TY - GEN A1 - Tchipilov, Teodor A1 - Meyer, Klas A1 - Weller, Michael G. T1 - Quantitative 1H Nuclear Magnetic Resonance (qNMR) of Aromatic Amino Acids for Protein Quantification T2 - Preprints N2 - qNMR is a valuable technique for metrological studies due to the uniformity of its signal response for all chemical species of an isotope of interest, which enables compound-independent calibration. However, protein quantification remained challenging as large molecules produce wide, low-intensity signals that reduce the already low sensitivity. Combining qNMR with the hydrolysis of protein samples into amino acids circumvents many of these issues and facilitates the use of NMR spectroscopy for absolute protein and peptide quantification.In this work, different conditions have been tested for quantifying aromatic amino acids and proteins. First, we examined the pH-based signal shifts in the aromatic region. The preferable pH depends on the selection of the amino acids for quantification and which internal standard substance should be used to avoid peak overlap. Several aromatic compounds, such as terephthalic acid, sulfoisophthalic acid, and benzene tricarboxylic acid, have been applied as internal standards. The quantification of amino acids from an amino acid standard, as well as from a certified reference material (bovine serum albumin), was performed. Using the first two suggested internal standards, recovery was ~ 97 % for histidine, phenylalanine, and tyrosine at a concentration of approximately 1 mM in solution. Acidic hydrolysis of a certified reference material (CRM) of bovine serum albumin (BSA) and subsequent quantification of Phe and Tyr yielded recoveries of 98 ± 2 and 88 ± 4 %, respectively, at a protein concentration of 16 g/L or 250 µM. KW - Amino acid analysis KW - AAA KW - Protein hydrolysis KW - Metrology KW - Traceability KW - Reference materials KW - Internal standards KW - Calibration PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-564520 DO - https://doi.org/10.20944/preprints202211.0569.v1 SP - 1 EP - 13 PB - MDPI CY - Basel AN - OPUS4-56452 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Völzke, Jule L. A1 - Hodjat Shamami, P. A1 - Gawlitza, Kornelia A1 - Feldmann, Ines A1 - Zimathies, Annett A1 - Weller, Michael G. T1 - High-purity corundum as support for affinity extractions from complex samples T2 - Preprints N2 - Nonporous corundum powder, known as an abrasive material in the industry, was functionalized covalently with protein binders to isolate and enrich specific proteins from complex matrices. The materials based on corundum were characterized by TEM, ESEM, BET, DLS, and zeta potential measurements. The strong Al-O-P bonds between the corundum surface and amino phosphonic acids are used to introduce functional groups for further conjugations. The common cross-linker glutaraldehyde was compared with a hyperbranched polyglycerol (PG) of around 10 kDa. The latter is oxidized with periodate to generate aldehyde groups that can covalently react with the amines of the surface and the amino groups from the protein via a reductive amination process. The amount of bound protein was quantified via aromatic amino acid analysis (AAAA). This work shows that oxidized polyglycerol can be used as an alternative to glutaraldehyde. With polyglycerol, more of the model protein bovine serum albumin (BSA) could be attached to the surface under the same conditions, and lower nonspecific binding (NSB) was observed. As a proof of concept, IgG was extracted with protein A from crude human plasma. The purity of the product was examined by SDS-PAGE. A binding capacity of 1.8 mg IgG per g of corundum powder was achieved. The advantages of corundum are the very low price, extremely high physical and chemical stability, pressure resistance, favorable binding kinetics, and flexible application. KW - Protein KW - Bioseparation KW - Purification KW - Immunoprecipitation KW - Affinity chromatography KW - Polyglycerol KW - Glutaraldehyde KW - Linker KW - Bioconjugation KW - Self-assembled monolayer (SAM) KW - Periodate oxidation KW - Reductive amination KW - Antibodies KW - Igg KW - Immunoglobulins KW - Carrier KW - Solid phase KW - Hyperbranched polymer KW - Aromatic amino acid analysis aaaa PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-555142 DO - https://doi.org/10.20944/preprints202208.0004.v1 SP - 1 EP - 13 PB - MDPI CY - Basel AN - OPUS4-55514 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN 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 T2 - Preprints 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 thirty-five monoclonal antibodies against SARS-CoV-2 to demonstrate how sequence-independent antibody identification can be achieved by simple means applied onto 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 45 minutes 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 °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 (https://gets.shinyapps.io/ABID/). 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 - SARS-CoV-2 antibody KW - Reproducibility crisis KW - Peptide mass fingerprinting KW - Monoclonal antibody KW - Traceability KW - Antibody identification KW - Identity KW - Antibody light chain KW - MALDI-TOF-MS KW - Trypsin KW - Acidic cleavage KW - Antibody subclass KW - Database KW - Peak overlap KW - ABID KW - Sulfuric acid KW - Online software KW - Sequencing KW - Peptide coverage PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-545182 DO - https://doi.org/10.20944/preprints202203.0229.v1 SN - 2310-287X SP - 1 EP - 24 PB - MDPI CY - Basel AN - OPUS4-54518 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Hartfiel, Reni T1 - Zweistufiges Screening von One-Bead-One-Peptide-Bibliotheken linearer & cyclischer Peptide gegen Pflanzenviren T2 - Masterarbeit N2 - In der Masterarbeit wurde ein Screening gegen den CCMV mit einer linearen Peptidbibliothek entwickelt, wobei zwei lineare Binder identifiziert wurden. Das resynthetisierte Peptid wurde auf seine Bindungseigenschaften mittels ELISA und MST untersucht. Aufgrund eines Aminosäurefehlers in der selbst durchgeführten Resynthese des Peptids sind die Ergebnisse nicht vollständig übertragbar. Um eine umsetzbare Cyclusgröße für die Peptidbibliothek zu finden, wurden Ringgrößen mit sechs bis acht Aminosäuren untersucht. Da keiner der gewählten Ringgrößen bevorzugt war, wurde die Ringgröße aus acht Aminosäuren für die Peptidbibliothek gewählt. Der Ringschluss wurde durch die Bildung einer Disulfidbrücke erreicht. Dadurch war die Alkylierung der vorhandenen Thiolgruppe in den Abbruchsequenzen notwendig. Neben den etablierten Alkylierungsreagenzien Iodessigsäure, Iodacetamid und Acrylamid wurden zwei Epoxide mituntersucht. Hierbei konnte nur bei Acrylamid und Propylenoxid eine vollständige Alkylierung beobachtet werden. Eine synthetische Peptidbibliothek aus zehn Aminosäuren pro Kopplungsschritt und einer Peptidlänge von acht Aminosäuren wurde erfolgreich nach der Split-and-Mix-Synthese hergestellt. Neben den kanonischen Aminosäuren wurde die synthetische Aminosäure 3-(3-Pyridyl)-alanin in die Peptidbibliothek mit eingebaut. Peptidsequenzen aus der cyclische Peptidbibliothek konnte mittels MALDI-TOF-MS identifiziert werden. Es konnte außerdem gezeigt werden, dass synthetische Aminosäuren mit proteinogenen Aminosäuren erfolgreich übersetzt werden. Anschließend wurde das entwickelte Screening auf eine cyclische Peptidbibliothek übertragen. Dabei konnte kein Binder identifiziert werden, da zu viele Nebenreaktionen auftraten. Ein alternativer Ringschluss über die Seitenketten von Lysin und Cystein wurden mit ortho-Phthaldialdehyd und 2,4,6-Trichloro-1,3,5-triazin (Cyanurchlorid) untersucht. Beide Bedingungen wiesen keinen erfolgreichen Ringschluss auf. Obwohl der Ringschluss über die Seitenketten von Lysin und Cystein nicht erfolgreich war, sollte ein Austausch von Cystein angestrebt werden, so dass kein freies Cystein in den Abbruchsequenzen vorhanden ist und die Alkylierung überflüssig wäre. Der Ringschluss durch Verwendung anderer Seitenketten bietet einen vielseitigen Ansatz. KW - CCMV KW - Pflanzenvirus KW - Peptidbibliothek KW - Peptid-Aptamer KW - Alkylierung KW - Cyclisierung KW - MALDI-TOF-MS KW - Fluoreszenz KW - Chip KW - Sequenzierung KW - Peptid-Synthese PY - 2022 SP - 1 EP - 81 PB - Humboldt-Universität zu Berlin CY - Berlin AN - OPUS4-54501 LA - deu AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Tchipilov, Teodor A1 - Raysyan, Anna A1 - Weller, Michael G. T1 - Methods for the quantification of particle-bound protein – Application to reagents for lateral-flow immunoassays (LFIA) T2 - Preprints N2 - Protein immobilization for the functionalization of particles is used in various applications, including biosensors, lateral-flow immunoassays (LFIA), bead-based assays, and others. Common methods for the quantification of bound protein are measuring protein in the supernatant before and after coating and calculating the difference. This popular approach has the potential for a significant overestimation of the amount of immobilized protein since layers not directly bound to the surface (soft protein corona) are usually lost during washing and handling. Only the layer directly bound to the surface (hard corona) can be used in subsequent assays. A simplified amino acid analysis method based on acidic hydrolysis and RP-HPLC-FLD of tyrosine and phenylalanine (aromatic amino acid analysis, AAAA) is proposed to directly quantify protein bound to the surface of gold nano- and latex microparticles. The results are compared with indirect methods such as colorimetric protein assays, such as Bradford, bicinchoninic acid (BCA), as well as AAAA of the supernatant. For both particle types, these indirect quantification techniques show a protein overestimation of up to 1700% compared to the direct AAAA measurements. In addition, protein coating on latex particles was performed both passively through adsorption and covalently through EDC/sulfo-NHS chemistry. Our results showed no difference between the immobilization methodologies. This finding suggests that usual protein determination methods are no unambiguous proof of a covalent conjugation on particles or beads. KW - Soft protein corona KW - Hard protein corona KW - Gold particles KW - Nanoparticles KW - Mikroparticles KW - Antibody KW - Bioconjugation KW - Protein quantification KW - Supernatant KW - Sodium chloride method KW - Covalent conjugation KW - Latex particles KW - Lateral flow immunoassays PY - 2022 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-545365 DO - https://doi.org/10.20944/preprints202203.0332.v1 SP - 1 EP - 8 PB - MDPI CY - Basel AN - OPUS4-54536 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Fischer, Janina T1 - Suspensionsarray-Fluoreszenzimmunoassay zur Multiplexbestimmung von SARS-CoV-2-Antikörpern T2 - Masterarbeit N2 - Übergeordnetes Ziel der Arbeit war die Entwicklung und Optimierung eines Suspensionsarray-Fluoreszenzimmunoassays (SAFIA) für die simultane Bestimmung verschiedener gegen SARS-CoV-2-Proteine gerichtete Antikörper mittels Multiplexdetektion in komplexen Matrices wie humanen Blutserumproben. KW - SARS-CoV-2 KW - Corona KW - COVID-19 KW - Coronavirus KW - Virus KW - Spike-Protein KW - Nucleocapsid-Protein KW - RBD KW - SAFIA KW - LFIA KW - ELISA KW - Partikel KW - Mutationen KW - Neutralisierende Antikörper KW - Durchflusszytometrie KW - ACE2 PY - 2022 SP - 1 EP - 99 PB - Humboldt-Universität zu Berlin CY - Berlin AN - OPUS4-54722 LA - deu AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -