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 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-547347 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 - CONF A1 - Tscheuschner, Georg A1 - Kaufmann, Jan Ole A1 - Kaiser, Melanie A1 - Weller, Michael G. T1 - MALDI-TOF MS Fingerprinting of Antibodies in Less Than One Hour N2 - Antibodies are the most used biomolecules in analytical research. Nevertheless, the sequence and structure information of antibodies is often limited, since manufacturers keep them secret or suppliers sell them under different names. This can make it difficult to reproduce even basic experiments performed in publications as the antibodies used might not be identifiable. To overcome these problems, we developed a simple and cheap method for antibody identification by MALDI-TOF-MS fingerprinting. This technique was used to generate a library of antibody fingerprints, which enables the identification and comparison of antibodies in short time. T2 - SALSA Make and Measure 2021 CY - Online meeting DA - 16.09.2021 KW - Hydrolysis KW - Acid KW - Trypsin KW - Digestion KW - Fragment KW - Peptides KW - Mass spectrometry KW - Database KW - Clones KW - Monoclonal antibodies PY - 2021 AN - OPUS4-53294 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 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-478973 UR - https://www.mdpi.com/2571-5135/8/2/11 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 - Diepeveen, L. E. A1 - Laarakkers, C. M. M. A1 - Martos, G. A1 - Pawlak, M. E. A1 - Uguz, F. F. A1 - Verbene, K. E. S. A. A1 - van Swelm, R. P. L. A1 - Klaver, S. A1 - de Haan, A. F. J. A1 - Pitts, K. R. A1 - Bansal, S. S. A1 - Abbas, Ioana M. A1 - Fillet, M. A1 - Lefebvre, T. A1 - Geurts-Moespot, A. J. A1 - Girelli, D. A1 - Castagna, A. A1 - Herkert, M. A1 - Itkonen, O. A1 - Olbina, G. A1 - Tomosugi, N. A1 - Westerman, M. E. A1 - Delatour, V. A1 - Weykamp, C. W. A1 - Swinkels, D. W. T1 - Provisional standardization of hepcidin assays: creating a traceability chain with a primary reference material, candidate reference method and a commutable secondary reference material N2 - 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. KW - Reference material KW - Peptide KW - Biomarker KW - Bioanalysis KW - Mass spectrometry KW - LC-MS/MS KW - Iron deficiency KW - MALDI-TOF MS KW - UHPLC-MS/MS KW - ELISA KW - Immunoassay PY - 2018 U6 - https://doi.org/10.1515/cclm-2018-0783 SN - 1437-4331 SN - 1434-6621 VL - 57 IS - 6 SP - 864 EP - 872 PB - De Gruyter CY - Berlin AN - OPUS4-47153 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Celasun, S. A1 - Remmler, D. A1 - Schwaar, Timm A1 - Weller, Michael G. A1 - Du Prez, F. A1 - Börner, H. G. T1 - Digging into the sequential space of thiolactone precision polymers: A combinatorial strategy to identify functional domains N2 - 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. KW - Combinatorial chemistry KW - Combinatorial polymer libraries KW - Sequence-defined oligomer KW - Precision polymer sequencing KW - Pseudo peptides KW - MALDI-TOF KW - ESI MS KW - Mass spectrometry KW - Sequencing KW - PEG KW - Polyethylene glycol KW - Solubilizer KW - Drug KW - Conjugates PY - 2019 U6 - https://doi.org/10.1002/anie.201810393 SN - 1521-3773 VL - 58 IS - 7 SP - 1960 EP - 1964 PB - Wiley-VCH CY - Weinheim AN - OPUS4-47323 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Beslic, D. A1 - Tscheuschner, Georg A1 - Renard, B. Y. A1 - Weller, Michael G. A1 - Muth, Thilo T1 - Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly N2 - 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. KW - De novo peptide sequencing KW - Bioinformatics KW - Benchmarking study KW - Monoclonal antibody KW - Mass spectrometry KW - Sequence coverage KW - Light chains KW - Heavy chains KW - IgG KW - Immunoglobulins KW - Error correction KW - Sequencing algorithm KW - Preprocessing KW - Missing fragmentation sites KW - Deep learning-based tools PY - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-570363 VL - 24 IS - 1 SP - 1 EP - 12 PB - Oxford University Press AN - OPUS4-57036 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 U6 - 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 - THES A1 - Abbas, Ioana M. T1 - Development of LC-MS/MS methods for the quantitative determination of hepcidin-25, a key regulator of iron metabolism N2 - Isotope-dilution liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS) is emerging in the field of clinical chemistry and laboratory medicine as an alternative to immunoassays and is acknowledged as the MS “gold standard” for small biomolecule quantification. Hepcidin-25, a key iron-regulatory peptide hormone discovered in 2000, has revolutionized the understanding of iron disorders and its quantitative determination in biological samples should advance the management of iron-related pathology (diagnosis, prognosis and treatment). This study applied LC-MS/MS, using the triple quadrupole (QqQ) mass spectrometer, in a rapid and robust analytical strategy for the quantification of hepcidin-25 in human serum, to be implemented in routine laboratories. For this purpose, two sample preparation strategies and two complementary chromatographic separation conditions were investigated, where the use of acidic mobile phases (0.1% trifluoroacetic acid) was compared with a novel approach involving solvents at high pH (containing 0.1% ammonia). The application of these LC-MS/MS methods to human samples in an intra-laboratory comparison, using the same hepcidin-25 calibrators, yielded a very good correlation of the results. The LC-MS/MS employing trifluoroacetic acid-based mobile phases was selected as a highly sensitive (limit of quantification LOQ of 0.5 μg/L) and precise (coefficient of variation CV<15%) method and was recommended as a reference method candidate for hepcidin-25 quantification in real samples (in the dynamic range of 0.5-40 μg/L). One of the novel aspects of the methodology was the use of amino- and fluoro-silanized autosampler vials to reduce the interaction of the 25-residue peptide to laboratory glassware surfaces. Moreover, this LC-MS/MS method was used for an international round robin study, applying a secondary reference material as a calibrator. By determining the degree of equivalence between the results of the ten participating methodologies, the performance of the method developed in this study was found to be in the optimal range as defined by the International Consortium for Harmonization of Clinical Laboratory Results (ICHCLR). In this work, the formation of hepcidin-25 complexes with copper(II) was investigated. The first reversed-phase chromatographic separation of hepcidin-25/Cu2+ and hepcidin-25 (copper “free”) was achieved by applying mobile phases containing 0.1% of ammonia (pH 11). LC-MS/MS and high-resolution mass spectrometry (Fourier-transform ion cyclotron resonance (FTICR) MS) were applied for the mass spectrometric characterization of the formed hepcidin-25-Cu(II) species at pH values of 11 and 7.4 respectively. A new species corresponding to hepcidin-25 complexed with two copper ions was identified at high pH. KW - Copper KW - LC-MS/MS KW - Chromatography KW - Mass spectrometry KW - Metal complex KW - Metalloprotein KW - Peptide KW - Metrology KW - Reference material PY - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:11-110-18452/20119-6 UR - https://edoc.hu-berlin.de/handle/18452/20119?show=full SP - 1 EP - 156 CY - Berlin AN - OPUS4-45780 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -