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MALDI-TOF-MS-based identification of monoclonal murine anti-SARS-CoV-2 antibodies within one hour
(2022)
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.
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.
Zellen, als Grundeinheit für Organismen, bilden einen wesentlichen Eckpfeiler für das Leben. Die Untersuchung von einzelnen Zellen liefert wertvolle Einblicke in fundamentale Prozesse des Lebens. So können Anomalien auf der Zelleebene Indikatoren für Krankheiten sein und durch eine Analyse früh erkannt werden. Weiterhin kann durch ein tiefgreifendes Verständnis von Vorgängen in Zellen auch gezielt Forschung zu z.B. neuen Medikamenten betrieben werden. Damit können die Wirksamkeit erhöht und die Nebenwirkungen reduziert werden.
T cells need to adapt their cellular metabolism for effector cell differentiation. This relies on alterations in mitochondrial physiology. Which signals and molecules regulate those alterations remains unclear. We recently reported, that the mitochondrial protein TCAIM inhibits activation-induced changes in mitochondrial morphology and function and thus, CD effector T cell formation. Using conditional TCAIM knock-in (KI) and knockout (KO) mice, w now show that it also applies to CD8+ T cells and more importantly, delineate the molecular processes in mitochondria by which TCAIM controls effector cell differentiation. TCAIM KI resulted in reduced activation-induced HIF1α protein expression. Metabolomics and transcriptional data in combination with mathematical flux modeling revealed an impaired induction of anabolic pathways, especially of the mevalonate pathway and cholesterol biosynthesis in TCAIM KI CD8+ T cells. Addition of cholesterol completely rescued HIF1α protein expression, activation and proliferation of TCAIM KI CD8+ T cells. At the molecular level, TCAIM delayed activation-induced mitochondria-ER contact (MERC) formation by binding to MERC promoting proteins such as RMD3 and VDAC2. In summary, we demonstrate that TCAIM suppresses effector cell differentiation by inhibiting MERC formation, which induce HIF1α-mediated increase in cellular metabolism and cholesterol biosynthesis.
The publicly available document encapsulates the first version of the Catalogue of Services of the future EC4Safenano Centre (CoS 2019).
The CoS 2019 is structured in 12 Service Categories and 27 Service Topics, for each of the 12 categories considered. This architecture configures a 12 x 27 matrix that allows ordering the potential EC4Safenano offer in 324 types of services/groups of services.
Each type of service/group of services is described, in a simple and friendly way, by means of a specific service sheet: the EC4Safenano - Service Data Sheet (EC4-SDS). These EC4-SDSs allow structuring and summarizing the information of each service, providing the customer with a concise view of characteristics of the service and also the contact details with the service provider.
The CoS 2019 deploys a map of services consisting of a set of 100 EC4-SDSs, covering 7 of the 12 Service Categories and 17 of the 27 Service Topics.
The harmonization of services is visualized as a future necessary step in EC4Safenano, in order to strengthen the offer and provide added value to customers with a growing offer of harmonized services in future versions of the CoS.
The information contained in this document is structured in 3 main sections, as follows:
• Catalogue structure. This section describes in short the main characteristics of the CoS 2019.
• Catalogue content. This section represents the core part of the document and encapsulates the set of 100 SDSs displaying the offer proposed by the CoS 2019.
• Online Catalogue. This section describes the resources implemented by EC4Safenano to facilitate the on-line consultation of the CoS 2019 by customers and other interested parties.
In the last years, the Process Analytical Technology (PAT) research field has become of great importance due to its connection with the industrial world. This industry related research, along with the evolutionary progress that technology has seen lately, has allowed that key analytical techniques in an industrial environment have undergone a radical development. One of these techniques has been the near-infrared spectroscopy (NIRS). This technique, currently common in "online" industrial analysis, has seen a remarkable revolution, especially since the introduction of the microelectromechanical systems technology (MEMS) in the spectroscopy field. Nowadays it is possible to find compact spectrometers no bigger than a wristwatch in the market. Although there is an unavoidable question: can these compact spectrometers actually compete against the traditional spectrometers?
In this project different calibration parameters of two compact NIR spectrometers ("Spectral Engines Oy NIR-One Sensor NM2.0", with 1550 to 1950 nm range; and "NeoSpectra Si-ware", with 1300 to 2550 nm range) were evaluated, and the obtained results were compared with a reference spectrometer ("Bruker Optik GmbH Matrix-F", with 15000 to 4000 cm–1 range). In order to obtain the different calibration parameters, a sequence of quality performance tests were conducted. The results obtained after the different experiments carried out with both compact spectrometers prove that their performance is more than acceptable for routine analysis.
Afterward, model samples of different microplastics in soil at different known concentration were analyzed with all three spectrometers. Chemometric models capable to identify and classify microplastics in soil were established. For this analysis five of the most used plastics worldwide were used: polyethylene (PE), polyethylene terephthalate (PET), polypropylene (PP), polystyrene (PS), and polyvinyl chloride (PVC). After the Principal component analysis (PCA), it can be seen that only the NIR-One NM2.0 is capable to differentiate all types of microplastics in soil at concentrations of 1–2 %, while the NeoSpectra Si-ware is unable to identify the PET sample.
Spec2Seq
(2018)
Roadmap for the purity determination of pure metallic elements – Basic rinciples and helpful advice
(2018)
High purity materials can serve as a realisation of the Système International d’Unitès (SI) unit amount of substance for the specific element. Solutions prepared from such high purity materials using gravimetric preparation and the concept of molar mass are used as calibration solutions in many fields of analytical chemistry. Calibration solutions prepared this way provide the traceability to the SI and are the metrological basis in elemental analysis.
The preparation and characterization of such primary pure substances, representing the realisation of the SI unit amount of substance, is undertaken only by a small number of National Metrology Institutes (NMI) and Designated Institutes (DI).
Many other NMIs and DIs, however, prepare elemental calibration solutions as calibrants for their measurement services, such as the certification of matrix Reference Materials or the provision of reference values for Proficiency Testing schemes. The elemental calibration solutions used for this purpose are not a direct service to customers, such as preparing secondary calibration solutions, but provide the source of traceability for the other services. Hence, it is necessary for the NMI or DI to obtain data on the purity of the pure metals or other materials used to prepare the solutions with measurement uncertainties meeting the needs of the above described services. This is commonly undertaken as a “fit for purpose” assessment, appropriate for the uncertainty requirement of the service provided to customers.
As a consequence, total purity measurements are a long-term strategy of CCQM-IAWG. Several studies were conducted (CCQM-P107, CCQM-K72 and CCQM-P149) on the measurement of the purity of zinc. From these studies, several conclusions can be drawn for the purity assessment of a pure (metallic) element. These conclusions will be put together in this document in order to assist all NMIs/DIs in performing a purity assessment, whenever needed.