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 - Vogl, Jochen T1 - Isotope Ratio Analysis N2 - Basic information on isotope ratio analysis is provided. Isotope fractionation is discussed and the measurement process is described. Additionally, practical examples are provided. T2 - Workshop & Training "Isotope Ratio Analysis" CY - Pathum Thani, Thailand DA - 06.12.2023 KW - Isotope fractionation KW - Mass spectrometry KW - Terminology PY - 2023 AN - OPUS4-59164 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - van Wasen, S. A1 - You, Yi A1 - Beck, S. A1 - Riedel, Jens A1 - Volmer, D. A. T1 - Miniaturized Protein Digestion Using Acoustic Levitation with Online High Resolution Mass Spectrometry N2 - 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. KW - Acoustic levitation KW - Protein analysis KW - Mass spectrometry PY - 2023 DO - https://doi.org/10.1021/acs.analchem.2c05334 VL - 95 SP - 4190 EP - 4195 PB - ACS Publications AN - OPUS4-57053 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Alcalde-Vasquez, R. A1 - Moreno-Pedraza, A. A1 - Rosas-Román, I. A1 - Guillén-Alonso, H. A1 - Riedel, Jens A1 - Partida-Martínez, L. P. A1 - Winkler, R. T1 - MoBiMS: A Modular Miniature Mass Analyzer for the Real-Time 2 Monitoring of Gases and Volatile Compounds in Biological Systems N2 - 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. KW - Mass spectrometry KW - Instrumentation KW - Miniaturization KW - Volatiles PY - 2022 DO - https://doi.org/10.1016/j.microc.2021.107090 SN - 0026-265X VL - 175 PB - Elsevier B.V. CY - Amsterdam AN - OPUS4-56528 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Flierl, Lukas A1 - Rienitz, Olaf A1 - Vogl, Jochen A1 - Pramann, Axel T1 - An advancement of the gravimetric isotope mixture method rendering the knowledge of the spike purity superfluous N2 - The gravimetric isotope mixture method is the primary method to determine absolute isotope ratios. This method, however, depends on the existence of suitable spike materials and knowledge of their purities. Determining the purity of the spikes can be tedious and labour-intensive. In this publication, an advancement of the gravimetric isotope mixture method, rendering the determination of the purity of the spike materials unnecessary, is presented. The advancement combines mass spectrometry and ion chromatography leading to an approach being independent of the purity of the spike materials. In the manuscript the mathematical background and the basic idea of the novel approach are described using a two-isotope system like copper or lithium. KW - Isotope amount ratios KW - Metrology KW - Mass spectrometry KW - Ion chromatography PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-608726 DO - https://doi.org/10.1007/s00216-024-05465-9 SP - 5325 EP - 5333 PB - Springer Science and Business Media LLC AN - OPUS4-60872 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Saeidfirozeh, H. A1 - Kubelík, P. A1 - Laitl, V. A1 - Krivkova, A. A1 - Vrabel, J. A1 - Rammelkamp, K. A1 - Schroder, S. A1 - Gornushkin, Igor B. A1 - Kepes, E. A1 - Zabka, J. A1 - Ferus, M. A1 - Porízka, P. A1 - Kaiser, J. T1 - Laser-induced breakdown spectroscopy in space applications: Review and prospects N2 - This review describes the principles and summarizes the challenges of analytical methods based on optical emission spectroscopy (OES) in space applications, with a particular focus on Laser-Induced Breakdown Spectroscopy (LIBS). Over the past decade, LIBS has emerged as a powerful analytical technique for space exploration and In-Situ Resource Utilization (ISRU) of celestial bodies. Its implementation has been suggested for various segments of the Space Resources Value Chain, including prospecting, mining, and beneficiation. Current missions to Mars, including the ChemCam instrument on the Curiosity rover, the SuperCam on the Perseverance rover, and the MarSCoDe on the Zhurong rover, are considered flagship applications of LIBS. Despite neither the Pragyan rover nor the Vikram lander waking from the lunar night, the success of the Chandrayaan-3 mission marks another milestone in the development of LIBS instruments, with further missions, including commercial ones, anticipated. This paper reviews the deployment of LIBS payloads on Mars rovers, upcoming missions prospecting the Moon and asteroids, and LIBS analysis of meteorites. Additionally, it highlights the importance of data processing specific to space applications, emphasizing recent trends in transfer learning. Furthermore, LIBS combined with other spectroscopic techniques (e.g., Raman Spectroscopy, Mass Spectrometry, and Fourier-Transform Infrared Spectroscopy) represents an intriguing platform with comprehensive analytical capabilities. The review concludes by emphasizing the significance of LIBS-based contributions in advancing our understanding of celestial bodies and paving the way for future space exploration endeavors KW - Laser-induced breakdown spectroscopy KW - Mars KW - Moon KW - Asteroids KW - Meteorites KW - Machine learning KW - Transfer learning KW - Raman spectroscopy KW - Mass spectrometry KW - Fourier-transform infrared spectroscopy PY - 2024 DO - https://doi.org/10.1016/j.trac.2024.117991 VL - 181 SP - 1 EP - 22 PB - Elsevier B.V. AN - OPUS4-62142 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Fricke, F. A1 - Mahmood, S. A1 - Hoffmann, J. A1 - Brandalero, M. A1 - Liehr, Sascha A1 - Kern, Simon A1 - Meyer, Klas A1 - Kowarik, S. A1 - Westerdick, S. A1 - Maiwald, Michael A1 - Hübner, M. T1 - Artificial Intelligence for Mass Spectrometry and Nuclear Magnetic Resonance Spectroscopy N2 - 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. T2 - 2021 Design, Automation & Test in Europe Conference & Exhibition (DATE) CY - Grenoble, France DA - 01.02.2021 KW - Industry 4.0, KW - Cyber-physical systems KW - Artificial neural networks KW - Mass spectrometry KW - Nuclear magnetic resonance spectroscopy PY - 2021 DO - https://doi.org/10.23919/DATE51398.2021.9473958 SP - 615 EP - 620 PB - IEEE AN - OPUS4-55360 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Winckelmann, Alexander T1 - Advantages of N2-MICAP-MS for Trace Metal Analysis in Steel N2 - The climate and energy crisis are extreme challenges. One possible solution could be hydrogen technology. Safety is a big concern. Steel used for pipelines and storage is under permanent stress from low temperatures and high pressures. The content of different alloyed metals determines the performance of the steel. Nitrogen microwave inductively coupled atmosphere pressure plasma mass spectrometry (N2-MICAP-MS) is a promising method for trace metal analysis in steel. Nitrogen is cheap and can be generated on site. It has fewer interferences than argon. Additionally, MICAP-MS is very matrix tolerant, proving the matrix-matched calibration expendable. Safety in technology and chemistry is the mission of BAM. Providing reference methods and materials can create trust in future technologies like hydrogen. T2 - SALSA Make and Measure 2022 CY - Berlin, Germany DA - 15.09.2022 KW - Trace analysis KW - Steel KW - Microwave plasma KW - Mass spectrometry KW - Safety PY - 2022 AN - OPUS4-55792 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Schneider, Rudolf A1 - Konthur, Zoltán A1 - Jaeger, Carsten T1 - Reference Material (IgG) for CCQM-PAWG Key Comparison N2 - BAM proposes a recombinant human IgG (anti-tetanus monoclonal antibody SA13) as candidate material for the 2027 CCQM-PAWG key comparison on antibody purity. The antibody is produced via hybridoma and recombinant expression systems, with detailed sequence and glycosylation profiling. Analytical methods include MALDI-TOF-MS, SEC, DLS, and UV-vis spectroscopy to assess purity, aggregation, and stability. Preliminary results show high purity, low heterogeneity, and consistent size distribution. A minimum of 40 mg IgG is required, with 100 mg preferred for deeper characterization. Production is expected to be completed by the end of 2026, with potential for a joint technical project. T2 - Spring Meeting of CCQM-PAWG CY - Sèvres, France DA - 06.04.2025 KW - Antibodies KW - Research Grade Test Material KW - Mass spectrometry KW - Affinity PY - 2025 AN - OPUS4-63503 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -