Biopharmaceutical quality control with mass spectrometry

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022

The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.

Addressing Acid-Catalyzed Deamidation and the Solubility of Hydrophobic Peptides in Multi-Attribute Method Workflows

Recently, we introduced an optimized and automated Multi-Attribute Method (MAM) workflow, which (a) significantly reduces the number of missed cleavages using an automated two-step digestion procedure and (b) dramatically reduces chromatographic peak tailing and carryover of hydrophobic peptides by implementing less retentive reversed-phase column chemistries. Here, further insights are provided on the impact of postdigest acidification and the importance of maintaining hydrophobic peptides in solution using strong chaotropic agents after digestion. We demonstrate how oxidation can significantly increase the solubility of hydrophobic peptides, a fact that can have a profound impact on quantitation of oxidation levels if care is not taken in MAM workflows. We conclude that (a) postdigestion acidification can result in significant acid-catalyzed deamidation during storage in an autosampler at 5 °C and (b) a strong chaotropic agent, such as guanidine hydrochloride, is critical for preventing loss of hydrophobic peptides through adsorption, which can result in (sometimes extreme) biases in quantitation of tryptophan oxidation levels. An optimized method is presented, which effectively addressed acid-catalyzed deamidation and solubility of hydrophobic peptides in MAM workflows.

Dissecting the structural heterogeneity of proteins by native mass spectrometry

A single gene yields many forms of proteins via combinations of post-transcriptional/post-translational modifications. Proteins also fold into higher-order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the "bottom-up" approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher-order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the "top-down" approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in-depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero-complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near-native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding molecular heterogeneity of proteins. This article is protected by copyright. All rights reserved.

Extractive electrospray ionization mass spectrometry for analytical evaluation and synthetic preparation of pharmaceutical chemicals

Extraction electrospray ionization mass spectrometry (EESI-MS), due to the unique configuration of its ionization module, enables the effective ionization of trace molecules of interest in samples containing complex matrices with high sensitivity, high selectivity and high responding speed without requiring sample pretreatment, and allows high-energy molecular species to undergo specially designed reactions for advanced functionalization. The typical effects of operating conditions on the analytical performance of extraction electrospray ionization mass spectrometry for various pharmaceutical compounds, pharmaceutical preparations and herbal materials were systematically reviewed. The application prospect of extraction electrospray ionization in molecular functionalization for advanced drug discovery is also briefly introduced.

Optimized Multi-Attribute Method Workflow Addressing Missed Cleavages and Chromatographic Tailing/Carry-Over of Hydrophobic Peptides

Peptide mapping by liquid chromatography mass spectrometry (LC-MS) and the related multi-attribute method (MAM) are well-established analytical tools for verification of the primary structure and mapping/quantitation of co- and post-translational modifications (PTMs) or product quality attributes in biopharmaceutical development. Proteolytic digestion is a key step in peptide mapping workflows, which traditionally is labor-intensive, involving multiple manual steps. Recently, simple high-temperature workflows with automatic digestion were introduced, which facilitate robustness and reproducibility across laboratories. Here, a modified workflow with an automatic digestion step is presented, which includes a two-step digestion at high and low temperatures, as opposed to the original one-step digestion at a high temperature. The new automatic digestion workflow significantly reduces the number of missed cleavages, obtaining a more complete digestion profile. In addition, we describe how chromatographic peak tailing and carry-over is dramatically reduced for hydrophobic peptides by switching from the traditional C18 reversed-phase (RP) column chemistry used for peptide mapping to a less retentive C4 column chemistry. No negative impact is observed on MS/MS-derived sequence coverage when switching to a C4 column chemistry. Overall, the new peptide mapping workflow significantly reduces the number of missed cleavages, yielding more robust and simple data interpretation, while providing dramatically reduced tailing and carry-over of hydrophobic peptides.

Mass spectrometric stochastic dynamic 3D structural analysis of mixture of steroids in solution - Experimental and theoretical study

There is explored, herein, functional relation: Experimental mass spectrometric phenomenon, obeying a certain scientific law ⇔ 3D molecular conformations and electronic structures of analytes obtained for quantum chemical theories. The paper answers to questions: (a) What evidence claims these actual relations among measurable and theoretical parameters, experimental factors and molecular properties; (b) how the provided evidence is collected and used; and (c) how empirical proof relates to assign and explain mass spectrometric phenomena of steroids afforded by our innovative stochastic dynamic mass spectrometric formula, D″_SD = 2.6388.10^-17.(<I²>-<I>²), quantum chemical 3D conformations, electronic structures and energetics of molecules, respectively. The paper address issue concerning empirical evidence at very high-to-exact level of assignment of 3D molecular conformations of steroids to experimental mass spectrometric fragment ions, accounting precisely for (i) effect of protonation; (ii) intramolecular rearrangement for A-D rings of steroidal skeleton and proton transfer effect, if any; in addition to (iii) examination of enantiomers of steroids in mixture with different stereochemistry, (R) and (S), of a set of six atoms of the molecular backbone of hydrocortisone (1), deoxycorticosterone (2), progesterone (3) and methyltestosterone (4), respectively. Results from testosterone (5) are discussed, as well. There are used ultra-high resolution atmospheric pressure chemical ionization mass spectrometric data on analytes (1)-(4) at ng.(mL)^-1 concentration levels in mixtures in solution obtained for positive operation mode. High accuracy static and molecular dynamic quantum chemical computations and chemometrics are also utilized. Experimental 3D structural parameters of steroids obtained for stochastic dynamic diffusion theory are correlated with available crystallographic data.