TY - JOUR A1 - Nowatzky, Yannek A1 - Russo, Francesco Friedrich A1 - Lisec, Jan A1 - Kister, Alexander A1 - Reinert, Knut A1 - Muth, Thilo A1 - Benner, Philipp T1 - FIORA: Local neighborhood-based prediction of compound mass spectra from single fragmentation events N2 - Non-targeted metabolomics holds great promise for advancing precision medicine and biomarker discovery. However, identifying compounds from tandem mass spectra remains a challenging task due to the incomplete nature of spectral reference libraries. Augmenting these libraries with simulated mass spectra can provide the necessary references to resolve unmatched spectra, but generating high-quality data is difficult. In this study, we present FIORA, an open-source graph neural network designed to simulate tandem mass spectra. Our main contribution lies in utilizing the molecular neighborhood of bonds to learn breaking patterns and derive fragment ion probabilities. FIORA not only surpasses state-of-the-art fragmentation algorithms, ICEBERG and CFM-ID, in prediction quality, but also facilitates the prediction of additional features, such as retention time and collision cross section. Utilizing GPU acceleration, FIORA enables rapid validation of putative compound annotations and large-scale expansion of spectral reference libraries with high-quality predictions. KW - Metabolomics KW - Machine Learning KW - Mass spectrometry KW - Bioinformatics PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-627585 DO - https://doi.org/10.1038/s41467-025-57422-4 SN - 2041-1723 VL - 16 IS - 1 SP - 1 EP - 17 PB - Springer Science and Business Media LLC AN - OPUS4-62758 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Epping, Ruben A1 - Bliesener, Lilly A1 - Weiss, Tilman A1 - Koch, Matthias T1 - Marker Substances in the Aroma of Truffles N2 - 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. KW - Truffle KW - Volatile organic compounds; KW - Gas chromatography KW - Mass spectrometry KW - Canine olfactometry PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-556116 DO - https://doi.org/10.3390/molecules27165169 SN - 1420-3049 VL - 27 IS - 16 SP - 1 EP - 19 PB - MDPI CY - Basel AN - OPUS4-55611 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Temgoua Tonleu, Ranil C. A1 - Koch, Matthias T1 - Simulation of the Environmental Degradation of TBBPA by EC-LC-MS N2 - Oxidative degradation processes of tetrabromobisphenol A (TBBPA), a brominated flame retardant (BFR) in wood, plastics and electronics, were investigated by electrochemistry (EC) coupled online to electrospray ionization mass spectrometry (ESI/MS). Oxidative phase I and II metabolites production was achieved using an electrochemical flow-through cell equipped with a boron doped diamond electrode. Structural elucidation and prediction of oxidative metabolism pathways of TBBPA according to type II ipso-substitution were based on retention time, m/z ratio in negative mode and fragmentation pattern. Using the data obtained through high resolution MS analysis and the identification of single electron transfer (SET) as the initial step of a two-electron oxidation provided the necessary information to propose a mechanism for the electrochemical oxidation of TBBPA. Oxidation reactions involving aromatic hydroxylation and β-scission were the main degradation observed when studying the electrochemical behavior of TBBPA. Computational chemistry experiments using density functional theory (DFT) allowed to identify mono-hydroxylated reaction intermediate and dismissed the mechanism involving two concurrent hydroxylation. TBBPA oxidation products were compared to known metabolites of its biological and environmental degradation confirming the ability of electrochemistry to simulate β-scission reactions. T2 - Mass Spectrometry Forum 2024 CY - Vienna, Austria DA - 21.02.2024 KW - Emerging pollutants KW - Chemical characterization KW - Electrochemistry KW - Chemical and material safety KW - Mass spectrometry KW - Environment-material interactions PY - 2024 AN - OPUS4-59571 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Nowatzky, Yannek T1 - Fiora: Source Data for Training and Testing N2 - This repository contains source data for training and testing the Fiora model (see GitHub and DOI: 10.5281/zenodo.14651774). As part of the Fiora study (Nowatzky et al., 2025), which introduces a GNN-based fragmentation algorithm for simulating MS/MS spectra, this dataset enables the reproduction of the study’s findings and the training of new spectral prediction models. KW - Bioinformatics KW - Mass spectrometry KW - Machine Learning PY - 2025 DO - https://doi.org/10.5281/zenodo.14782249 PB - Zenodo CY - Geneva AN - OPUS4-64587 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Lisec, Jan A1 - Sommerfeld, Thomas A1 - Riedel, Juliane A1 - Mauch, Tatjana A1 - Koch, Matthias T1 - CRM BAM-B003 eCerto data file N2 - Data file (RData) containing measurement data recorded during the production process of the Certified Reference Material BAM-B003 containing per- and polyfluoroalkyl substances (PFAS) in textiles. The data can be most conveniently openend using the Shiny-App eCerto which is accessible at https://www.bam.de/eCerto. KW - Certified reference material KW - Mass spectrometry KW - PFAS PY - 2025 DO - https://doi.org/10.5281/zenodo.15907581 PB - Zenodo CY - Geneva AN - OPUS4-64544 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Jaeger, Carsten A1 - Lintelmann, Jutta A1 - Franke, Raimo A1 - Artati, Anna A1 - Cecil, Alexander A1 - Broda, Frank A1 - Klawonn, Frank A1 - Erban, Alexander A1 - Kopka, Joachim A1 - Fuchs, Beate A1 - Sommer, Ulf A1 - Neumann-Schaal, Meina A1 - O'Connor, Gavin T1 - Analytical practices, use and needs of standard and reference materials in the German-speaking metabolomics community: results of an online survey N2 - Introduction Since the early 2000s, metabolomics has grown rapidly, becoming integral to fields like life sciences, health, and environmental research. This expansion has led to the formation of national and international societies, such as Germany’s DGMet, to tackle emerging challenges. One of DGMet’s goals is to improve measurement quality by assessing community needs for harmonization and standardization. A recent survey within the German-speaking community aimed to identify current practices and gaps in the use of chemical standards and reference materials, to guide future standardization efforts and collaborative initiatives. Methods An online survey was conducted between June 2023 and April 2024. The survey consisted of 38 key questions and was open to research institutions from Germany, Austria, and Switzerland. Results The survey was accessed by 68 laboratories, with 23 institutes providing complete or partial responses (34% response rate), which is comparable to rates reported in similar surveys within the metabolomics and lipidomics communities. Respondents were mainly experienced researchers from Germany, focusing mainly on health-related (“red”) metabolomics, as indicated by 78% of the respondents, followed by microbial (“grey”, 48%) and plant (“green”, 39%) metabolomics (multiple answers possible). The use of targeted methods was reported more frequently (91%) than that of non-targeted methods (78%), whereas metabolite fractions studied were equally split between polar, midpolar and lipid fractions (83% each). Human (74%), mouse (61%) and Arabidopsis (30%) were the most frequently studied organisms. Most participants used synthetic chemical standards for instrument qualification (83%), calibration (78%), and metabolite identification (74%), while matrix reference materials were mainly applied for quality control (52%) and method validation (44%). There was a strong demand for more standards, especially for metabolite identification and quantification, with cost being a major barrier, particularly for isotopically labelled standards and certified reference materials. Conclusions Valuable insights into the use of standards and reference materials within the German-speaking metabolomics community were obtained. Moving forward, the community should address critical gaps in metabolomics standardization. To achieve this, it must share its knowledge, articulate its needs clearly, and actively engage in joint efforts with national metrology institutes and international standardization initiatives. KW - Reference material KW - Chemical standard KW - Metabolomics KW - Mass spectrometry PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-647303 DO - https://doi.org/10.1007/s11306-025-02360-x VL - 21 IS - 6 SP - 1 EP - 11 PB - Springer-Nature CY - Heidelberg AN - OPUS4-64730 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - You, Yi A1 - Danischewski, Julia A1 - Molnar, Brian A1 - Riedel, Jens A1 - Shelley, Jacob T1 - Manipulation of Gaseous Ions with Acoustic Fields at Atmospheric Pressure N2 - The ability to controllably move gaseous ions is an essential aspect of ion-based spectrometry (e.g., mass spectrometry and ion mobility spectrometry) as well as materials processing. At higher pressures, ion motion is largely governed by diffusion and multiple collisions with neutral gas molecules. Thus, high-pressure ion optics based on electrostatics require large