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Mistle: bringing spectral library predictions to metaproteomics with an efficient search index
(2023)
Motivation: Deep learning has moved to the forefront of tandem mass spectrometry-driven proteomics and authentic prediction for peptide fragmentation is more feasible than ever. Still, at this point spectral prediction is mainly used to validate database search results or for confined search spaces. Fully predicted spectral libraries have not yet been efficiently adapted to large search space problems that often occur in metaproteomics or proteogenomics.
Results: In this study, we showcase a workflow that uses Prosit for spectral library predictions on two common metaproteomes and implement an indexing and search algorithm, Mistle, to efficiently identify experimental mass spectra within the library. Hence, the workflow emulates a classic protein sequence database search with protein digestion but builds a searchable index from spectral predictions as an in-between step.
We compare Mistle to popular search engines, both on a spectral and database search level, and provide evidence that this approach is more accurate than a database search using MSFragger. Mistle outperforms other spectral library search engines in terms of run time and proves to be extremely memory efficient with a 4- to 22-fold decrease in RAM usage. This makes Mistle universally applicable to large search spaces, e.g. covering comprehensive sequence databases of diverse microbiomes.
Availability and implementation: Mistle is freely available on GitHub at https://github.com/BAMeScience/Mistle.
Thermo-Desorption Gas Chromatography-Mass Spectrometry (TD-GC-MS) was used to investigate the thermal degradation of two different polyurethanes (PU). PU samples were heated at different heating rates and the desorbed products were collected in a cold injection system and thereafter submitted to GC-MS. Prospects and limitations of the detection and quantification of semi-volatile degradation products were investigated. A temperature dependent PU depolymerization was
found at temperatures above 200 °C proved by an increasing release of 1,4-butanediol and methylene diphenyl diisocyanate (MDI) representing the main building blocks of both polymers. Their release was monitored quantitatively based on external calibration with authentic compounds. Size Exclusion Chromatography (SEC) of the residues obtained after thermodesorption confirmed the initial competitive degradation mechanism indicating an equilibrium of crosslinking and depolymerization as previously suggested. Matrix-Assisted Laser Desorption Ionization (MALDI) mass spectrometry of SEC fractions of thermally degraded PUs provided additional hints on degradation mechanism.
The combination of acoustically levitated droplets, mid-IR laser evaporation, and subsequent post-ionization by secondary electrospray ionization was applied for monitoring the enzymatic digestion of various proteins. Acoustically levitated droplets are an ideal, wall-free model reactor, readily allowing compartmentalized microfluidic trypsin digestions. Time-resolved interrogation of the droplets yielded real-time information on the progress of the reaction and thus provided insights into reaction kinetics. After 30 min of digestion in the acoustic levitator, the obtained protein sequence coverages were identical to the reference overnight digestions. Importantly, our results clearly demonstrate that the applied experimental setup can be used for the real-time investigation of chemical reactions. Furthermore, the described methodology only uses a fraction of the typically applied amounts of solvent, analyte, and trypsin. Thus, the results exemplify the use of acoustic levitation as a green analytical chemistry alternative to the currently used batch reactions.
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly
(2023)
Monoclonal antibodies are biotechnologically produced proteins with various applications in research, therapeutics and diagnostics. Their ability to recognize and bind to specific molecule structures makes them essential research tools and therapeutic agents. Sequence information of antibodies is helpful for understanding antibody–antigen interactions and ensuring their affinity and specificity. De novo protein sequencing based on mass spectrometry is a valuable method to obtain the amino acid sequence of peptides and proteins without a priori knowledge. In this study, we evaluated six recently developed de novo peptide sequencing algorithms (Novor, pNovo 3, DeepNovo, SMSNet, PointNovo and Casanovo), which were not specifically designed for antibody data. We validated their ability to identify and assemble antibody sequences on three multi-enzymatic data sets. The deep learning-based tools Casanovo and PointNovo showed an increased peptide recall across different enzymes and data sets compared with spectrum-graph-based approaches. We evaluated different error types of de novo peptide sequencing tools and their performance for different numbers of missing cleavage sites, noisy spectra and peptides of various lengths. We achieved a sequence coverage of 97.69–99.53% on the light chains of three different antibody data sets using the de Bruijn assembler ALPS and the predictions from Casanovo. However, low sequence coverage and accuracy on the heavy chains demonstrate that complete de novo protein sequencing remains a challenging issue in proteomics that requires improved de novo error correction, alternative digestion strategies and hybrid approaches such as homology search to achieve high accuracy on long protein sequences.
The composition of acoustically levitated droplets was probed by a novel combination of mid-IR laser evaporation and subsequent postionization via secondary electrospray ionization. The combination of microliter samples and subnanoliter sampling provided time-resolved interrogation of droplets and allowed for a kinetic investigation of the laser-induced release of the analyte, which was found to strongly depend on the analytes. The observed substancespecific delayed release of the analytes permitted baseline-separated discrimination of the analytes, ideal for the study of complex samples.
The additionally applied postionization scheme was found to enable efficient detection of small volatile compounds as well as peptides. The detection of small molecules and peptides occurred under very different sampling geometries, pointing to two distinct underlying ionization mechanisms. Overall, our results suggest that the experimental setup presented in this study can serve as a widely applicable platform to study chemical reactions in acoustically levitated droplets as model reactors.
Living organisms constantly interact with their environment, including through the exchange of gases. Respiration and the release and uptake of volatile organic compounds (VOCs) create dynamic microenvironments in biological systems. Studying the kinetics of volatiles in biological systems requires expensive instruments, and data analysis is challenging. Therefore, we aimed to design a minimal analytical device for measuring the composition of gaseous mixtures in realtime.
We built the ‘Modular Biological Mass Spectrometer’ (MoBiMS) from 3D-printed parts and custom sensors to fit a wide array of experimental set-ups. We tested the chemical detection range and temporal resolution of the MoBiMS employing pure compounds and complex biological samples.
Compounds with a higher than 0.4 mmHg vapor pressure and a molecular weight up to 154 g/mol were reliably sensed within seconds. The generated electron impact (EI) spectra were directly comparable with standard databases like the NIST EI library. Under a direct analysis approach, the MoBiMS identified the characteristic odor of banana (Musa sp.), that is, isoamyl acetate; tracked the dynamics of CO2 release while the Alka-Seltzer® reaction occurred showed the kinetics of the transient production and consumption of carbon dioxide during photosynthesis. MoBiMS also discriminated between volatile compounds ions coming from tobacco (Nicotiana benthamiana) leaves and the surrounding air through untargeted analysis. The small footprint of the MoBiMS and its relatively low energy consumption facilitate in situ analyses, as an additional gas supply is not necessary with EI ionization. The MoBiMS is easy to assemble, and its construction and operation are very cost-efficient compared to commercial devices. The analytical performance of the MoBiMS is suitable for real-time studies of biological systems, environmental monitoring, and medical diagnostics.
The aim of this study was to identify specific truffle marker substances within the truffle aroma. The aroma profile of different truffle species was analyzed using static headspace sampling with gas chromatography mass spectrometry analysis (SHS/GC-MS). Possible marker substances were identified, taking the additional literature into account. The selected marker substances were tested in an experiment with 19 truffle dogs. The hypothesis “If trained truffle dogs recognize the substances as supposed truffles in the context of an experiment, they can be regarded as specific” was made. As it would be nearly impossible to investigate every other possible emitter of the same compounds to determine their specificity, this hypothesis was a reasonable approximation. We were interested in the question of what it is the dogs actually search for on a chemical level and whether we can link their ability to find truffles to one or more specific marker substances. The results of the dog experiment are not as unambiguous as could have been expected based on the SHS/GC-MS measurements. Presumably, the truffle aroma is mainly characterized and perceived by dogs by dimethyl sulfide and dimethyl disulfide. However, as dogs are living beings and not analytical instruments, it seems unavoidable that one must live with some degree of uncertainty regarding these results.
Mass Spectrometry (MS) and Nuclear Magnetic Resonance Spectroscopy (NMR) are critical components of every industrial chemical process as they provide information on the concentrations of individual compounds and by-products. These processes are carried out manually and by a specialist, which takes a substantial amount of time and prevents their utilization for real-time closed-loop process control. This paper presents recent advances from two projects that use Artificial Neural Networks (ANNs) to address the challenges of automation and performance-efficient realizations of MS and NMR. In the first part, a complete toolchain has been developed to develop simulated spectra and train ANNs to identify compounds in MS. In the second part, a limited number of experimental NMR spectra have been augmented by simulated spectra to train an ANN with better prediction performance and speed than state-of-theart analysis. These results suggest that, in the context of the digital transformation of the process industry, we are now on the threshold of a possible strongly simplified use of MS and MRS and the accompanying data evaluation by machine-supported procedures, and can utilize both methods much wider for reaction and process monitoring or quality control.
Mass spectrometry-based proteomics provides a holistic snapshot of the entire protein set of living cells on a molecular level. Currently, only a few deep learning approaches exist that involve peptide fragmentation spectra, which represent partial sequence information of proteins. Commonly, these approaches lack the ability to characterize less studied or even unknown patterns in spectra because of their use of explicit domain knowledge. Here, to elevate unrestricted learning from spectra, we introduce ‘ad hoc learning of fragmentation’ (AHLF), a deep learning model that is end-to-end trained on 19.2 million spectra from several phosphoproteomic datasets. AHLF is interpretable, and we show that peak-level feature importance values and pairwise interactions between peaks are in line with corresponding peptide fragments. We demonstrate our approach by detecting post-translational modifications, specifically protein phosphorylation based on only the fragmentation spectrum without a database search. AHLF increases the area under the receiver operating characteristic curve (AUC) by an average of 9.4% on recent phosphoproteomic data compared with the current state of the art on this task. Furthermore, use of AHLF in rescoring search results increases the number of phosphopeptide identifications by a margin of up to 15.1% at a constant false discovery rate. To show the broad applicability of AHLF, we use transfer learning to also detect cross-linked peptides, as used in protein structure analysis, with an AUC of up to 94%.
MALDI-TOF-MS-Based Identification of Monoclonal Murine Anti-SARS-CoV-2 Antibodies within One Hour
(2022)
During the SARS-CoV-2 pandemic, many virus-binding monoclonal antibodies have been developed for clinical and diagnostic purposes. This underlines the importance of antibodies as universal bioanalytical reagents. However, little attention is given to the reproducibility crisis that scientific studies are still facing to date. In a recent study, not even half of all research antibodies mentioned in publications could be identified at all. This should spark more efforts in the search for practical solutions for the traceability of antibodies. For this purpose, we used 35 monoclonal antibodies against SARS-CoV-2 to demonstrate how sequence-independent antibody identification can be achieved by simple means applied to the protein. First, we examined the intact and light chain masses of the antibodies relative to the reference material NIST-mAb 8671. Already half of the antibodies could be identified based solely on these two parameters. In addition, we developed two complementary peptide mass fingerprinting methods with MALDI-TOF-MS that can be performed in 60 min and had a combined sequence coverage of over 80%. One method is based on the partial acidic hydrolysis of the protein by 5 mM of sulfuric acid at 99 degrees C. Furthermore, we established a fast way for a tryptic digest without an alkylation step. We were able to show that the distinction of clones is possible simply by a brief visual comparison of the mass spectra. In this work, two clones originating from the same immunization gave the same fingerprints. Later, a hybridoma sequencing confirmed the sequence identity of these sister clones. In order to automate the spectral comparison for larger libraries of antibodies, we developed the online software ABID 2.0. This open-source software determines the number of matching peptides in the fingerprint spectra. We propose that publications and other documents critically relying on monoclonal antibodies with unknown amino acid sequences should include at least one antibody fingerprint. By fingerprinting an antibody in question, its identity can be confirmed by comparison with a library spectrum at any time and context.
Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
Sequence-defined poly(amino phosphodiester)s containing main-chain tertiary amines were synthesized by automated solid-phase phosphoramidite chemistry. These polymers were prepared using four monomers with different substituents. The formed polymers were characterized by HPLC and mass spectrometry. These methods evidenced preparation of molecularly-defined polymers. Furthermore, the presence of tertiary amines in the polymer backbones facilitates sequencing by tandem mass spectrometry.
One of the most widely used methods to detect an acute viral infection in clinical specimens is diagnostic real-time polymerase chain reaction. However, because of the COVID-19 pandemic, mass-spectrometry-based proteomics is currently being discussed as a potential diagnostic method for viral infections. Because proteomics is not yet applied in routine virus diagnostics, here we discuss its potential to detect viral infections. Apart from theoretical considerations, the current status and technical limitations are considered. Finally, the challenges that have to be overcome to establish proteomics in routine virus diagnostics are highlighted.
To gain a thorough appreciation of microbiome dynamics, researchers characterize the functional relevance of expressed microbial genes or proteins. This can be accomplished through metaproteomics, which characterizes the protein expression of microbiomes. Several software tools exist for analyzing microbiomes at the functional level by measuring their combined proteome-level response to environmental perturbations. In this survey, we explore the performance of six available tools, to enable researchers to make informed decisions regarding software choice based on their research goals. Tandem mass spectrometry-based proteomic data obtained from dental caries plaque samples grown with and without sucrose in paired biofilm reactors were used as representative data for this evaluation. Microbial peptides from one sample pair were identified by the X! tandem search algorithm via SearchGUI and subjected to functional analysis using software tools including eggNOG-mapper, MEGAN5, MetaGOmics, MetaProteomeAnalyzer (MPA), ProPHAnE, and Unipept to generate functional annotation through Gene Ontology (GO) terms. Among these software tools, notable differences in functional annotation were detected after comparing differentially expressed protein functional groups. Based on the generated GO terms of these tools we performed a peptide-level comparison to evaluate the quality of their functional annotations. A BLAST analysis against the NCBI non-redundant database revealed that the sensitivity and specificity of functional annotation varied between tools. For example, eggNOG-mapper mapped to the most number of GO terms, while Unipept generated more accurate GO terms. Based on our evaluation, metaproteomics researchers can choose the software according to their analytical needs and developers can use the resulting feedback to further optimize their algorithms. To make more of these tools accessible via scalable metaproteomics workflows, eggNOG-mapper and Unipept 4.0 were incorporated into the Galaxy platform.
The theory of a new calibration approach for obtaining absolute isotope ratios of multi-isotopic elements without the use of any standard has been developed. The calibration approach basically uses the difference in the instrumental isotope fractionation of two different types of mass spectrometers, leading to two different fractionation lines in a three-isotope diagram. When measuring the same sample with both mass spectrometers, the different fractionation lines have one point in common: this is the ‘true’ logarithmized isotope ratio pair of the sample. Thus, the intersection of both fractionation lines provides us with the absolute isotope ratios of the sample. This theory has been tested in practice by measuring Cd and of Pb isotope ratios in the certified reference materials BAM-I012 and NIST SRM981 by thermal ionization mass spectrometry and by inductively coupled plasma mass spectrometry while varying the ionization conditions for both mass spectrometers. With this experiment, the theory could be verified, and absolute isotope ratios were obtained, which were metrologically compatible with the certified isotope ratios. The so-obtained absolute isotope ratios are biased by − 0.5% in average, which should be improved with further developments of the method. This calibration approach is universal, as it can be applied to all elements with three or more isotopes and it is not limited to the type of mass spectrometers applied; it can be applied as well to secondary ion mass spectrometry or others. Additionally, this approach provides information on the fractionation process itself via the triple-isotope fractionation exponent θ.
We studied the dissolution behavior of β NaYF4:Yb(20%), Er(2%) UCNP of two different sizes in biologically relevant media i.e., water (neutral pH), phosphate buffered saline (PBS), and Dulbecco’s modified Eagle medium (DMEM) at different temperatures and particle concentrations. Special emphasis was dedicated to assess the influence of different surface functionalizations, particularly the potential of mesoporous and microporous silica shells of different thicknesses for UCNP stabilization and protection. Dissolution was quantified electrochemically using a fluoride ion selective electrode (ISE) and by inductively coupled plasma optical emission spectrometry (ICP OES). In addition, dissolution was monitored fluorometrically. These experiments revealed that a thick microporous silica shell drastically decreased dissolution. Our results also underline the critical influence of the chemical composition of the aqueous environment on UCNP dissolution. In DMEM, we observed the formation of a layer of adsorbed molecules on the UCNP surface that protected the UCNP from dissolution and enhanced their fluorescence. Examination of this layer by X ray photoelectron spectroscopy (XPS) and mass spectrometry (MS) suggested that mainly phenylalanine, lysine, and glucose are adsorbed from DMEM. These findings should be considered in the future for cellular toxicity studies with UCNP and other nanoparticles and the design of new biocompatible surface coatings.
The structure and composition of polycarbonate polydimethylsiloxane copolymer (PC-co-PDMS) was investigated by applying various analytical approaches including chromatographic separation methods, spectrometric, and spectroscopic detection techniques. In particular, size exclusion chromatography (SEC) and liquid adsorption chromatography operating at different conditions (e.g. using gradient solvent systems) were used to achieve separations according to molar mass and functionality distribution. The coupling of both techniques resulted in fingerprint two-dimensional plots, which could be used to easily compare different copolymer batches. Matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) mass spectrometry was applied for structural investigations. The different ionization behavior of both comonomers, however, strongly limited the applicability of this technique. In contrast to that, Fourier-transform Infrared (FTIR) spectroscopy could be used to quantify the amount of PDMS in the copolymer at different points in the chromatogram. The resulting methodology was capable of distinguishing PC-co-PDMS copolymer from PC homopolymer chains present in the material.
Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similar tools, metaproteome annotation benefits from the most comprehensive set of available databases (such as NCBI, UniProt, EggNOG, PFAM, and CAZy). The workflow described in this protocol combines both tools and leads the user through the entire data analysis process, including protein database creation, database search, protein grouping and annotation, and results visualization. To the best of our knowledge, this protocol presents the most comprehensive, detailed and flexible guide to metaproteomics data analysis to date. While beginners are provided with robust, easy-to-use, state-of-the-art data analysis in a reasonable time (a few hours, depending on, among other factors, the protein database size and the number of identified peptides and inferred proteins), advanced users benefit from the flexibility and adaptability of the workflow.
Untargeted accurate strain-level classification of a priori unidentified organisms using tandem mass spectrometry is a challenging task. Reference databases often lack taxonomic depth, limiting peptide assignments to the species level. However, the extension with detailed strain information increases runtime and decreases statistical power. In addition, larger databases contain a higher number of similar proteomes. We present TaxIt, an iterative workflow to address the increasing search space required for MS/MS-based strain-level classification of samples with unknown taxonomic origin. TaxIt first applies reference sequence data for initial identification of species candidates, followed by automated acquisition of relevant strain sequences for low level classification. Furthermore, proteome similarities resulting in ambiguous taxonomic assignments are addressed with an abundance weighting strategy to increase the confidence in candidate taxa. For benchmarking the performance of our method, we apply our iterative workflow on several samples of bacterial and viral origin. In comparison to noniterative approaches using unique peptides or advanced abundance correction, TaxIt identifies microbial strains correctly in all examples presented (with one tie), thereby demonstrating the potential for untargeted and deeper taxonomic classification. TaxIt makes extensive use of public, unrestricted, and continuously growing sequence resources such as the NCBI databases and is available under open-source BSD license at https://gitlab.com/rki_bioinformatics/TaxIt.
Tandem mass spectrometry represents an important analytical tool to unravel molecular structures and to study the gas-phase behavior of organic molecules. Besides commonly used methods like collision-induced dissociation and electron capture or transfer dissociation, new ultraviolet light–based techniques have the potential to synergistically add to the activation methods. Here, we present a new simple, yet robust, experimental design for polychromatic activation of trapped ions using the 115–160 nm output of a commercially available deuterium lamp. The resulting continuous dissociative excitation with photons of a wide energy range from 7.7 to 10.8 eV is studied for a comprehensive set of analyte classes in both positive and negative ion modes. While being simple, affordable, compact, and of low maintenance, the new setup initiates fragmentation of most precursor ions via their known dissociation pathways. Additionally, some new fragmentation patterns were discovered. Especially, electron loss and electron capture reactions with subsequent fragmentations were observed. For oligonucleotides, peptides, carbohydrates, and organic dyes, in comparison to collision-induced dissociation, a significantly wider fragment distribution was obtained, resulting in an information increase. Since the individual photons carry enough energy to post-ionize the nascent fragments, a permanent vacuum ultraviolet light exposure inside the ion trap potentially goes along with a general increase in detection capability.
In this study, the thermal decomposition of 1,3,5-tris-(2,3-dibromopropyl)-1,3,5-triazine-2,4,6-trione (TDBPTAZTO) and 2,4,6-tris-(2,4,6-tribromo-phenoxy)-1,3,5-triazine (TTBP-TAZ) were investigated for the first time by thermogravimetric analysis. Both compounds were thermal degraded between 225 and 350 °C (TDBP-TAZTO) as well as 300 and 400 °C (TTBP-TAZ).
As a result, mass loss (%) of 98.5% for TTBP-TAZ and 95.4% for TDBP-TAZTO at 600 °C under N2 were observed. The major pyrolytic degradation products of TTBP-TAZ were formed in a single step and identified by FTIR analysis as 2,4,6-tribromophenol and further bromine-substituted aromatic compounds. In comparison, TDBP-TAZTO was pyrolytic degraded in two steps, whereby on the first step the release of hydrogen Bromide and 1,3,5-triallyl-1,3,5-triazine-2,4,6-trione could be detected. In the second minor step, isocyanic acid could be additionally identified.
Subsequently, the obtained products of the TGA-FTIR measurements were used for a targeted search for mass fragments in mass spectrometry measurements. For TTBP-TAZ, only the degradation product 1,3,5-tribromobenzene could be detected by MS/MS analyzes. No comparable thermal degradation products, except hydrogen bromide, were observed in the MS/MS spectra of TDBP-TAZTO. Therefore, the search of further mass fragments was not possible compared to the findings of the TGA-FTIR measurements.
ICP-MS has played a key role in inorganic chemical metrology for 25 years, from the 1993 CIPM feasibility study which led to establishment of the CCQM. Since that time, the Inorganic Analysis Working Group of the CCQM has organised 56 international comparisons involving measurements by ICP-MS and, in a recent comparison, 16 different national institutes submitted their results using the technique. Metrological applications of ICP-MS currently address an enormous range of measurements using a wide variety of instrumentation, calibration strategies and methodologies. This review provides an overview of the ICP-MS field with an emphasis on developments which are of particular relevance to chemical metrology.
Examples from CCQM comparisons and the services available from the participants are used to illustrate how the capability and scope of ICP-MS methods have expanded far beyond the expectations of 1993. This is due in part to the research and development Programmes of the national institutes which participate in the CCQM. They have played a key role in advancing new instrumentation and applications for elemental analysis, isotope dilution mass spectrometry, determination of isotopic ratio or composition, and speciation of organometallic compounds. These developments are continuing today, as demonstrated by work in new fields such as heteroatom quantitation of proteins, characterisation and counting of nanoparticles using spICP-MS, and LA-ICP-MS analysis of solid materials.
Screening of one-bead-one-compound (OBOC) libraries is a proven procedure for the identification of protein-binding ligands. The demand for binders with high affinity and specificity towards various targets has surged in the biomedical and pharmaceutical field in recent years. The traditional peptide screening involves tedious steps such as affinity selection, bead picking, sequencing, and characterization. Herein, we present a high-throughput “all-on-one chip” system to avoid slow and technically complex bead picking steps. On a traditional glass slide provided with an electrically conductive tape, beads of a combinatorial peptide library are aligned and immobilized by application of a precision sieve. Subsequently, the chip is incubated with a fluorophore-labeled target protein. In a fluorescence scan followed by matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry, high-affinity binders are directly and unambiguously sequenced with high accuracy without picking of the positive beads. The use of an optimized ladder sequencing approach improved the accuracy of the de-novo sequencing step to nearly 100%. The new technique was validated by employing a FLAG-based model system, identifying new peptide binders for the monoclonal M2 anti-FLAG antibody, and was finally utilized to search for IgG-binding peptides. In the present format, more than 30,000 beads can be screened on one slide.
Functional sequences of precision polymers based on thiolactone/Michael chemistry are identified from a large one-bead one-compound library. Single-bead readout by MALDI-TOF MS/MS identifies sequences that host m-THPC that is a second Generation photo-sensitizer drug. The corresponding Tla/Michael-PEG conjugates make m-THPC available in solution and drug payload as well as drug release kinetics can be fine-tuned by the precision segment.
Metal tags find application in a multitude of biomedical systems and the combination with laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) offers an opportunity for multiplexing. To lay the foundation for an increase of the signal intensities in such processes, we herein present a general approach for efficient functionalization of a well-defined metal oxido cluster [Bi6O4(OH)(4)(SO3CF3)(6)(CH3CN)(6)].2 CH3CN (1), which can be realized by selecting 7mer peptide sequences via combinatorial means from large one-bead one-compound peptide libraries. Selective cluster-binding peptide sequences (CBS) for 1 were discriminated from non-binders by treatment with H2S gas to form the reduction product Bi2S3, clearly visible to the naked eye. Interactions were further confirmed by NMR experiments. Extension of a binding peptide with a maleimide linker (Mal) introduces the possibility to covalently attach thiol-bearing moieties such as biological probes and for their analysis the presence of the cluster instead of mononuclear entities should lead to an increase of signal intensities in LA-ICP-MS measurements. To prove this, CBS-Mal was covalently bound onto thiol-presenting glass substrates, which then captured 1 effectively, so that LA-ICP-MS measurements demonstrated drastic signal amplification compared to single lanthanide tags.
Hepcidin-25 concentrations measured by various methods differ considerably, complicating interpretation. Here, a previously identified plasma-based candidate secondary reference material (csRM) was modified into a serum-based two-leveled sRM. We validated its functionality to increase the equivalence between methods for international standardization. We applied technical procedures developed by the International Consortium for Harmonization of Clinical Laboratory Results. The sRM, consisting of lyophilized serum with cryolyoprotectant, appeared commutable among nine different measurement procedures using 16 native human serum samples in a first round robin (RR1). Harmonization potential of the sRM was simulated in RR1 and evaluated in practice in RR2 among 11 measurement procedures using three native human plasma samples. Comprehensive purity analysis of a candidate primary RM (cpRM) was performed by state-of-the-art procedures. The sRM was value assigned with an isotope dilution mass spectrometry-based candidate reference method calibrated using the certified pRM. The inter-assay CV without harmonization was 42.1% and 52.8% in RR1 and RR2, respectively. In RR1, simulation of harmonization with sRM resulted in an inter-assay CV of 11.0%, whereas in RR2 calibration with the material resulted in an inter-assay CV of 19.1%. Both the sRM and pRM passed international homogeneity criteria and showed long-term stability. We assigned values to the low (0.95 ± 0.11 nmol/L) and middle concentration (3.75 ± 0.17 nmol/L) calibrators of the sRM. Standardization of hepcidin is possible with our sRM, which value is assigned by a pRM. We propose the implementation of this material as an international calibrator for hepcidin-25.
Mass spectrometry-based methods play a crucial role in the quantification of the main iron metabolism regulator hepcidin by singling out the bioactive 25-residue peptide from the other naturally occurring N-truncated isoforms (hepcidin-20, -22, -24), which seem to be inactive in iron homeostasis. However, several difficulties arise in the MS analysis of hepcidin due to the sticky character of the peptide and the lack of suitable standards. Here, we propose the use of amino- and fluoro-silanized autosampler vials to reduce hepcidin interaction to laboratory glassware surfaces after testing several types of vials for the preparation of stock solutions and serum samples for isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS). Furthermore, we have investigated two sample preparation strategies and two chromatographic separation conditions with the aim of developing an LC-MS/MS method for the sensitive and reliable quantification of hepcidin-25 in serum samples. A chromatographic separation based on usual acidic mobile phases was compared with a novel approach involving the separation of hepcidin-25 with solvents at high pH containing 0.1% of ammonia. Both methods were applied to clinical samples in an intra-laboratory comparison of two LC-MS/MS methods using the same hepcidin-25 calibrators with good correlation of the results. Finally, we recommend an LC-MS/MS-based quantification method with a dynamic range of 0.5–40 μg/L for the assessment of hepcidin-25 in human serum that uses TFA-based mobile phases and silanized glass vials.
This study aimed to assess the measurement capabilities of participating National Metrology Institutes/ Designated Institutes (NMIs/DIs) and expert laboratories in determining of low-polarity organics in surface water. This comparison was organized by Government Laboratory, Hong Kong (GLHK).
At the CCQM Organic Analysis Working Group (OAWG) Meeting held in November 2012 in Hong Kong, GLHK initially proposed a CCQM key comparison and a parallel pilot study programme on pharmaceuticals in surface water. Further discussion at the CCQM Meeting held in April 2014 in Paris, the OAWG approved a CCQM Track C comparison (CCQM-K126) on low polarity pharmaceuticals in surface water. In the meeting, the programme was supported by more than six National Metrology Institutes/ Designated Institutes (NMIs/ DIs).
CCQM-K126 officially commenced in July 2014 and had registration from nine NMIs/DIs. Participants were provided two bottles (40 mL each) of surface water and were requested to determine the mass fraction of spiked carbamazepinein in surface water. The coordinator received nine sets of results from eight NMIs/DIs in February 2015. Apart from one using an immunoassay technique, all participants applied isotope dilution liquid chromatography-tandem mass spectrometry (ID-LCMS/MS) technique as their determination technique.
2-Amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) and ethylene-diaminetetraacetic acid (EDTA) are key components of biological buffers and are frequently used as DNA stabilizers in irradiation studies. Such surface or liquid phase studies are done with the aim to understand the fundamental mechanisms of DNA radiation damage and to improve cancer radiotherapy. When ionizing radiation is used, abundant secondary electrons are formed during the irradiation process, which are able to attach to the molecular compounds present on the surface. In the present study we experimentally investigate low energy electron attachment to TRIS and methyliminodiacetic acid (MIDA), an analogue of EDTA, supported by quantum chemical calculations. The most prominent dissociation channel for TRIS is through hydroperoxyl radical formation, whereas the dissociation of MIDA results in the formation of formic and acetic acid. These compounds are well-known to cause DNA modifications, like strand breaks. The present results indicate that buffer compounds may not have an exclusive protecting effect on DNA as suggested previously.
Mass spectrometry is applied as a tool for the elucidation of molecular structures. This premises that gas-phase structures reflect the original geometry of the analytes, while it requires a thorough understanding and investigation of the forces controlling and affecting the gas-phase structures. However, only little is known about conformational changes of oligonucleotides in the gas phase. In this study, a series of multiply charged DNA oligonucleotides (n¼15–40) has been subjected to a comprehensive tandem mass spectrometric study to unravel transitions between different ionic gas-phase structures. The nucleobase sequence and the chain length were varied to gain insights into their influence on the geometrical oligonucleotide organization. Altogether, 23 oligonucleotides were analyzed using collision-induced fragmentation. All sequences showed comparable correlation regarding the characteristic collision energy. This value that is also a measure for stability, strongly correlates with the net charge density of the precursor ions. With decreasing charge of the oligonucleotides, an increase in the fragmentation energy was observed. At a distinct charge density, a deviation from linearity was observed for all studied species, indicating a structural reorganization. To corroborate the proposed geometrical change, collisional cross-sections of the oligonucleotides at different charge states were determined using ion mobility-mass spectrometry. The results clearly indicate that an increase in charge density and thus Coulomb repulsion results in the transition from a folded, compact form to elongated structures of the precursor ions. Our data show this structural transition to depend mainly on the charge density, whereas sequence and size do not have an influence.
Unprecedented Ionization Processes in Mass SpectrometryProvide Missing Link between ESI and MALDI
(2018)
In the field of mass spectrometry,producing intact, highly-charged protein ions from surfaces is a conundrum with significant potential payoff in application areas ranging from bio-medical to clinical research. Here, we report on the ability to form intact, highly-charged protein ions on high vacuum time-of-flight mass spectrometers in the linear and reflectron modes achievable using experimental conditions that allow effective matrix removal from both the sample surfaces and from the charged clusters formed by the laser Ablation event. The charge states are the highest reported on high vacuum mass spectrometers, yet they remain at only around athird of the highest charge obtained using laser ablation with a suitable matrix at atmospheric pressure. Other than physical instrument modifications, the key to forming abundant and stable highly-charged ions appears to be the volatility of the matrix used. Cumulative results suggest mechanistic links between the ionization process reported here and traditional ionization methods of electrospray ionization and matrix-assisted laser desorp-tion/ionization.
An immunohistochemical method is described to visualize the distribution of metallothioneins 1/2 (MT 1/2) and metallothionein 3 (MT 3) in human ocular tissue. It is making use of (a) antibodies conjugated to gold nanoclusters (AuNCs) acting as labels, and (b) laser ablation (LA) coupled to inductively coupled plasma – mass spectrometry (ICP-MS).Water-soluble fluorescent AuNCs (with an average size of 2.7 nm) were synthesized and then conjugated to antibody by carbodiimide coupling. The surface of the modified AuNCs was then blocked with hydroxylamine to avoid nonspecific interactions with biological tissue. Immunoassays for MT 1/2 and MT 3 in ocular tissue sections (5 μm thick) from two post mortem human donors were performed. Imaging studies were then performed by fluorescence using confocal microscopy, and LA-ICP-MS was performed in the retina to measure the signal for gold. Signal amplification by the >500 gold atoms in each nanocluster allowed the antigens (MT 1/2 and MT 3) to be imaged by LA-ICP-MS using a laser spot size as small as 4 μm. The image patterns found in retina are in good agreement with those obtained by conventional fluorescence immunohistochemistry which was used as an established reference method.
8-Bromoadenine (8BrA) is a potential DNA radiosensitizer for cancer radiation therapy due to its efficient interaction with low-energy electrons (LEEs). LEEs are a short-living species generated during the radiation damage of DNA by high-energy radiation as it is applied in cancer radiation therapy. Electron attachment to 8BrA in the gas phase results in a stable parent anion below 3 eV electron energy in addition to fragmentation products formed by resonant exocyclic bond cleavages. Density functional theory (DFT) calculations of the 8BrA– anion reveal an exotic bond between the bromine and the C8 atom with a bond length of 2.6 Å, where the majority of the charge is located on bromine and the spin is mainly located on the C8 atom. The detailed understanding of such long-lived anionic states of nucleobase analogues supports the rational development of new therapeutic agents, in which the enhancement of dissociative electron transfer to the DNA backbone is critical to induce DNA strand breaks in cancerous tissue.
Amphibians are undergoing a global decline. One poorly investigated reason could be the pollution of aquatic habitats by endocrine disrupting compounds (EDCs). We tested the susceptibility to the synthetically stabilized estrogen 17α-ethinylestradiol (EE2) in three deeply diverged anuran species, differing in sex determination systems, types of gonadogenesis and larval ecologies. To understand whether data from the amphibian model Xenopus laevis (Pipidae) are analogous and applicable to only distantly related non-model amphibians, tadpoles of X. laevis, Hyla arborea (Hylidae) and Bufo viridis (Bufonidae) were simultaneously exposed to 50, 500 and 5000 ng/L EE2 from hatching until completion of metamorphosis, using a flow-through-system under identical experimental conditions. Comparing molecularly established genetic with histologically assessed phenotypic sex in all species, we have recently shown that EE2 provoked numerous genetic-male-to-phenotypic-female sex reversals and mixed sex individuals, confirming overall its expected feminizing effect. In the present study, we focus on the influence of EE2 on gonadal and somatic development. Anatomy and histology revealed several species-specific effects. In both non-model species, H. arborea and B. viridis, high numbers of anatomically impaired gonads were observed. In H. arborea, exposed to 5000 ng/L EE2, numerous underdeveloped gonads were detected. Whereas EE2 did not alter snout-to-vent length and body weight of X. laevis metamorphs, H. arborea showed a treatment-dependent decrease, while B. viridis exhibited an increase in body weight and snout-to-vent length. Apart from a concentration-dependent occurrence of yellowish skin color in several H. arborea, no organ-specific effects were detected. Since EE2 ubiquitously occurs in many aquatic ecosystems and affects sexual and somatic development, among EDCs, it may indeed contribute to amphibian decline. The inter-species variation in developmental EE2-effects corroborates species-specific vulnerability differences towards EDCs between deeply diverged amphibian groups
Multiple anthropogenic stressors cause worldwide amphibian declines. Among several poorly investigated causes is global pollution of aquatic ecosystems with endocrine disrupting compounds (EDCs). These substances interfere with the endocrine system and can affect the sexual development of vertebrates including amphibians. We test the susceptibility to an environmentally relevant contraceptive, the artificial estrogen 17α-ethinylestradiol (EE2), simultaneously in three deeply divergent systematic anuran families, a model-species, Xenopus laevis (Pipidae), and two non-models, Hyla arborea (Hylidae) and Bufo viridis (Bufonidae). Our new approach combines synchronized tadpole exposure to three EE2-concentrations (50, 500, 5,000 ng/L) in a flow-through-system and pioneers genetic and histological sexing of metamorphs in non-model anurans for EDC-studies. This novel methodology reveals striking quantitative differences in genetic-male-to-phenotypic-female sex reversal in non-model vs. model species. Our findings qualify molecular sexing in EDC-analyses as requirement to identify sex reversals and state-of-the-art approaches as mandatory to detect speciesspecific vulnerabilities to EDCs in amphibians.
Real Time Imaging of Deuterium in a Duplex Stainless Steel Microstructure by Time-of-Flight SIMS
(2016)
For more than one century, hydrogen assisted degradation of metallic microstructures has been identified as origin for severe technical component failures but the mechanisms behind have not yet been completely understood so far. Any in-situ observation of hydrogen transport phenomena in microstructures will provide more details for further elucidation of these degradation mechanisms. A novel experiment is presented which is designed to elucidate the permeation behaviour of deuterium in a microstructure of duplex stainless steel (DSS). A hydrogen permeation cell within a TOF-SIMS instrument enables electrochemical charging with deuterium through the inner surface of the cell made from DSS. The outer surface of the DSS permeation cell exposed to the vacuum has been imaged by TOF-SIMS vs. increasing time of charging with subsequent chemometric treatment of image data. This in-situ experiment showed evidently that deuterium is permeating much faster through the ferrite phase than through the austenite phase. Moreover, a direct proof for deuterium enrichment at the austenite-ferrite interface has been found.
Mycotoxins are among the most abundant contaminants in food and feed worldwide. Therefore, in the EU maximum levels are established, e.g. for the frequently occurring Fusarium toxins deoxynivalenol (DON) and zearalenone (ZEA). Additional to DON and ZEA, modified mycotoxins are present in naturally contaminated grain products contributing significantly to the exposure of humans and animals with mycotoxins. Up to now data on the spatial distribution of many (masked) mycotoxins in the kernels of wheat are missing. The aim of the present study was to investigate the amounts of DON and ZEA as well as their most abundant derivatives DON-3-glucoside (DON-3G), 3- and 15-acetyl-DON, ZEA-14- and 16-glucoside and ZEA-14-sulphate (ZEA-14S) in mill fractions of naturally contaminated wheat batches using HPLC-MS/MS. The investigated distribution pattern in ten milling fractions is comparable among the three investigated different wheat batches. Interestingly, DON and DON-3G were found to be present to similar amounts in all fractions. In bran, the levels were only slightly higher than in the endosperm. By contrast, for ZEA and ZEA-14S a significantly higher amount of toxin is located in the fibre-rich fractions. The relative mass proportion of DON-3G comprises for only between 2.9 and 11.2% of the free DON, while the relative mass proportion of ZEA-14S is estimated to even exceed the amount of free ZEA in certain fractions. Acetylated DON derivatives and ZEA-glucosides were only detected in low amounts. The experimental results show that a significant reduction of the ZEA and ZEA-14S level in wheat flour is feasible by applying milling technology strategies. However, the almost evenly distribution of DON and DON-3G in all fractions does not allow for the technological removal of relevant toxin amounts. Furthermore, the relative share of masked forms was higher for ZEA derivatives than for the DON conjugates in the investigated wheat lots.
Here, we study the metastable decay of 5'-d(TTGCTT) in the presence of 0–6 alkaline metal ions (Li+, Na+, K+, Rb+) and 0–3 alkaline earth metal ions (Mg2+ and Ca2+), which replace the corresponding number of protons in the oligonucleotide. We find that all ions studied here stabilize the oligonucleotide with respect to simple 3'-C–O backbone cleavage, but at the same time these metal ions promote a central oligonucleotide deletion accompanied by a concomitant recombination of the terminal d(TT) groups. We find that the quenching of the 3'-C–O backbone cleavage is not ion specific, since it is due to the removal of the phosphate protons upon replacement with the respective metal ions. The central nucleotide deletion competes with the 3'-C–O backbone cleavage channels and is thus promoted through the replacement of the exchangeable protons against metal ions. However, with increasing positive charge density of the metal ions the yield of the central nucleotide deletion further increases. We attribute this effect to the necessity of sufficient proximity of the terminal d(TT) group to allow for their recombination on this reaction path. Hence, the formation of a reactive conformer is mediated by the metal ions.
New-found interest in the development of ionization sources for mass spectrometry, inspired by the advent of ambient desorption/ionization mass spectrometry, has led to a resurgence in plasma-source development and characterization. Dielectric-barrier discharges, particularly the low-temperature plasma (LTP) probe format, have been at the forefront of this field due to their low power consumption and relatively simple design. However, better fundamental understanding of this desorption/ionization source is needed to improve the analytical capabilities of such a device. Here, we use relatively fast (2.5 ms per spectrum) time-resolved mass spectrometry to characterize the temporal reagent-ion distribution from a low-frequency LTP probe. Different voltage waveforms were found to heavily influence the discharge properties and, consequently, ion production. Ion signals from short discharge pulses, ca. 40 µs, were found to be significantly broadened, ca. 10 ms, prior to extraction into the mass spectrometer. Additionally, higher frequencies of a sine-wave LTP produced the largest flux of reagent ions, which existed for most of the voltage waveforms. Finally, temporal signals for reagent and analyte ions were measured and related to specific ionization processes: proton transfer and charge transfer.
A commercially available airbrush gun as a new source for spray ionization is presented. It is best operated employing moderate stagnation pressures, resulting in a sonic gas flow. A mass spectrometric investigation on the amino acid lysine and several peptides reveals that this inexpensive approach results in reproducible mass spectra. The ion patterns strongly resemble the results from other studies obtained with custom made sonic spray vaporizers. The patterns as well resemble the mass spectra recorded with electrospray devices. For a better understanding of the vaporization process, the mass spectrometry experiments are accompanied by laser induced fluorescence experiments. Inverse Abel transform of the obtained fluorescence maps allows the determination of the full 3D distribution of the spray cone. Furthermore, via exploitation of the solvatochromism of the used dye the solvation state distribution can be visualized. In addition, expansion parameters like droplet size and velocity are obtained by laser stroboscopy. The experiments demonstrate that the analyte is hardly desolvated throughout the expansion. This indicates a subsequent vaporization of the residual solvent in the intermediate pressure region of the mass spectrometer.
Assessment of international reference materials for isotope-ratio analysis (IUPAC Technical report)
(2014)
A detailed characterization of metal-tagged antibodies is the prerequisite for the implementation of quantitative concepts in inductively coupled plasma–mass spectrometry (ICP-MS)-based bioanalysis or future medical diagnosis. In this paper, the common modification with bifunctional ligands containing maleimide residues as a reactive group was investigated in detail via size exclusion chromatography (SEC)-ICP-MS and liquid chromatography–time-of-flight (LC-TOF)-MS to determine the preservation of the antibody structure after tagging. Mouse monoclonal IgG modified with metal-coded tags (MeCATs) was used as a model system. Several antibody fragments were identified carrying different numbers of metal tags. In a second step, a functionality test was performed with isolated fragments where the antigen specificity was tested in a dot blot immunoassay.
Biotin is an essential vitamin that is, on the one hand, relevant for the metabolism, gene expression and in the cellular response to DNA damage and, on the other hand, finds numerous applications in biotechnology. The functionality of biotin is due to two particular sub-structures, the ring structure and the side chain with carboxyl group. The heterocyclic ring structure results in the capability of biotin to form strong intermolecular hydrogen and van der Waals bonds with proteins such as streptavidin, whereas the carboxyl group can be employed to covalently bind biotin to other complex molecules. Dissociative electron attachment (DEA) to biotin results in a decomposition of the ring structure and the carboxyl group, respectively, within resonant features in the energy range 012 eV, thereby preventing the capability of biotin for intermolecular binding and covalent coupling to other molecules. Specifically, the fragment anions (M–H)-, (M–O)-, C3N2O-, CH2O2-, OCN-, CN-, OH- and O- are observed, and exemplarily the DEA cross section of OCN- formation is determined to be 3 × 10-19 cm². To study the response of biotin to electrons within a complex condensed environment, we use the DNA origami technique and determine a dissociation yield of (1.1 ± 0.2) × 10-14 cm² at 18 eV electron energy, which represents the most relevant energy for biomolecular damage induced by secondary electrons. The present results thus have important implications for the use of biotin as a label in radiation experiments.
The development of a facile covalent strategy for the fabrication of organic conducting polymers (OCPs)/carbon nanotubes (CNTs) based molecular hybrid materials remains a challenge and is expected to address the detrimental intrinsic bundling issue of CNTs. In view of the pristine CNTs' ability to undergo Diels–Alder reactions with dienes, we report the synthesis of a novel poly(3-hexylthiophene) (P3HT) based organic conducting polymer (OCP) with terminal cyclopentadienyl (Cp) groups. The synthetic strategy employed is based on a combination of in situ end group functionalization via Grignard metathesis (GRIM) polymerization and a subsequent end group switching via reaction with nickelocene. Characterization data from Matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDITOF MS) fully support the successful synthesis of monofunctional Cp-capped P3HT, which was found to be highly reactive toward dienophile end-capped polystyrene (PS). The Cp-capped P3HT was subsequently ligated to the surface of pristine single walled CNTs (SWCNTs). The resulting P3HT/SWCNTs molecular hybrid material was characterized using thermogravimetric analysis (TGA), elemental analysis (EA), X-ray photoelectron spectroscopy (XPS), and high resolution transmission electron microscopy (HRTEM). The data from TGA, EA, and XPS were used to quantitatively deduce the grafting density. P3HT/SWCNTs prepared with Cp capped P3HT was found to contain 2 times more P3HT than the reference sample, featuring a grafting density of 0.0510 chains·nm–2 and a periodicity of 1 P3HT chain per 748 carbon atoms of the SWCNTs. HRTEM revealed individual SWCNTs wrapped with P3HT whereas in the reference sample P3HT was adsorbed on the bundles of the SWCNTs. The results presented here provide a new avenue for designing novel materials based on CNTs and OCPs.
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 pgmL-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 %.
Isotope reference materials are needed to calibrate and validate analytical procedures used for the determination of isotope amount ratios, procedurally defined isotope ratios or so-called δ values. In contrast to the huge analytical progress in isotope ratio analytics, the production of isotope reference materials has not kept pace with the increasing needs of isotope analysts. Three representative isotope systems are used to explain the technical and non-technical difficulties and drawbacks, on one hand, and to demonstrate what can be achieved at its best, on the other hand. A clear statement is given that new isotope reference materials are needed to obtain traceable and thus comparable data, which is essential for all kinds of isotope research. The range of available isotope reference materials and δ reference materials should be increased and matrix reference materials certified for isotope compositions or δ values, which do not exist yet, should be provided.
The nature and concentrations of volatile organic compounds (VOCs) in chars generated by hydrothermal carbonization (HTC) is of concern considering their application as soil amendment. Therefore, the presence of VOCs in solid HTC products obtained from wheat straw, biogas digestate and four woody materials was investigated using headspace gas chromatography. A variety of potentially harmful benzenic, phenolic and furanic volatiles along with various aldehydes and ketones were identified in feedstock- and temperature-specific patterns. The total amount of VOCs observed after equilibration between headspace and char samples produced at 270 °C ranged between 2000 and 16,000 µg/g (0.2–1.6 wt.%). Depending on feedstock 50–9000 µg/g of benzenes and 300–1800 µg/g of phenols were observed. Substances potentially harmful to soil ecology such as benzofurans (200–800 µg/g) and p-cymene (up to 6000 µg/g in pine wood char) exhibited concentrations that suggest restrained application of fresh hydrochar as soil amendment or for water purification.
The derivatization of organoarsenic compounds by different reagents like thioglycolates or dithiols and the subsequent analysis by GC–MS as a molecular specific technique was investigated and described. The possible derivatization reagents methyl- and ethylthioglycolate (TGM and TGE), 1,3-propane- and 1,5-pentanedithiol (PDT and PeDT), which transfer the polar and nonvolatile analytes dimethylarsenate (DMA), monomethylarsonate (MMA), arsenite and arsenate into volatile compounds, were evaluated. The application for real samples like fish material was also studied.
In addition the gas chromatographic separation and resolution was optimized and experiments were carried out to determine the highest derivatization rates. Derivatization reagents were evaluated in terms of quantity and stability of the formed chemical species.
All derivatization products were characterized by mass spectrometry in order to identify the separated arsenic species.
The most efficient conversion of DMA and MMA was observed by using ethylthioglycolate as derivatization agent. Finally, the derivatization procedure and the GC–MS-method were validated to determine linearity, precision, selectivity, analytical limiting values and recoveries. For the proposed method a limit of detection (LOD) of 5.8 pg for DMA and 14.0 pg for MMA was found. The accuracy was established by comparing the mean value measured for DMA in the certified reference material BCR-627 (tuna fish) with the certified one.
MMA was not quantified in marine samples due to its low content. In shrimp samples DMA was not detectable. For codfish a DMA-content of 0.20±0.004 mg kg-1, for 'Surströmming' an amount of 0.38±0.02 mg kg-1 and for herring, which showed the highest amount of DMA, a content of 1.15±0.03 mg kg-1 was determined.
Commercially available linear alkylbenzenesulfonates (LASs) are a mixture of various homologues and isomers, leading to 20 major species. In this work we investigated the commercial product by liquid chromatography-solid phase extraction-nuclear magnetic resonance spectroscopy-mass spectrometry (LC-SPE-NMR/MS). The commercial product was separated into 17 fractions by liquid chromatography (LC). After chromatographic separation, 5% of the flow was split to a mass spectrometer (MS) while 95% was send to post-column solid phase extraction cartridges for enrichment of the analytes (LC-SPE). After elution from the SPE-cartridges a NMR-spectrometer equipped with a cryo-probe was used for the characterisation of the different LASs species. For the first time H-1-1D and H-H-COSY spectra for 14 LASs species out of 20 major isomers are presented, whereas the 6 remaining species are detected as mixtures in 3 H-1-1D and H-H-COSY spectra. These data were used to correlate the chromatographic retention of the LASs isomers to the substitution pattern of the alkyl chain.
Besides protein identification via mass spectrometric methods, protein and peptide quantification has become more and more important in order to tackle biological questions. Methods like differential gel electrophoresis or enzyme-linked immunosorbent assays have been used to assess protein concentrations, while stable isotope labeling methods are also well established in quantitative proteomics. Recently, we developed metalcoded affinity tagging (MeCAT) as an alternative for accurate and sensitive quantification of peptides and
proteins. In addition to absolute quantification via inductively coupled plasma mass spectrometry, MeCAT also enables sequence analysis via electrospray ionization tandem mass spectrometry. In the current study, we developed a new labeling approach utilizing an iodoacetamide MeCAT reagent (MeCAT-IA). The MeCAT-IA approach shows distinct advantages over the previously used MeCAT with maleinimide reactivity such as higher labelling efficiency and the lack of diastereomer formation during labeling. Here, we present a careful characterization of this new method focusing on the labeling process, which yields complete tagging with an excess of reagent of 1.6 to 1, less complex chromatographic behavior, and fragmentation characteristics of the tagged peptides using the iodoacetamide MeCAT reagent.
Two decades after the introduction of matrix assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI), soft ionization mass spectrometry represents a powerful toolset for the structural investigation of synthetic polymers. The present review highlights the current state-of-the-art, covering the latest developments of novel techniques, enabling instrumentation as well as the important applications of soft ionization MS from the beginning of 2008. Special attention is paid to the role that soft ionization MS has played in the mechanistic investigation of radical polymerization processes since 2005.
The strontium isotope composition of food samples has been successfully used to trace the provenance of both herbal and animal agricultural products. Adequately accurate and precise 87Sr/86Sr ratios, however, are key to unravel environmental and anthropogenic strontium contributions of specific growing areas. In a recently published analytical method in Food Chemistry by Choi et al. (2008) a demonstrably inadequate protocol for the determination of 87Sr/86Sr ratios of ginseng is presented. Based on well established geological and analytical fundamentals the 87Sr/86Sr ratios presented by Choi et al. (2008) are too inaccurate and imprecise to be used to trace the origin of the ginseng. Appropriate wet chemical separation techniques and mass spectrometric instrumentation enables the generation of 87Sr/86Sr data with very low expanded uncertainties (<0.05%, k = 2). Those high quality data allow the identification of even small strontium contributions of source reservoirs or physical and anthropogenic processes if diagnostic isotope compositions are present.
Open cell rigid foams made from polyurethane (PU) are frequently used in ceramic processing for preparation of porous ceramics by the so-called replica technique. This work presents data regarding the PU burnout, shrinkage characteristics as well as the morphology of the ceramic coated PU sponges during heating up. Shrinkage of the ceramic coated PU sponges closely follows the mass loss due to PU decomposition. Two temperatures (i) 267 °C and (ii) 380 °C were identified at which PU decomposition reaches local maxima. Shrinkage measurements on ceramic coated PU sponges reveal that both PU decomposition stages lead to similar extends of shrinkage in the ceramic coated PU sponge. Differential thermal analysis (DTA) showed that the two decomposition related temperatures (267 and 380 °C) differ concerning the energy release. While the low-temperature signal is endothermic, an exothermic signal was detected at 380 °C. The morphology of the ceramic coated PU sponges was investigated with scanning electron microscopy (SEM) which gave insight into the formation of hollow ceramic struts-a well known feature of ceramics being prepared by the replica technique.
A method for the determination of the novel brominated flame retardant tetrabromobisphenol A bis(2,3-dibromopropylether), 1,1'-(isopropylidene)bis[3,5-dibromo-4-(2,3-dibromo-propoxy)-benzene] (TBBPA-dbpe), was developed. Technical TBBPA-dbpe was purified and the results of a thorough physical characterisation are reported. The application of APCI-MS is discussed and the fragmentation patterns are described. Quantification of TBBPA-dbpe was done by HPLC-DAD using external calibration. The validation of the method was accomplished using sediment and sewage sludge samples spiked with defined amounts of authentic TBBPA-dbpe. The average recovery rates of TBBPA-dbpe from spiked samples ranged from 35 to 91% (sediment) and from 57 to 98% (sewage sludge) depending on the respective extraction method. Pressurised fluid extraction (PFE) and fluidised bed extraction were superior to classical Soxhlet and sonication procedures and yielded recovery rates between 90 and 98% with relative standard deviations of 2%. The limits of detection (DTC), identification (ID) and determination (DTM) using HPLC-DAD were 10, 21 and 30 ng g-1 in sediment and 22, 44 and 72 ng g-1 in sewage sludge, respectively.
Two synthetic isotope mixtures for the calibration of sulfur isotope amount ratio measurements were gravimetrically prepared from high purity Ag2S materials enriched in 32S, 33S, and 34S. The mixtures were made so as to closely resemble the (natural) isotopic composition of the materials to be calibrated. This allowed a totally independent evaluation, on the same samples, of the relative combined uncertainty of: (a) the procedure to perform direct measurements of the amount of substance ratios of gas isotopes in the redetermination of the Avogadro constant and (b) the gravimetric preparation procedure. The result of both procedures, mass spectrometry and gravimetry, agree to a relative uncertainty of 3 × 10-4 for sulfur amount ratio measurements of the major abundant isotopes. Thus it seems that a direct measurement of isotopic gas mixtures (e.g. of natural isotopic composition) is now possible for sulfurand probably also for other gaseous isotopeswithout necessarily having to rely on calibration by means of values provided by measurements of gravimetrically prepared isotope mixtures. However, synthetic mixtures may be needed for validation and verification purposes, in particular for quality assurance.