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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.
Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly
(2023)
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.
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.
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.
The theory of a new calibration approach for obtaining absolute isotope ratios of multi-isotopic elements without the use of any standard has been developed. The calibration approach basically uses the difference in the instrumental isotope fractionation of two different types of mass spectrometers, leading to two different fractionation lines in a three-isotope diagram. When measuring the same sample with both mass spectrometers, the different fractionation lines have one point in common: this is the ‘true’ logarithmized isotope ratio pair of the sample. Thus, the intersection of both fractionation lines provides us with the absolute isotope ratios of the sample. This theory has been tested in practice by measuring Cd and of Pb isotope ratios in the certified reference materials BAM-I012 and NIST SRM981 by thermal ionization mass spectrometry and by inductively coupled plasma mass spectrometry while varying the ionization conditions for both mass spectrometers. With this experiment, the theory could be verified, and absolute isotope ratios were obtained, which were metrologically compatible with the certified isotope ratios. The so-obtained absolute isotope ratios are biased by − 0.5% in average, which should be improved with further developments of the method. This calibration approach is universal, as it can be applied to all elements with three or more isotopes and it is not limited to the type of mass spectrometers applied; it can be applied as well to secondary ion mass spectrometry or others. Additionally, this approach provides information on the fractionation process itself via the triple-isotope fractionation exponent θ.
We studied the dissolution behavior of β NaYF4:Yb(20%), Er(2%) UCNP of two different sizes in biologically relevant media i.e., water (neutral pH), phosphate buffered saline (PBS), and Dulbecco’s modified Eagle medium (DMEM) at different temperatures and particle concentrations. Special emphasis was dedicated to assess the influence of different surface functionalizations, particularly the potential of mesoporous and microporous silica shells of different thicknesses for UCNP stabilization and protection. Dissolution was quantified electrochemically using a fluoride ion selective electrode (ISE) and by inductively coupled plasma optical emission spectrometry (ICP OES). In addition, dissolution was monitored fluorometrically. These experiments revealed that a thick microporous silica shell drastically decreased dissolution. Our results also underline the critical influence of the chemical composition of the aqueous environment on UCNP dissolution. In DMEM, we observed the formation of a layer of adsorbed molecules on the UCNP surface that protected the UCNP from dissolution and enhanced their fluorescence. Examination of this layer by X ray photoelectron spectroscopy (XPS) and mass spectrometry (MS) suggested that mainly phenylalanine, lysine, and glucose are adsorbed from DMEM. These findings should be considered in the future for cellular toxicity studies with UCNP and other nanoparticles and the design of new biocompatible surface coatings.
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.