources and transformation of CPs in the environment.

A modified lead-matrix separation procedure shown for lead isotope analysis in Trojan silver artefacts as an example.

A modified Pb-matrix separation procedure using NH4HCO3 solution as eluent has been developed and validated for determination of Pb isotope amount ratios by thermal ionization mass spectrometry. The procedure is based on chromatographic separation using the Pb·Spec resin and an in-house-prepared NH4HCO3 solution serving as eluent. The advantages of this eluent are low Pb blanks (<40 pg mL(-1)) and the property that NH4HCO3 can be easily removed by use of a heating step (>60 °C). Pb recovery is >95 % for water samples. For archaeological silver samples, however, the Pb recovery is reduced to approximately 50 %, but causes no bias in the determination of Pb isotope amount ratios. The validated procedure was used to determine lead isotope amount ratios in Trojan silver artefacts with expanded uncertainties (k = 2) <0.09 %.

Recycling of 3He from lung magnetic resonance imaging.

We have developed the means to recycle (3) He exhaled by patients after imaging the lungs using magnetic resonance of hyperpolarized (3) He. The exhaled gas is collected in a helium leak proof bag and further compressed into a steel bottle. The collected gas contains about 1-2% of (3) He, depending on the amount administered and the number of breaths collected to wash out the (3) He gas from the lungs. (3) He is separated from the exhaled air using zeolite molecular sieve adsorbent at 77 K followed by a cold head at 8 K. Residual gaseous impurities are finally absorbed by a commercial nonevaporative getter. The recycled (3) He gas features high purity, which is required for repolarization by metastability exchange optical pumping. At present, we achieve a collection efficiency of 80-84% for exhaled gas from healthy volunteers and cryogenic separation efficiency of 95%.

Solution speciation controls mercury isotope fractionation of Hg(II) sorption to goethite.

The application of Hg isotope signatures as tracers for environmental Hg cycling requires the determination of isotope fractionation factors and mechanisms for individual processes. Here, we investigated Hg isotope fractionation of Hg(II) sorption to goethite in batch systems under different experimental conditions. We observed a mass-dependent enrichment of light Hg isotopes on the goethite surface relative to dissolved Hg (ε(202)Hg of -0.30‰ to -0.44‰) which was independent of the pH, chloride and sulfate concentration, type of surface complex, and equilibration time. Based on previous theoretical equilibrium fractionation factors, we propose that Hg isotope fractionation of Hg(II) sorption to goethite is controlled by an equilibrium isotope effect between Hg(II) solution species, expressed on the mineral surface by the adsorption of the cationic solution species. In contrast, the formation of outer-sphere complexes and subsequent conformation changes to different inner-sphere complexes appeared to have insignificant effects on the observed isotope fractionation. Our findings emphasize the importance of solution speciation in metal isotope sorption studies and suggest that the dissolved Hg(II) pool in soils and sediments, which is the most mobile and bioavailable, should be isotopically heavy, as light Hg isotopes are preferentially sequestered during binding to both mineral phases and natural organic matter.

Treatise on the measurement of molecular masses with ion mobility spectrometry.

The ability to separate isotopes by high-resolution ion mobility spectrometry techniques is considered as a direct means for determining mass at ambient pressures. Calculations of peak shapes from the transport equation show that it should be possible to separate isotopes for low-mass ions (<200) by utilizing heavy collision gases and high-resolution ion mobility analyzers. The mass accuracy associated with this isotopic separation approach based on ion mobility separation is considered. Finally, we predict several isotopes that should be separable.

Isotope fractionation due to aqueous phase diffusion - What do diffusion models and experiments tell? - A review.

For the interpretation of stable isotope ratio trends in saturated geochemical systems, the magnitude of aqueous phase diffusion-induced isotope fractionation needs to be known. This study reviews how five diffusion models (Fick, Maxwell-Stefan, Einstein, Langevin, Mode-Coupling Theory Analysis (MCTA) of diffusion) predict isotope fractionation due to aqueous phase diffusion and compares them with experimental results. The reviewed diffusion models were not consistent regarding the prediction of the mass (m) dependency of the aqueous phase diffusion coefficient (D). The predictions range from a square root power law (D ∝ m-0.5) to an opposite mass dependency of D (D ∝ mß). Experimental studies exhibited consistently a weak power law mass dependency of the diffusion coefficient (D ∝ m-ß with ß < 0.5) for the vast majority of dissolved species and a larger diffusion-induced isotope effect for low weight noble gases (D ∝ m-0.5). The weak power law mass dependency of D for the species other than low weight noble gases is consistent with the MCTA of diffusion. The MCTA suggests that the weak power law mass dependency of D originates from interplays between strongly mass dependent short-term and mass independent long-term solute-solvent interactions. The larger isotope fractionation for low weight noble gases could be attributed to quantum isotope effects significantly magnifying the aqueous phase diffusion-induced isotope fractionation. Our review shows, that except for low weight noble gases a weak power law mass dependency of D is likely the most adequate assumption for aqueous phase diffusion-induced isotope fractionation in geochemical systems.

Polysulfone-graft-4'- aminobenzo-15-crown-5-ether based tandem membrane chromatography for efficient adsorptive separation of lithium isotopes.

Adsorptive membrane-based chromatography can provide the high separation efficiency common to column chromatography but at a lower working pressure. Herein, a novel membrane chromatography system for lithium isotope adsorptive separation is reported. It uses polysulfone-graft-4'-aminobenzo-15-crown-5-ether (PSf-g-AB15C5) porous membranes (0.52 mmol/g of immobilization crown ether, average pore size of 62.7 nm, porosity of 80.4%) as a stationary phase packed in a chromatography column (Ø 25 × 100 mm). Furthermore, a four-stage tandem membrane chromatography system was designed to enhance lithium isotope separation performance. The partial eluate from the former column was used as the feed solution for the next stage. Results show that the flow rate of the eluent could reach 18 mL/h owing to the lower internal diffusion resistance of membranes. Meanwhile, adsorption isotherms and adsorption kinetics show that Li+ adsorption was an exothermic and spontaneous process. The surface diffusion, multilayer adsorption and ion-pore electrostatic interaction between Li+ and the crown ether groups on the membranes played a key role in the separation of 7Li+ and 6Li+ by membrane chromatography. The separation factor obtained from the single-stage membrane chromatography was up to 1.0232. The abundances of 7Li+ and 6Li+ gradually increased with an increase in the elution stages. The relative abundances of 7Li+ and 6Li+ obtained from the four-stage tandem membrane chromatography increased by 0.26% (from 92.40 to 92.66%) and 0.2% (from 7.60 to 7.80%), respectively. In conclusion, our current research opens a new avenue for the simultaneous enrichment of 7Li+ and 6Li+ during lithium isotope adsorptive separation.

Evaluation of 72Se/72As generator and production of 72Se for supplying 72As as a potential PET imaging radionuclide.

Positron-emitting 72As is the PET imaging counterpart for beta-emitting 77As. Its parent, no carrier added (n.c.a.) 72Se, was produced for a 72Se/72As generator by irradiating an enriched 7°Ge metal-graphite target via the 70Ge(α, 2 n)72Se reaction. Target dissolution used a fast, environmentally friendly method with 93% radioactivity recovery. Chromatographic parameters of the 72Se/72As generator were evaluated, the eluted n.c.a. 72As was characterized with a phantom imaging study, and the previously reported trithiol and aryl-dithiol ligand systems were radiolabeled with the separated n.c.a. 72As in high yield.

Development of a remote purification apparatus with disposable evaporator for the routine production of high-quality 64Cu for clinical use.

We developed a new apparatus for the routine production of 64Cu in clinical use. The apparatus has many disposable parts that stabilize the product quality (such that there is a low deviation of the concentrations of impurity metals in the product) and reduce the work load of preparation for routine production. We also developed a new evaporator using near-infrared heaters for disposable use. We conducted a production test using the new apparatus and evaluated product quality. The product yield was 6.3 ±â€¯0.32 GBq (end of bombardment) (N = 4), the product quality in terms of the concentrations of impurity metals (Cu2+, Ni2+, Fe3+, Zn2+, Mn2+) was as good as that usually achieved, likely on the order of parts per billion, and the preparation time was reduced from 2 days to 1 day.