fields, radio frequency drives, complicated geometries, and/or partially transmissive grids that become contaminated. Here, we demonstrate that low-power standing acoustic waves can be used to guide, block, focus, and separate beams of ions akin to electrostatic ion optics. Ions preferentially travel through the static-pressure regions (“nodes”) while neutral gas does not appear to be impacted by the acoustic field structure and continues along a straight trajectory. This acoustic ion manipulation (AIM) approach has broad implications for ion manipulation techniques at high pressure, while expanding our fundamental understanding of the behavior of ions in gases. KW - Ion mobility spectrometry KW - Acoustic KW - Mass spectrometry PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-600704 DO - https://doi.org/10.1021/jacs.4c01224 SP - 1 EP - 6 PB - ACS Publications AN - OPUS4-60070 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 - Laser Ablation Secondary Electrospray Ionization for In Situ Mass Spectrometric Interrogation of Acoustically-Levitated Droplets N2 - 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. KW - Acoustic levitation KW - Mass spectrometry KW - Electrospray KW - Laser ablation PY - 2022 DO - https://doi.org/10.1021/acs.analchem.2c03800 SN - 0003-2700 VL - 2022 SP - 1 EP - 5 PB - ACS Publications CY - Washington AN - OPUS4-56531 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Hufgard, Josefin T1 - Traveling Wave Acoustic Ion Manipulation (AIM) for Ion Trajectory Alteration N2 - Acoustic ion manipulation (AIM) is a recent discovery reliant on the sound-ion interactions under ambient conditions. Instead of relying upon conventional electric or magnetic fields, this technique initially exploits standing acoustic waves to focus, gate, deflect, and separate ions. Compared to AIM in a standing wave scenario, the transportation of ions and their response to traveling acoustic waves remain less understood. In contrast to standing waves, which establish stationary pressure domains, traveling waves engender continuously propagating pressure variations. Here, we report on AIM effects induced by traveling acoustic waves that occur from a single-transducer setup. The changes in ion trajectory induced by acoustic traveling waves, ion-specific responses to the traveling wave and its analytical applications will be investigated. A home-built alternating-current (AC) plasma source was used to produce a laminar ion stream, positioned ~10 cm from the inlet capillary of an Orbitrap mass spectrometer. A Langevin-type ultrasonic transducer operated at 40 kHz and ~50 W was used to introduce a diverging sound gradient arranged perpendicular to the ion beam direction. Small model analytes, such as methanol, isopropanol, and acetone, were doped in the discharge gas flow as traces produced in the source, to differentiate from ions produced between the source and MS inlet capillary. Aerodynamic information on both the sound field and the gas stream is provided by defocusing shadowgraphy images. T2 - ASMS 73rd Conference on Mass spectrometry and Allied topics CY - Baltimore, Maryland, USA DA - 01.06.2025 KW - Mass spectrometry KW - Acoustic Ion Manipulation (AIM) KW - Traveling acoustic wave PY - 2025 AN - OPUS4-63380 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Becker, Roland A1 - Scholz, Philipp A1 - Jung, Christian A1 - Weidner, Steffen T1 - Thermo-Desorption Gas Chromatography-Mass Spectrometry for investigating the thermal degradation of polyurethanes N2 - 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. KW - Thermo-desorption KW - Mass spectrometry KW - Polyurethanes KW - Thermal degradation PY - 2023 DO - https://doi.org/10.1039/D3AY00173C SN - 1759-9660 SP - 1 EP - 6 PB - Royal Society for Chemistry AN - OPUS4-57307 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Rodriguez, Santiago A1 - Kumanski, Sylvain A1 - Ayed, Zeineb A1 - Fournet, Aurélie A1 - Bouanchaud, Charlène A1 - Sagar, Amin A1 - Allemand, Frédéric A1 - Baulin, Vladimir A. A1 - Resch‐Genger, Ute A1 - Cortés, Juan A1 - Sibille, Nathalie A1 - Chirot, Fabien A1 - Wegner, Karl David A1 - Antoine, Rodolphe A1 - Le Guével, Xavier A1 - Bernadó, Pau T1 - Programming the Optoelectronic Properties of Atomically Precise Gold Nanoclusters Using the Conformational Landscape of Intrinsically Disordered Proteins N2 - The rational design of hybrid nanomaterials with precisely controlled properties remains a central challenge in materials science. While atomically precise gold nanoclusters (Au‐NCs) offer molecule‐like control over a metallic core, tuning their optoelectronic behavior via surface engineering is often empirically driven. Here, we establish a design principle by demonstrating that the conformational landscape of intrinsically disordered proteins (IDP) can be used as a programmable scaffold to rationally modulate the photophysical properties of a covalently bound Au‐NC. We synthesized a series of bioconjugates between Au 25 nanoclusters and bioengineered IDPs containing a variable number of cysteine anchoring points. A combination of mass spectrometry, small‐angle X‐ray scattering, and modeling on the conjugates indicates that increasing the number of covalent anchors systematically restricts the conformational ensemble, inducing a progressively more compact protein shell around nanoclusters. This structural rigidification at the interface directly translates into a 15‐fold enhancement of the Au‐NC near‐infrared photoluminescence and a six‐fold increase in its average lifetime. Our findings demonstrate that the conformational plasticity of IDPs and the capacity to engineer them can be harnessed as a molecular tuning knob, moving to a new regime of programmable soft‐matter control over the properties of quantum‐confined nanomaterials for tailored biotechnological applications. KW - Fluorescence KW - Custer KW - Nano KW - Advanced material KW - Characterization KW - Fluorescence quantum yield KW - Integrating sphere spectroscopy KW - Thiol ligands KW - Gold KW - Surface chemistry KW - SWIR KW - Mass spectrometry KW - Protein PY - 2026 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-655086 DO - https://doi.org/10.1002/chem.202502991 SN - 0947-6539 SP - 1 EP - 9 PB - Wiley VHC-Verlag AN - OPUS4-65508 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Trimpin, Sarah A1 - Yenchick, Frank S. A1 - Lee, Chuping A1 - Hoang, Khoa A1 - Pophristic, Milan A1 - Karki, Santosh A1 - Marshall, Darrell D. A1 - Lu, I-Chung A1 - Lutomski, Corinne A. A1 - El-Baba, Tarick J. A1 - Wang, Beixi A1 - Pagnotti, Vincent S. A1 - Meher, Anil K. A1 - Chakrabarty, Shubhashis A1 - Imperial, Lorelei F. A1 - Madarshahian, Sara A1 - Richards, Alicia L. A1 - Lietz, Christopher B. A1 - Moreno-Pedraza, Abigail A1 - Leach, Samantha M. A1 - Gibson, Stephen C. A1 - Elia, Efstathios A. A1 - Thawoos, Shameemah M. A1 - Woodall, Daniel W. A1 - Jarois, Dean R. A1 - Davis, Eric T.J. A1 - Liao, Guochao A1 - Muthunayake, Nisansala S. A1 - Redding, McKenna J. A1 - Reynolds, Christian A. A1 - Anthony, Thilani M. A1 - Vithanarachchi, Sashiprabha M. A1 - DeMent, Paul A1 - Adewale, Adeleye O. A1 - Yan, Lu A1 - Wager-Miller, James A1 - Ahn, Young-Hoon A1 - Sanderson, Thomas H. A1 - Przyklenk, Karin A1 - Greenberg, Miriam L. A1 - Suits, Arthur G. A1 - Allen, Matthew J. A1 - Narayan, Srinivas B. A1 - Caruso, Joseph A. A1 - Stemmer, Paul M. A1 - Nguyen, Hien M. A1 - Weidner, Steffen A1 - Rackers, Kevin J. A1 - Djuric, Ana A1 - Shulaev, Vladimir A1 - Hendrickson, Tamara L. A1 - Chow, Christine S. A1 - Pflum, Mary Kay H. A1 - Grayson, Scott M. A1 - Lobodin, Vladislav V. A1 - Guo, Zhongwu A1 - Ni, Chi-Kung A1 - Walker, J. Michael A1 - Mackie, Ken A1 - Inutan, Ellen D. A1 - McEwen, Charles N. T1 - New Processes for Ionizing Nonvolatile Compounds in Mass Spectrometry: The Road of Discovery to Current State-of-the-Art N2 - This Perspective covers discovery and mechanistic aspects aswell as initial applications of novel ionization processes for use in massspectrometry that guided us in a series of subsequent discoveries, instrumentdevelopments, and commercialization. Vacuum matrix-assisted ionization onan intermediate pressure matrix-assisted laser desorption/ionization sourcewithout the use of a laser, high voltages, or any other added energy wassimply unbelievable, at first. Individually and as a whole, the variousdiscoveries and inventions started to paint, inter alia, an exciting new pictureand outlook in mass spectrometry from which key developments grew thatwere at the time unimaginable, and continue to surprise us in its simplisticpreeminence. We, and others, have demonstrated exceptional analyticalutility. Our current research is focused on how best to understand, improve, and use these novel ionization processes throughdedicated platforms and source developments. These ionization processes convert volatile and nonvolatile compounds from solid orliquid matrixes into gas-phase ions for analysis by mass spectrometry using, e.g., mass-selected fragmentation and ion mobilityspectrometry to provide accurate, and sometimes improved, mass and drift time resolution. The combination of research anddiscoveries demonstrated multiple advantages of the new ionization processes and established the basis of the successes that lead tothe Biemann Medal and this Perspective. How the new ionization processes relate to traditional ionization is also presented, as wellas how these technologies can be utilized in tandem through instrument modification and implementation to increase coverage ofcomplex materials through complementary strengths. KW - Mass spectrometry PY - 2024 DO - https://doi.org/10.1021/jasms.3c00122 SN - 1879-1123 VL - 35 IS - 12 SP - 2753 EP - 2784 PB - American Chemical Society (ACS) AN - OPUS4-61417 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - You, Yi T1 - Acoustic Ion Manipulation (AIM) N2 - The precise control of gaseous ions is a cornerstone in ion-based spectrometry and other disciplines such as materials processing. Traditional high-pressure ion optics rely on electrostatic and magnetic fields that often demand the use of intense electric fields, radio frequency activation, complex geometrical arrangements, or partially transmissive grids. Consequently, the efficiencies of such devices tend to be low or they require large footprints, as ion motions under ambient conditions are governed aerodynamically by collisions and fluid dynamics. However, from a different perspective and holistic reasoning, the limitations posed by collisions, aerodynamics, and other factors that hinder ion control in the open-air suggested an innovative direction for ion manipulation. Our study introduces a novel method that employs low-power standing acoustic waves to effectively manipulate ion beams. We observe that ions distinctively prefer traveling through areas of static pressure within the acoustic field, identified as "nodes." In contrast, neutral gases are unaffected by the acoustic field structure and continue to move along a straight trajectory. We have named this method Acoustic Ion Manipulation (AIM). Initial studies demonstrated selective and efficient manipulations of ion with AIM, including gating, redirection, regional dispersion, and focusing. This technique broadens the scope of ion manipulation strategies at high pressures while enriching our fundamental understanding of ion-acoustic kinetics. The potential applications of this method are vast, promising significant advancements in the fields of analytical chemistry, environmental science, and beyond. T2 - ANAKON 2025 CY - Leipzig, Germany DA - 10.03.2025 KW - Acoustic ion manipulation KW - Mass spectrometry PY - 2025 AN - OPUS4-64110 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Riedel, Jens T1 - Acoustic Ion Manipulation: Electric-field-free Approach to Gate, Focus, and Separate Ions at Atmospheric Pressure N2 - Approaches to control the motion and direction of ionized particles and mole-cules are an essential aspect of ion-based spectrometries, such as mass spec-trometry (MS) and ion mobility spectrometry (IMS). A wide variety of ion optics exist to reflect, focus, separate, gate, and filter ions based on physical proper-ties. Notably all rely on electric and magnetic fields to alter the trajectory of ionized atoms and molecules. While these optics are quite efficient at low pressures due to the large mean free path, diffusion and electrostatic repulsion between ions dominate at higher pressures. Conventional ion optics, that use electric or magnetic fields, can guide ions at atmospheric pressure (AP), but require high field strengths to overcome the dominating aerodynamic effects. Here, we describe a remarkable phenomenon whereby low-power acoustic fields are used to move, shape, gate, and separate beams of gaseous ions at atmospheric pressure. We refer to this approach as Acoustic Ion Manipulation (AIM). Gaseous ions at AP are directed towards and separated by the presence of the acoustic field. To better understand the phenomenon, an ion-detector array provided a measure of bulk ion movement, while mass spectrometry (MS) offered chemical-specific information. As one example of an AIM setup, a standing acoustic wave was formed with two ultrasonic speakers and placed between an ionization source and ion detector. Ion beams preferentially travel through regions of stable pressure gradients (i.e. nodes) and deflect from un-stable regions (i.e. antinodes). Shadowgraphy revealed that the ions are sepa-rated from a neutral gas stream. Specific examples of ion focusing, gating, and separation (based on ion size) will be shown. In addition, experimental findings will be used to postulate a theory to develop a better understand of the behav-ior of gas-phase ions in acoustic fields. This discovery could have profound im-pacts in IMS/MS instrumentation as well as materials processing and charac-terization. T2 - 56. Jahrestagung der DGMS CY - Göttingen, Germany DA - 04.03.2025 KW - Acoustic Ion Manipulation KW - Mass spectrometry KW - Ultrasound PY - 2025 AN - OPUS4-64208 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - INPR A1 - Battistella, Beatrice A1 - Revill, Adam A1 - Venzago, Cornel A1 - Hoffmann, Volker A1 - Agudo Jacome, Leonardo A1 - Al-Sabbagh, Dominik A1 - Recknagel, Sebastian A1 - Abad Andrade, Carlos Enrique T1 - Depth-Resolved Lithium Isotope Fractionation as a Diagnostic of Interphase Evolution and Degradation in Lithium Ion Batteries N2 - Lithium isotopic fractionation is well-established in dynamic geochemical systems; however, its role in lithium-ion batteries (LIBs) remains uninvestigated. Herein, we report the first depth-resolved demonstration that isotopic separation occurs during Li-ion cell operation whose magnitude depends on the cycling history. Using depth-resolved glow discharge mass spectrometry, we monitored the 7Li/6Li ratio in LiNi0.333Mn0.333Co0.333O2 (NMC111)||graphite coin cell electrodes at defined life-cycle stages. Different charging rates were examined to get mechanistic insight into kinetic and thermodynamic control in the fractionation process. Although pristine electrodes exhibit a uniform isotopic ratio, cycled electrodes show a distinct 7Li enrichment in the positive electrode and a corresponding accumulation of 6Li at the surface of the negative electrode. The degree of isotopic separation varies with the charging rate. Isotopic signatures correlate with capacity fading, indicating lithium isotope mapping as a sensitive diagnostic tool for tracking electrode degradation and the evolution of the electrode–electrolyte interphases in LIBs. KW - Li-ion batteries KW - Lithium isotopes KW - Post-mortem analysis KW - GD-MS KW - Depth profile KW - Mass spectrometry PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-651287 DO - https://doi.org/10.26434/chemrxiv-2025-5rvlk SP - 1 EP - 19 AN - OPUS4-65128 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Döring, Sarah A1 - Konthur, Zoltán A1 - Weller, Michael G. A1 - Jaeger, Carsten A1 - Reinders, Yvonne T1 - Challenges and Insights in Absolute Quantification of Recombinant Therapeutic Antibodies by Mass Spectrometry: An Introductory Review N2 - This review describes mass spectrometry (MS)-based approaches for the absolute quantification of therapeutic monoclonal antibodies (mAbs), focusing on technical challenges in sample treatment and calibration. Therapeutic mAbs are crucial for treating cancer and inflammatory, infectious, and autoimmune diseases. We trace their development from hybridoma technology and the first murine mAbs in 1975 to today’s chimeric and fully human mAbs. With increasing commercial relevance, the absolute quantification of mAbs, traceable to an international standard system of units (SI units), has attracted attention from science, industry, and national metrology institutes (NMIs). Quantification of proteotypic peptides after enzymatic digestion using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) has emerged as the most viable strategy, though methods targeting intact mAbs are still being explored. We review peptide-based quantification, focusing on critical experimental steps like denaturation, reduction, alkylation, choice of digestion enzyme, and selection of signature peptides. Challenges in amino acid analysis (AAA) for quantifying pure mAbs and peptide calibrators, along with software tools for targeted MS data analysis, are also discussed. Short explanations within each chapter provide newcomers with an overview of the field’s challenges. We conclude that, despite recent progress, further efforts are needed to overcome the many technical hurdles along the quantification workflow and discuss the prospects of developing standardized protocols and certified reference materials (CRMs) for this goal. We also suggest future applications of newer technologies for absolute mAb quantification. KW - Monoclonal antibody KW - Therapeutic antibodies KW - Mass spectrometry KW - Liquid chromatography KW - Absolute quantification KW - Metrology KW - Traceability KW - Certified reference material PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-623707 DO - https://doi.org/10.3390/antib14010003 SN - 2073-4468 VL - 14 IS - 1 SP - 1 EP - 26 PB - MDPI CY - Basel, Schweiz AN - OPUS4-62370 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - INPR A1 - Döring, Sarah A1 - Weller, Michael G. A1 - Reinders, Yvonne A1 - Konthur, Zoltán A1 - Jaeger, Carsten T1 - Challenges and Insights in Absolute Quantification of Recombinant Therapeutic Antibodies by Mass Spectrometry: An Introductory Review N2 - This review describes mass spectrometry (MS)-based approaches for the absolute quantification of therapeutic monoclonal antibodies (mAbs), focusing on technical challenges in sample treatment and calibration. Therapeutic mAbs are crucial for treating cancer, inflammatory, infectious, and autoimmune diseases. We trace their development from hybridoma technology and the first murine mAbs in 1975 to today’s chimeric and fully human mAbs. With increasing commercial relevance, absolute quantification of mAbs, traceable to SI units, has attracted attention from science, industry, and national metrology institutes (NMIs). Quantification of proteotypic peptides after enzymatic digestion using liquid chromatography-tandem mass spectrometry (LC-MS/MS) has emerged as the most viable strategy, though methods targeting intact mAbs are still being explored. We review peptide-based quantification, focusing on critical experimental steps like denaturation, reduction, alkylation, choice of digestion enzyme, and selection of signature peptides. Challenges in amino acid analysis (AAA) for quantifying pure mAbs and peptide calibrators, along with software tools for targeted MS data analysis, are also discussed. Short explanations within each chapter provide newcomers an overview of the field’s challenges. Finally, we discuss prospects and limitations of developing standardized protocols and certified reference materials (CRMs) and suggest future applications of newer technologies for the absolute quantification of therapeutic antibodies. KW - Antibody KW - Mass spectrometry KW - Absolute quantification KW - Metrology KW - Reference products PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-621841 DO - https://doi.org/10.20944/preprints202412.1081.v1 SP - 1 EP - 22 PB - MDPI AN - OPUS4-62184 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - INPR A1 - Döring, Sarah A1 - Wulfes, Birte S. A1 - Atanasova, Aleksandra A1 - Jaeger, Carsten A1 - Walzel, Leopold A1 - Tscheuschner, Georg A1 - Flemig, Sabine A1 - Gawlitza, Kornelia A1 - Feldmann, Ines A1 - Konthur, Zoltán A1 - Weller, Michael G. T1 - Corundum Particles as Trypsin Carrier for Efficient Protein Digestion N2 - Reusable enzyme carriers are valuable for proteomic workflows, yet many supports are expensive or lack robustness. This study describes the covalent immobilization of recombinant trypsin on micrometer-sized corundum particles and assesses their performance in protein digestion and antibody analysis. The corundum surface was cleaned with potassium hydroxide, silanized with 3-aminopropyltriethoxysilane and activated with glutaraldehyde. Recombinant trypsin was then attached, and the resulting imines were reduced with sodium cyanoborohydride. Aromatic amino acid analysis (AAAA) estimated an enzyme loading of approximately 1 µg/mg. Non-specific adsorption of human plasma proteins was suppressed by blocking residual aldehydes with a Tris-glycine-lysine buffer. Compared with free trypsin, immobilization shifted the temperature optimum from 50 to 60 °C and greatly improved stability in 1 M guanidinium hydrochloride. Activity remained above 80 % across several reuse cycles, and storage at 4 °C preserved functionality for weeks. When applied to digesting the NISTmAb, immobilized trypsin provided peptide yields and sequence coverage comparable to soluble enzyme and outperformed it at elevated temperatures. MALDI-TOF MS analysis of Herceptin digests yielded fingerprint spectra that correctly identified the antibody and achieved >60 % sequence coverage. The combination of low cost, robustness and analytical performance makes corundum-immobilized trypsin an attractive option for research and routine proteomic workflows. KW - Aluminum oxide KW - Mass spectrometry KW - Enzyme immobilization KW - Antibodies KW - Protein quantification PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-647944 DO - https://doi.org/10.20944/preprints202510.2002.v1 SP - 1 EP - 22 PB - Preprints.org AN - OPUS4-64794 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Tscheuschner, Georg A1 - Kaiser, Melanie N. A1 - Lisec, Jan A1 - Beslic, D. A1 - Muth, Thilo A1 - Krüger, M. A1 - Mages, H. W. A1 - Dorner, B. G. A1 - Knospe, J. A1 - Schenk, J. A. A1 - Sellrie, F. A1 - Weller, Michael G. T1 - MALDI-TOF-MS-Based Identification of Monoclonal Murine Anti-SARS-CoV-2 Antibodies within One Hour N2 - 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. KW - Reproducibility KW - Quality control KW - Traceability KW - Peptides KW - Peptide mass fingerprinting KW - Monoclonal antibody KW - Recombinant antibody KW - Identity KW - Antibody identification KW - Sequencing KW - Light chain KW - Mass spectrometry KW - Software KW - Open science KW - Library KW - COVID-19 KW - Corona virus KW - Sequence coverage KW - NIST-mAb 8671 KW - Reference material KW - RBD KW - Spike protein KW - Nucleocapsid KW - Cleavage KW - Tryptic digest KW - MALDI KW - DHAP KW - 2,5-dihydroxyacetophenone KW - Github KW - Zenodo KW - ABID PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-547347 DO - https://doi.org/10.3390/antib11020027 VL - 11 IS - 2 SP - 1 EP - 22 PB - MDPI CY - Basel AN - OPUS4-54734 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Bosc-Bierne, Gaby A1 - Ewald, Shireen A1 - Kreuzer, Oliver J. A1 - Weller, Michael G. T1 - Efficient Quality Control of Peptide Pools by UHPLC and Simultaneous UV and HRMS Detection N2 - Peptide pools consist of short amino acid sequences and have proven to be versatile tools in various research areas in immunology and clinical applications. They are commercially available in many different compositions and variants. However, unlike other reagents that consist of only one or a few compounds, peptide pools are highly complex products which makes their quality control a major challenge. Quantitative peptide analysis usually requires sophisticated methods, in most cases isotope-labeled standards and reference materials. Usually, this would be prohibitively laborious and expensive. Therefore, an approach is needed to provide a practical and feasible method for quality control of peptide pools. With insufficient quality control, the use of such products could lead to incorrect experimental results, worsening the well-known reproducibility crisis in the biomedical sciences. Here we propose the use of ultra-high performance liquid chromatography (UHPLC) with two detectors, a standard UV detector at 214 nm for quantitative analysis and a high-resolution mass spectrometer (HRMS) for identity confirmation. To be cost-efficient and fast, quantification and identification are performed in one chromatographic run. An optimized protocol is shown, and different peak integration methods are compared and discussed. This work was performed using a peptide pool known as CEF advanced, which consists of 32 peptides derived from cytomegalovirus (CMV), Epstein–Barr virus (EBV) and influenza virus, ranging from 8 to 12 amino acids in length. N2 - Peptidpools bestehen aus kurzen Aminosäuresequenzen und haben sich als vielseitige Werkzeuge in verschiedenen Forschungsbereichen der Immunologie und bei klinischen Anwendungen erwiesen. Sie sind in vielen verschiedenen Zusammensetzungen und Varianten im Handel erhältlich. Im Gegensatz zu anderen Reagenzien, die nur aus einer oder wenigen Verbindungen bestehen, sind Peptidpools jedoch hochkomplexe Produkte, was ihre Qualitätskontrolle zu einer großen Herausforderung macht. Die quantitative Peptidanalyse erfordert in der Regel ausgefeilte Methoden, in den meisten Fällen isotopenmarkierte Standards und Referenzmaterialien. Dies ist in der Regel sehr aufwändig und teuer. Daher wird ein Ansatz benötigt, der eine praktische und praktikable Methode zur Qualitätskontrolle von Peptidpools bietet. Bei unzureichender Qualitätskontrolle könnte die Verwendung solcher Produkte zu falschen Versuchsergebnissen führen, was das bekannte Problem der Reproduzierbarkeit in den biomedizinischen Wissenschaften noch verschärfen würde. Hier schlagen wir die Verwendung der Ultrahochleistungs-Flüssigkeitschromatographie (UHPLC) mit zwei Detektoren vor, einem Standard-UV-Detektor bei 214 nm für die quantitative Analyse und einem hochauflösenden Massenspektrometer (HRMS) für die Identitätsbestätigung. Um kosteneffizient und schnell zu sein, werden Quantifizierung und Identifizierung in einem einzigen chromatographischen Lauf durchgeführt. Es wird ein optimiertes Protokoll gezeigt, und es werden verschiedene Peak-Integrationsmethoden verglichen und diskutiert. Für diese Arbeit wurde ein Peptidpool verwendet, der als CEF advanced bekannt ist und aus 32 Peptiden besteht, die vom Cytomegalovirus (CMV), Epstein-Barr-Virus (EBV) und Influenzavirus stammen und zwischen 8 und 12 Aminosäuren lang sind. KW - Synthetic peptides KW - Quality control KW - Impurites KW - Byproducts KW - Degradation KW - Mass spectrometry KW - Orbitrap PY - 2024 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-602299 DO - https://doi.org/10.3390/separations11050156 SN - 2297-8739 VL - 11 IS - 5 SP - 1 EP - 18 PB - MDPI CY - Basel AN - OPUS4-60229 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -