Review
Chemistry, Analytical
Ketki Bagwe, Noah Gould, Kendall R. Johnson, Alexander R. Ivanov
Summary: Tissues and cell populations exhibit high levels of heterogeneity at the cellular level, making it important to analyze smaller sample sizes to capture subtle differences between cells. Capillary electrophoresis coupled with mass spectrometry (CE-MS) is a powerful technique for proteomics and metabolomics analysis at the single-cell level, and this review focuses on its applications and recent advances in sample preparation, separation, MS acquisition, and data analysis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Kendall R. Johnson, Michal Gregus, Alexander R. Ivanov
Summary: In this study, the combination of high-field asymmetric waveform ion mobility spectrometry (FAIMS) with ultrasensitive capillary electrophoresis hyphenated with tandem mass spectrometry (CE-MS/MS) was used for deep proteome coverage of low nanogram amounts of digested cell lysates. The optimized CE-FAIMS-MS/MS method showed significant improvements in protein and peptide identification, as well as detection of multiphosphorylated peptides.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Chemistry, Multidisciplinary
Tian Xu, Liangliang Sun
Summary: Capillary isoelectric focusing (cIEF) combined with electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS) is an ideal method for characterizing proteoforms based on their isoelectric points, but faces technical challenges that impede widespread adoption.
FRONTIERS IN CHEMISTRY
(2021)
Article
Biochemical Research Methods
Meng Li, Xueyu Zhao, Danfeng Shen, Gang Wu, Wenbo Wang, Chuanfei Yu, John Sausen, Hanmei Xu, Lan Wang
Summary: This article describes the method of using capillary electrophoresis-mass spectrometry (CE-MS) to characterize the critical quality attributes (CQAs) of recombinant monoclonal antibody therapeutics. By combining the CZE-MS and cIEF-MS methods with the traditional CE-SDS analysis workflow, a comprehensive profile of monoclonal antibody size variants can be obtained.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Biochemical Research Methods
Jennifer Roemer, Steffen Kiessig, Bernd Moritz, Christian Neusuess
Summary: Capillary sieving electrophoresis utilizing SDS (CE(SDS)) is commonly used in the biopharmaceutical industry for analyzing antibody size heterogeneity, but inadequate peak identification of observed protein fragments is a major issue. A recent publication introduced an electrophoretic 2D system for online mass spectrometric detection and identification of mAb fragments, but improvements in system stability and handling were desired. The novel 8-port valve and optimized decomplexation strategy presented here demonstrate increased robustness in impurity characterization of proteins for routine application in the biopharmaceutical field.
Article
Chemistry, Analytical
Bo Liu, Wentao Wang, Tie Gao, Lu Huang, Huihong Fan, Hong-Xu Chen
Summary: Cobratide, a peptide drug extracted from Chinese cobra venom, has shown potential in treating not only chronic pain but also COVID-19. A protocol combining sheathless CE-MS and CE-UV methods was established for the separation, identification, and quantification of cobratide and its impurities, providing valuable information for quality control and process analysis of peptide drugs.
ANALYTICAL METHODS
(2021)
Article
Chemistry, Analytical
Daoyang Chen, Zhichang Yang, Xiaojing Shen, Liangliang Sun
Summary: Top-down proteomics (TDP) is an ideal approach for deciphering the histone code and requires new analytical tools with high-capacity separation and highly sensitive detection of proteoforms. In this study, capillary zone electrophoresis (CZE) -MS/MS was used to identify a large number of histone proteoforms with higher sensitivity compared to traditional methods.
ANALYTICAL CHEMISTRY
(2021)
Article
Immunology
Christoph Gstottner, Alexander Knaupp, Gestur Vidarsson, Dietmar Reusch, Tilman Schlothauer, Manfred Wuhrer, Elena Dominguez-Vega
Summary: The impact of antibody glycoforms on Fc gamma RIIa activation and immune responses was investigated using an affinity capillary electrophoresis-mass spectrometry approach. The results showed clear differences in binding between different glycoforms of antibodies, and the assay was also evaluated for different variants of the Fc gamma RIIa receptor. This method provides a fast and efficient way to establish the structure-function relationships of different antibody species.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Chemistry, Analytical
Sille Stepanova, Vaclav Kasicka
Summary: This review provides an overview of recent advances and applications of capillary electrophoresis and microchip capillary electrophoresis methods in proteomics and peptidomics. It covers topics such as sample preparation, hyphenation with mass spectrometry, and multidimensional separations. New developments in both bottom-up and top-down approaches in proteomics are discussed, along with various applications in protein posttranslational modifications, biological and biochemical research, clinical peptidomics and proteomics, and food analysis.
JOURNAL OF SEPARATION SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Emmanouil Mavrogeorgis, Harald Mischak, Agnieszka Latosinska, Justyna Siwy, Vera Jankowski, Joachim Jankowski
Summary: In recent years, CE-MS has been increasingly used in clinical research for chronic and age-associated diseases, allowing for comprehensive assessment of small molecular weight proteins and peptides. The study evaluated the analytical performance of CE-MS in terms of reproducibility, variability, and efficiency in peptide detection, showing high correlation among different runs and low variation in signal intensity. These findings support the value of CE-MS for clinical application.
Article
Chemistry, Analytical
Jennifer Roemer, Alexander Stolz, Steffen Kiessig, Bernd Moritz, Christian Neususs
Summary: This study presents a comprehensive platform for full characterization of individual CE(SDS)-separated peaks by CE(SDS)-capillary zone electrophoresis-top-down-MS, enabling reliable and unambiguous online MS2 identification of unknown compounds of low-abundant individual CE(SDS) peaks.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2021)
Article
Chemistry, Analytical
Yongling Ai, Harsha P. Gunawardena, Xuanwen Li, Yong-Ick Kim, Howard D. Dewald, Hao Chen
Summary: This study developed a method for absolute quantitation of proteins without using standards, based on the electrochemical oxidation of surrogate peptides and mass spectrometry measurement of the peptide oxidation yield. The method was successfully applied for quantitation of multiple proteins in a mixture and for quantitation of low-level target proteins in the presence of highly abundant proteins. Additionally, the study demonstrated the unprecedented quantitative analysis of deamidated peptide products arising from a specific reaction.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Denis Beslic, Georg Tscheuschner, Bernhard Y. Renard, Michael G. Weller, Thilo Muth
Summary: Monoclonal antibodies are important proteins used in research, therapeutics, and diagnostics. Mass spectrometry-based de novo protein sequencing is a valuable method to obtain amino acid sequences without prior knowledge. Evaluating different sequencing algorithms is crucial for improving accuracy and coverage.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Marie-Jia Gou, Murat Cem Kose, Jacques Crommen, Cindy Nix, Gael Cobraiville, Jo Caers, Marianne Fillet
Summary: By combining different separation strategies to increase the number of identified proteins in a sample, it can aid in antigen discovery research. Studies have shown that the combination of CZE-DTIMS-QTOF and microfluidic RPLC can provide unique information.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Chemistry, Analytical
Blanca H. Lapizco-Encinas, Y. Victoria Zhang, Putuma P. Gqamana, Jana Lavicka, Frantisek Foret
Summary: Capillary electrophoresis (CE) is a powerful separation technique that offers high resolution, great sensitivity, and short processing times. When combined with mass spectrometry (MS), CE-MS systems provide accurate characterization of ionized species and significantly enhance the capabilities of MS. This review article introduces the analytical potential of CE-MS systems and discusses recent advances and future developments.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Nadhiratul-Farihin Semail, Aemi Syazwani Abdul Keyon, Bahruddin Saad, Sazlinda Kamaruzaman, Nur Nadhirah Mohamad Zain, Vuanghao Lim, Mazidatulakmam Miskam, Wan Nazwanie Wan Abdullah, Noorfatimah Yahaya, David D. Y. Chen
Summary: A dynamic pH junction was utilized in capillary electrophoresis to preconcentrate, separate, and determine trace amounts of sulfonamide antibiotics in milk and yoghurt samples. The method demonstrated good linearity, low limits of detection, and acceptable analytes recovery, with quantification limits below the maximum residue limit approved by the European Union. Sensitivity enhancement factors of up to 129 were achieved with the optimized dynamic pH junction using CE with a diode array detector.
Article
Biochemical Research Methods
Rongfan Ren, Hongli Li, Qing Jiang, Xing Wang, David Da Yong Chen
Summary: Characterization of structural isomers of bioactive molecules is important but challenging due to their similar structures. This study demonstrated a simple and robust method using in situ methylation reaction with TMAH and DART ion source to characterize saponin isomers. The method allowed for the identification of ginsenosides in Panax ginseng without the need for chromatographic separation or offline sample pretreatment.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Min Liu, Simin Wang, Wuxia Ge, Wentao Bi, David Da Yong Chen
Summary: This study systematically investigated the influence of host-guest interactions on the analytical performance of direct analysis in real time mass spectrometry (DART-MS) by studying the interactions between cyclodextrins (CDs) and Sudan dyes. The results showed that the host-guest interaction between CDs and Sudan dyes affected the quantitative analysis of the target compounds by lowering the signal intensity. Furthermore, the addition of organic solvents weakened the host-guest interaction and improved the signal intensity in DART-MS, particularly in solid-phase microextraction (SPME).
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Rongfan Ren, Minghui Yuan, Hongli Li, David Da Yong Chen
Summary: Carbohydrates are essential for energy supply and biological functions, but identifying and distinguishing their isomers has been challenging due to their similar structures and possible glycosidic linkages. This study developed an ionization tandem mass spectrometry method to characterize disaccharide isomers by in situ methylation. The method allowed for immediate methylation of hydroxyl groups on disaccharides, enabling their ionization and distinction through mass spectrometry. This approach was used to directly identify disaccharide isomers in real commercial products without complex pretreatment or chromatographic separation.
ANALYTICAL CHEMISTRY
(2023)
Editorial Material
Microbiology
Robert A. Holt
Summary: There is growing recognition of the various connections between host-microbe interactions and the onset and progression of cancer. Vaccines targeting oncomicrobes like F. nucleatum, which promote tumorigenesis, may offer novel and successful interventions against colorectal cancer and other diseases.
CELL HOST & MICROBE
(2023)
Article
Chemistry, Applied
Min Liu, Simin Wang, Wentao Bi, David Da Yong Chen
Summary: Deep eutectic systems (DESys) formed by hydrogen bond acceptor (HBA) and polysaccharide (hydrogen bond donor, HBD) in water can enhance the extraction efficiency and retain the physicochemical properties of polysaccharides. This method simplifies the recovery and purification process of polysaccharides.
Article
Biochemical Research Methods
Ryan M. Riley, Sandra E. Spencer Miko, Ryan D. Morin, Gregg B. Morin, Gian Luca Negri
Summary: Targeted and semitargeted mass spectrometry-based approaches are reliable methods to consistently detect and quantify low abundance proteins of clinical significance. However, their development is time-consuming and often requires costly libraries of synthetic peptides. To address this, we developed PeptideRanger, an R package that identifies peptides from proteins of interest with physiochemical properties suitable for mass spectrometry analysis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Immunology
Natasha Kekre, Kevin A. Hay, John R. Webb, Ranjeeta Mallick, Miruna Balasundaram, Mhairi K. Sigrist, Anne-Marie Clement, Julie S. Nielsen, Jennifer Quizi, Eric Yung, Scott D. Brown, Lisa Dreolini, Daniel D. Waller, Julian Smazynski, Nicole S. Gierc, Bianca C. Loveless, Kayla Clark, Tyler Dyer, Richard Hogg, Leah McCormick, Michael Gignac, Shanti Bell, D. Maria Chapman, David Bond, Siao Yong, Rachel Fung, Heather M. Lockyer, Victoria Hodgson, Catherine Murphy, Ana Subramanian, Evelyn Wiebe, Piriya Yoganathan, Liana Medynski, Dominique C. Vaillan, Alice Black, Sheryl McDiarmid, Michael Kennah, Linda Hamelin, Kevin Song, Sujaatha Narayanan, Judith A. Rodrigo, Stefany Dupont, Terry Hawrysh, Justin Presseau, Kednapa Thavorn, Manoj M. Lalu, Dean A. Fergusson, John C. Bell, Harold Atkins, Brad H. Nelson, Robert A. Holt
Summary: Access to commercial CD19 CAR-T cells remains limited even in wealthy countries like Canada. Therefore, we established a non-commercial academic platform for end-to-end manufacturing of CAR-T cells within Canada's publicly funded healthcare system. Our study demonstrated the safety and efficacy of in-house manufactured CD19 CAR-T cells (CLIC-1901) in patients with relapsed/refractory CD19 positive hematologic malignancies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemical Research Methods
Scott D. Brown, Lisa Dreolini, Jessica F. Wilson, Miruna Balasundaram, Robert A. Holt
Summary: This study presents a cost-effective and accurate plasmid sequencing method using the MinION device from Oxford Nanopore Technologies as an alternative to capillary-based sequencing. The procedure allows for the identification of plasmid identity and mutations, achieving high accuracy in consensus sequence generation. This pipeline offers significant cost savings compared to outsourcing clinical-grade sequencing, providing accessible high-quality plasmid sequence verification.
BMC BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Yuanli Dai, Chang Sun, Yunhe Yang, Shuanghao Wang, Huihui Li, David Da Yong Chen
Summary: The thermodynamic properties of molecular recognition in host-guest inclusion complexes were studied using Taylor dispersion analysis (TDA). TDA provided rapid and convergent results for the binding properties of cyclodextrins (CDs) and their derivatives with physiologically active substances. The TDA results were compared with those obtained by nuclear magnetic resonance and affinity capillary electrophoresis (ACE), showing slightly lower binding constants from ACE.
Article
Chemistry, Applied
Zhixin Xiao, Min Liu, Wentao Bi, David Da Yong Chen
Summary: In-depth studies of extraction mechanism using deep eutectic solvents (DES) and ionic liquids (IL) reveal similarities between the two systems. New applications of ILs and DES in the extraction of nutritional natural products are presented. The study systematically investigates the extraction behavior of ChCl and [HMIm][Cl] in DES and IL, respectively, for target compound extraction from Moringa oleifera leaves. The results show that both extraction methods are based on the formation of a DESys, which can be improved by the formation of a new IL deep eutectic system based on hydrogen bond interaction.
Article
Chemistry, Analytical
Xin Geng, Kai Zhang, Hongli Li, David Da Yong Chen
Summary: A robust ambient ionization mass spectrometry method using a modified direct analysis in real time (DART) ion source was developed for online analysis of breath volatiles. The method is fast, simple, versatile, and has the potential to evaluate the true state of human exhaled breath.
Article
Biochemical Research Methods
Fraser D. Johnson, Christopher S. Hughes, Alvin Liu, William W. Lockwood, Gregg B. Morin
Summary: In this study, the authors present a protocol using thermal proteome profiling (TPP) to identify effector drug-protein interactions in lysates from cancer cell lines. The protocol includes a streamlined sample preparation technique, nonparametric analysis for protein ranking, and a follow-up strategy for identifying effector interactors. Overall, this study is valuable for understanding the mechanisms of action of novel small molecules.
Article
Chemistry, Analytical
Binjun Yan, Mengtian Shi, Siyu Cai, Yuan Su, Renhui Chen, Chiyuan Huang, David Da Yong Chen
Summary: Proteomics is essential for understanding biology and diseases, with liquid chromatography-tandem mass spectrometry (LC-MS/MS) being a widely used platform. Data-independent acquisition (DIA) improves the reproducibility of LC-MS/MS in proteomics research. However, existing DIA data processing tools sometimes lead to significant deviations in quantification. This study presents a cross-run ion selection and peak-picking (CRISP) tool that takes advantage of the consistency of DIA data across runs to filter out interfering signals, resulting in improved quantification accuracy.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Ryan M. Riley, Sandra E. Spencer Miko, