Application of sample displacement batch chromatography for fractionation of proteoforms.

Fractionation of proteoforms is currently the most challenging topic in the field of proteoform analysis. The need for considering the existence of proteoforms in experimental approaches is not only important in Life Science research in general but especially in the manufacturing of therapeutic proteins (TPs) like recombinant therapeutic antibodies (mAbs). Some of the proteoforms of TPs have significantly decreased actions or even cause side effects. The identification and removal of proteoforms differing from the main species, having the desired action, is challenging because the difference in the composition of atoms is often very small and their concentration in comparison to the main proteoform can be low. In this study, we demonstrate that sample displacement batch chromatography (SDBC) is an easy-to-handle, economical, and efficient method for fractionating proteoforms. As a model sample a commercial ovalbumin fraction was used, containing many ovalbumin proteoforms. The most promising parameters for the SDBC were determined by a screening approach and applied for a 10-segment fractionation of ovalbumin with cation exchange chromatography resins. Mass spectrometry of intact proteoforms was used for characterizing the SDBC fractionation process. By SDBC, a significant separation of different proteoforms was obtained.

Site-Specific Structural Changes in Long-Term-Stressed Monoclonal Antibody Revealed with DEPC Covalent-Labeling and Quantitative Mass Spectrometry.

Studies of structural changes in mAbs under forced stress and storage conditions are essential for the recognition of degradation hotspots, which can be further remodeled to improve the stability of the respective protein. Herein, we used diethyl pyrocarbonate (DEPC)-based covalent labeling mass spectrometry (CL-MS) to assess structural changes in a model mAb (SILuMAb). Structural changes in the heat-stressed mAb samples were confirmed at specific amino acid positions from the DEPC label mass seen in the fragment ion mass spectrum. The degree of structural change was also quantified by increased or decreased DEPC labeling at specific sites; an increase or decrease indicated an unfolded or aggregated state of the mAb, respectively. Strikingly, for heat-stressed SILuMAb samples, an aggregation-prone area was identified in the CDR region. In the case of longterm stress, the structural consequences for SILuMAb samples stored for up to two years at 2-8 °C were studied with SEC-UV and DEPC-based CL-MS. While SEC-UV analysis only indicated fragmentation of SILuMAb, DEPC-based CL-MS analysis further pinpointed the finding to structural disturbances of disulfide bonds at specific cysteines. This emphasized the utility of DEPC CL-MS for studying disulfide rearrangement. Taken together, our data suggests that DEPC CL-MS can complement more technically challenging methods in the evaluation of the structural stability of mAbs.

An Integrated Strategy Reveals Complex Glycosylation of Erythropoietin Using Mass Spectrometry.

The characterization of therapeutic glycoproteins is challenging due to the structural heterogeneity of the therapeutic protein glycosylation. This study presents an in-depth analytical strategy for glycosylation of first-generation erythropoietin (epoetin beta), including a developed mass spectrometric workflow for N-glycan analysis, bottom-up mass spectrometric methods for site-specific N-glycosylation, and a LC-MS approach for O-glycan identification. Permethylated N-glycans, peptides, and enriched glycopeptides of erythropoietin were analyzed by nanoLC-MS/MS, and de-N-glycosylated erythropoietin was measured by LC-MS, enabling the qualitative and quantitative analysis of glycosylation and different glycan modifications (e.g., phosphorylation and O-acetylation). The newly developed Python scripts enabled the identification of 140 N-glycan compositions (237 N-glycan structures) from erythropoietin, especially including 8 phosphorylated N-glycan species. The site-specificity of N-glycans was revealed at the glycopeptide level by pGlyco software using different proteases. In total, 114 N-glycan compositions were identified from glycopeptide analysis. Moreover, LC-MS analysis of de-N-glycosylated erythropoietin species identified two O-glycan compositions based on the mass shifts between non-O-glycosylated and O-glycosylated species. Finally, this integrated strategy was proved to realize the in-depth glycosylation analysis of a therapeutic glycoprotein to understand its pharmacological properties and improving the manufacturing processes.

FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics.

Top-down mass spectrometry (TD-MS)-based proteomics analyzes intact proteoforms and thus preserves information about individual protein species. The MS signal of these high-mass analytes is complex and challenges the accurate determination of proteoform masses. Fast and accurate feature deconvolution (i.e., the determination of intact proteoform masses) is, therefore, an essential step for TD data analysis. Here, we present FLASHDeconv, an algorithm achieving higher deconvolution quality, with an execution speed two orders of magnitude faster than existing approaches. FLASHDeconv transforms peak positions (m/z) within spectra into log m/z space. This simple transformation turns the deconvolution problem into a search for constant patterns, thereby greatly accelerating the process. In both simple and complex samples, FLASHDeconv reports more genuine feature masses and substantially fewer artifacts than other existing methods. FLASHDeconv is freely available for download here: https://www.openms.org/flashdeconv/. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.

Structural and In Vitro Functional Comparability Analysis of Altebrel™, a Proposed Etanercept Biosimilar: Focus on Primary Sequence and Glycosylation.

The demand for reliable comparability studies of biosimilars grows with their increased market share. These studies focus on physicochemical, structural, functional and clinical properties to ensure that a biosimilar has no significant differences to the originator product and can be released into the market without extensive clinical trials. In the current study, Enbrel® (etanercept, the originator) and Altebrel™ (the proposed biosimilar) underwent direct comparison. "Bottom-up" mass spectrometric analysis was used for primary sequence analysis, evaluation of N/O-glycosylation sites and quantification of methionine oxidation. N/O-glycans were analyzed after permethylation derivatization and the effect of N-glycans on in-vitro functionality of etanercept was assayed. Three enzyme peptide mapping resulted in complete identification of the primary structure. It was confirmed that total ion chromatograms are valuable datasets for the analysis of the primary structure of biodrugs. New N/O-glycan structures were identified and all the N-glycans were quantified. Finally, investigation of the functional properties of N-deglycosylated and non-modified etanercept samples using surface plasmon resonance analysis and in-vitro bioassay showed that N-glycosylation has no significant effect on its in-vitro functionality. Analysis of etanercept and its biosimilar, revealed a high similarity in terms of glycosylation, primary structure and in-vitro functionality.

Factors Associated with Vitamin D Testing, Deficiency, Intake, and Supplementation in Patients with Chronic Pain.

Vitamin D deficiency is a public health issue, with reports of six- to twenty-five-fold rise in vitamin D testing. Vitamin D deficiency has been linked to many chronic diseases such as diabetes mellitus, cardiovascular disease, depression, and chronic pain. Identifying factors associated with risk of deficiency in individuals with chronic pain will help minimize time and cost. This study aims to examine the factors associated with vitamin D testing, intake, and physician-advised supplementation in individuals with chronic pain. Using a cross-sectional design, data were collected from 465 individuals with chronic pain. These data were analyzed using penalized logistic regression with the LASSO technique. Fifty-seven percent reported being tested for vitamin D, about 40% reported being diagnosed with vitamin D deficiency, and of those who had been tested, 60% reported taking vitamin D supplementation. The findings suggest older age (OR 3.12, CI [1.02, 9.50]) and higher mean pain intensity score (OR 2.02, CI [1.13, 3.59]) increased an individual's chance of being vitamin D deficient. Unemployment or on leave due to pain (OR 1.79, [CI 1.03, 3.11]), part-time employment (OR 1.86, CI [1.02, 3.39]), and being a resident of Australia (OR 2.32, CI [1.13, 4.72]) increased chances of being tested for vitamin D. Being diagnosed with vitamin D deficiency (OR 6.67, CI [2.75, 16.19]), unemployed or on leave due to pain (OR 3.71, CI [1.25, 11.00]), and in part-time employment (OR 2.69, CI [0.86, 8.38]) were associated with physician-advised vitamin D supplementation. Our results may have practical implications, as identifying pretest risk factors may assist in identifying who is at risk of vitamin D deficiency, whom to test, and when to treat.

Understanding patient perspectives on management of their chronic pain - online survey protocol.

BACKGROUND: It is widely recognized that both doctors and patients report discontent regarding pain management provided and received. The impact of chronic pain on an individual's life resonates beyond physical and mental suffering; equal or at times even greater impact is observed on an individual's personal relationships, ability to work, and social interactions. The degree of these effects in each individual varies, mainly because of differences in biological factors, social environment, past experiences, support, and belief systems. Therefore, it is equally possible that these individual patient characteristics could influence their treatment outcome. Research shows that meeting patient expectations is a major challenge for health care systems attempting to provide optimal treatment strategies. However, patient perspectives and expectations in chronic pain management have not been studied extensively. The aim of this study is to investigate the views, perceptions, beliefs, and expectations of individuals who experience chronic pain on a daily basis, and the strategies used by them in managing chronic pain. This paper describes the study protocol to be used in a cross sectional survey of chronic pain patients. METHODS AND ANALYSIS: The study population will comprise of individuals aged ≥18 years, who have experienced pain for ≥3 months with no restrictions of sex, ethnicity, or region of residence. Ethics approval for our study was obtained from Humans research ethics committees, University of Adelaide and University of South Australia. Multinomial logistic regression will be used to estimate the effect of duration and character of pain, on patient's perception of time to recovery and supplement intake. Logistic regression will also be used for estimating the effect of patient-provider relationship and pain education on patient-reported recovery and pain intensity. DISCUSSION: Knowledge about the perceptions and beliefs of patients with chronic pain could inform future policies, research, health care professional education, and development of individualized treatment strategies.