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ABID
(2022)
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.
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 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.
Nearly all disease processes are associated with variations of components of the extracellular matrix (ECM) that are typically observed during the development of inflammation. This concerns for example proteoglycans and their associated glycosaminoglycans (GAG), which have been shown to bind to cationic metal imaging probes due to their strong complexing activity. The complexing activity largely depends on the degree of GAG sulfation and/or carboxylation as well as on the GAG isomericity. In this central project, we investigate GAG structures from inflammatory disorders (namely cardiovascular diseases, inflammatory intestinal diseases and neuroinflammation) provided by researchers of the Collaborative Research Center at the molecular disaccharidic level using chromatographic and mass spectrometric methods. In parallel, the spatial localization and quantification of metal-based imaging probes are evaluated by LA-ICP-MS imaging.
Die MALDI-TOF Massenspektrometrie stellt eine wichtige Methode zur simultanen Bestimmung von Molmassen, Molmassenverteilungen und Endgruppen von synthetischen Polymeren dar. In dem Vortrag wird gezeigt, welche zusätzlichen Informationen über die Art der Polymerisation, der Nebenreaktionen und der Topologie der gebildeten hochmolekularen Polylaktid-Homo- und Copolymere im Verlauf ihrer Synthese erhalten werden können.
In addition to molar mass distribution (MMD) synthetic polymers often exhibit an additional chemical heterogeneity distribution, expressed by different end groups and other structural variations (e.g. tacticity, copolymer composition etc.). Ionization in MALDI MS is always strongly affected by such chemical properties. For example, the abundance of cyclics in MALDI TOF mass spectra is frequently reported to greatly exceed that of linears. Thus, the MALDI ionization behavior of various neat end-capped linear poly(L-lactide)s and one cyclic poly(L-lactide) was investigated and compared with that of blends of both structures. Moreover, the influence of the cationizing salt was investigated too.
Neat compounds and various blends of cyclic and linear species were prepared and studied using two MALDI TOF mass spectrometers under identical conditions with regard to sample preparation and instrumental conditions, except for the laser power and the salt used for cationization. Polymer samples were additionally characterized by NMR and SEC.
The steady increase of the laser intensity caused an exponential increase of the peak intensities of both linear and cyclic polylactides.The response of linear polylactides (in the investigated molecular mass range), whether as neat polymer or in blends with other linear polylactides was almost similar. This clearly supports our assumption that ionization in MALDI is probably unaffected by the end group structure.The variation of the laser power shows only little effect on the intensity ratio of linear-to linear and cyclic-to-linear polylactides in blends. Whereas neat linear polylactides at all laser intensities have a significantly higher abundance than neat cyclics, in mixtures of both an overestimation of cyclic species in MALDI TOF mass spectra of polylactides was found. However, this is far less distinct than frequently reported for other polymers.Concluding, peak suppression of linear polymers in mixtures of both architectures can be excluded, which also means, that polylactides showing only peaks of cyclic compounds in their MALDI - TOF mass spectra do not contain a significant fraction of linear analogues.
Our study is the first systematic comparison of the MALDI ionization of neat and blended cyclic and linear polylactides.
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.
A method is described for high-resolution label-free molecular imaging of human bone tissue. To preserve the lipid content and the heterogeneous structure of osseous tissue, 4 μm thick human bone sections were prepared via cryoembedding and tape-assisted cryosectioning, circumventing the application of organic solvents and a decalcification step. A protocol for comparative mass spectrometry imaging (MSI) on the same section was established for initial analysis with time-of-flight secondary ion mass spectrometry (TOF-SIMS) at a lateral resolution of 10 μm to <500 nm, followed by atmospheric pressure scanning microprobe matrix-assisted laser desorption/ionization (AP-SMALDI) Orbitrap MSI at a lateral resolution of 10 μm. This procedure ultimately enabled MSI of lipids, providing the lateral localization of major lipid classes such as glycero-, glycerophospho-, and sphingolipids. Additionally, the applicability of the recently emerged Orbitrap-TOF-SIMS hybrid system was exemplarily examined and compared to the before-mentioned MSI methods.
The common characterization and identification of pollen is a time-consuming task that mainly relies on microscopic determination of the genus-specific pollen morphology. A variety of spectroscopic and spectrometric approaches have been proposed to develop a fast and reliable pollen identification using specific molecular information. Amongst them, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) shows a high potential for the successful investigation of such complex biological samples. Based on optimized MALDI sample preparation using conductive carbon tape, the application of multivariate statistics (e.g. principal components analysis, PCA) yields an enormous improvement concerning taxonomic classification of pollen species compared to common microscopic techniques.
Since multivariate evaluation of the recorded mass spectra is of vital importance for classification, it’s helpful to implement the applied sequence of standard Matlab functions into a graphical user interface (GUI). In this presentation, a stand-alone application (GUI) is shown, which provides multiple functions to perform fast multivariate analysis on multiple datasets. The use of a GUI enables a first overview on the measured dataset, conducts spectral pretreatment and can give classification information based on HCA and PCA evaluation. Moreover, it can be used to improve fast spectral classification and supports the development of a simple routine method to identify pollen based on mass spectrometry.
Unprecedented Ionization Processes in Mass SpectrometryProvide Missing Link between ESI and MALDI
(2018)
In the field of mass spectrometry,producing intact, highly-charged protein ions from surfaces is a conundrum with significant potential payoff in application areas ranging from bio-medical to clinical research. Here, we report on the ability to form intact, highly-charged protein ions on high vacuum time-of-flight mass spectrometers in the linear and reflectron modes achievable using experimental conditions that allow effective matrix removal from both the sample surfaces and from the charged clusters formed by the laser Ablation event. The charge states are the highest reported on high vacuum mass spectrometers, yet they remain at only around athird of the highest charge obtained using laser ablation with a suitable matrix at atmospheric pressure. Other than physical instrument modifications, the key to forming abundant and stable highly-charged ions appears to be the volatility of the matrix used. Cumulative results suggest mechanistic links between the ionization process reported here and traditional ionization methods of electrospray ionization and matrix-assisted laser desorp-tion/ionization.