TY - JOUR A1 - Ribar, A. A1 - Huber, S. E. A1 - Smiałek, M. A. A1 - Tanzer, K. A1 - Neustetter, M. A1 - Schürmann, Robin A1 - Bald, Ilko A1 - Denifl, S. T1 - Hydroperoxyl radical and formic acid formation from common DNA stabilizers upon low energy electron attachment N2 - 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. KW - DEA KW - DNA KW - Low energy electrons KW - Mass spectrometry PY - 2018 UR - http://pubs.rsc.org/en/content/articlepdf/2018/cp/c7cp07697e DO - https://doi.org/10.1039/c7cp07697e VL - 20 IS - 8 SP - 5578 EP - 5585 PB - Royal Society of Chemistry AN - OPUS4-44703 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Abbas, Ioana M. A1 - Hoffmann, Holger A1 - Montes-Bayón, M. A1 - Weller, Michael G. T1 - Improved LC-MS/MS method for the quantification of hepcidin-25 in clinical samples N2 - 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. KW - HPLC KW - Liquid chromatography KW - Mass spectrometry KW - Silanization KW - Mobile phase KW - Adsorption KW - Peptide losses KW - Recovery KW - Validation KW - Quality control KW - QC KW - Iron disorders KW - Chronic kidney disease KW - Metrology KW - Round robin exercise KW - Basic solvent KW - Peptide analysis PY - 2018 DO - https://doi.org/10.1007/s00216-018-1056-0 SN - 1618-2642 SN - 1618-2650 VL - 410 IS - 16 SP - 3835 EP - 3846 PB - Springer Nature CY - Heidelberg AN - OPUS4-45053 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Schwaar, Timm A1 - Lettow, Maike A1 - Remmler, Dario A1 - Börner, H. G. A1 - Weller, Michael G. T1 - Efficient Screening of Combinatorial Peptide Libraries by Spatially Ordered Beads Immobilized on Conventional Glass Slides N2 - 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. KW - Peptide library KW - HTS KW - Target KW - MALDI KW - Mass spectrometry KW - Biochip KW - Lab-on-a-Chip KW - Array KW - Screening KW - Ladder sequencing KW - Binder KW - Pharmaceutical PY - 2019 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-478973 UR - https://www.mdpi.com/2571-5135/8/2/11 DO - https://doi.org/10.3390/ht8020011 VL - 8 IS - 2 SP - 1 EP - 15 PB - MDPI CY - Basel AN - OPUS4-47897 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Cruz-Alonso, M. A1 - Fernandez, B. A1 - Álvarez, L. A1 - González-Iglesias, H. A1 - Traub, Heike A1 - Jakubowski, Norbert A1 - Pereiro, R. T1 - Bioimaging of metallothioneins in ocular tissue sections by laser ablation-ICP-MS using bioconjugated gold nanoclusters as specific tags N2 - 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. KW - Metal nanoclusters KW - Fluorescence KW - Protein imaging KW - Thin tissue sections KW - Immunohistochemistry KW - Bioconjugation KW - Carbodiimide crosslinking KW - Laser ablation KW - Mass spectrometry PY - 2018 DO - https://doi.org/10.1007/s00604-017-2597-1 VL - 185 IS - 1 SP - 1 EP - 9 PB - Springer AN - OPUS4-44022 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ickert, Stefanie A1 - Beck, S. A1 - Linscheid, M. A1 - Riedel, Jens T1 - VUV Photodissociation Induced by a Deuterium Lamp in an Ion Trap N2 - 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. KW - Fragmentation activation KW - Vacuum ultraviolet (VUV) light KW - Mass spectrometry KW - Tandem MS PY - 2019 DO - https://doi.org/10.1007/s13361-019-02282-8 SN - 1044-0305 VL - 30 IS - 10 SP - 2114 EP - 2122 PB - Springer Nature CY - Heidelberg AN - OPUS4-48756 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Jaeger, Carsten T1 - Improving Small Molecule Annotation In Nontargeted Soft Ionization GC/LC High Resolution Mass Spectrometry N2 - High-resolution mass spectrometry, either combined with gas or liquid chromatography (GC/LC-HR-MS), is currently the most powerful analytical option for broad nontargeted small molecule analysis. To transform HR-MS raw data from metabolomics or environmental studies into chemically meaningful data, several computational steps are needed, including peak detection, deconvolution of these peaks into compounds and putative identification of compounds using databases. Each of these steps can cause problems and still requires methodological advancements. Computational compound annotation as one of the steps, however, has proven particularly challenging, mainly due to the chemical diversity of organic analytes. In addition, different annotation approaches are needed for the different platforms used in HR-MS screening. We recently introduced InterpretMSSpectrum as an annotation workflow for GC-HR-MS using atmospheric pressure chemical ionization (APCI). InterpretMSSpectrum locates molecular ion, fragment and adduct peaks, calculates their most likely sum formula combination and graphically summarizes results as an annotated mass spectrum. As a complementary approach for LC-HR-MS, we presented findMAIN, which scores MS1 spectra based on explained intensity, mass accuracy and isotope charge agreement of adducts and related electrospray ionization (ESI) products to determine the neutral mass of unknown compounds. Both approaches were validated against large spectral libraries containing more than 600 compounds, for which correct annotation was achieved in over 80% of the cases. Based on the experiences from this validation, we here compare soft-ionization GC/LC-HR-MS regarding “annotatability” of unknown compounds from a computational perspective. As a main advantage for GC-HR-MS, the relatively uniform ionization behavior of commonly used trimethylsilyl (TMS) derivatives observed under APCI allowed differentiation of molecular ion peaks from in-source fragments based on relatively compact set of rules. By contrast, neutral mass inference in ESI required a more complex evaluation scheme, due to the higher diversity of ionization products observable in ESI. We demonstrate such differences by practical examples of both software packages applied to metabolomics studies and discuss the challenges connected to transferring the approaches to environmental screening. T2 - ACS Fall Meeting 2019 CY - San Diego, CA, USA DA - 25.09.2019 KW - Compound annotation KW - Mass spectrometry KW - Electrospray ionization KW - Nontarget analysis KW - Accurate mass PY - 2019 AN - OPUS4-49200 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Kuhring, M. A1 - Doellinger, J. A1 - Nitsche, A. A1 - Muth, Thilo A1 - Renard, B. Y. T1 - TaxIt: An Iterative Computational Pipeline for Untargeted Strain-Level Identification Using MS/MS Spectra from Pathogenic Single-Organism Samples N2 - 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. KW - Bioinformatics KW - Mass spectrometry KW - Microbial proteomics KW - Strain identification KW - MS/MS PY - 2020 DO - https://doi.org/10.1021/acs.jproteome.9b00714 VL - 19 IS - 6 SP - 2501 EP - 2510 PB - ACS AN - OPUS4-50942 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Vogl, Jochen T1 - The triple-isotope calibration approach: a universal and standard-free calibration approach for obtaining absolute isotope ratios of multi-isotopic elements N2 - 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. KW - Triple isotope fractionation KW - Absolute isotope ratio KW - Mass spectrometry KW - Calibration KW - Uncertainty PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-516364 DO - https://doi.org/10.1007/s00216-020-03050-4 VL - 413 IS - 3 SP - 821 EP - 826 PB - Springer Verlag AN - OPUS4-51636 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Jaeger, Carsten T1 - Rapid characterization of ionization products for chemistry-aware compound annotation in nontargeted small molecule mass spectrometry N2 - Nontargeted high-resolution mass spectrometry (HRMS) is widely used for small molecule screening in biotic or abiotic samples. However, HRMS approaches like metabolomics or environmental nontarget screening currently still lack confidence in chemical annotation, i.e. computational structure assignment to all measured mass signals. As a crucial step within the annotation pipeline, molecular weight inference (MWI) deduces a compound’s intact mass from diagnostic mass differences between MS1 peaks, allowing precise database queries in subsequent steps. As the common practice of considering all possible ionization products such as adducts, multimers, multiple charges etc. in MWI suffers from high false positive rates, we aimed at selecting candidate ionization products in a chemically sensitive way. Generally, electrospray ionization produces different types of adducts depending on chromatographic system and sample matrix, necessitating application-specific optimization for optimum MWI performance. To avoid, however, the tedious and potentially biased manual data curation connected to optimization, we established an R-based workflow for automating this task. The workflow consists of two parts. Part 1 creates an MS1 spectral library by performing peak detection, spectral deconvolution and target peak assignment based on density estimation. Part 2 analyzes ion relationships within the library and returns a list of detected ionization products ranked by their frequency. We applied the workflow to a commercial 634-compound library that was acquired for two chromatographic methods (reverse phase, RP; hydrophilic liquid interaction chromatographic, HILIC) and the two ESI modes (positive, negative). As expected, different frequency distributions of ionization products were found for the two chromatographies. Interestingly, however, some of the differences were expected in terms of solvent chemistries (e.g. [M+NH4]+ in ammonium formate-buffered HILIC) while others indicated more complex ion competition (e.g. abundant [M+K]+, [M+2K-H]+ in HILIC). This demonstrated the relevance of this empirical approach. We further show that MWI accuracy clearly benefitted from derived optimized adduct lists – by adding filters or weighting terms – and present FDR calculations supporting this observation. We conclude that chemistry-aware compound annotation based on the combination of high-throughput library acquisition and statistical analysis holds significant potential for further improvements in nontargeted small molecule HRMS. T2 - ANAKON 2019 CY - Münster, Germany DA - 25.03.2019 KW - Compound annotation KW - Mass spectrometry KW - Electrospray ionization KW - Nontarget analysis KW - Accurate mass PY - 2019 AN - OPUS4-48332 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Lörchner, Dominique A1 - Dittmann, Daniel A1 - Braun, Ulrike A1 - Kroh, L. W. A1 - Köppen, Robert T1 - Investigation of two triazine-based heterocyclic brominated flame retardants by coupled thermogravimetry-Fourier transform infrared spectroscopy N2 - 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. KW - Pyrolysis KW - Thermal decomposition KW - TGA-FTIR KW - Mass spectrometry PY - 2019 DO - https://doi.org/10.1016/j.jaap.2019.104635 VL - 141 SP - 104635-1 EP - 104635-5 PB - Elsevier B.V. AN - OPUS4-48506 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -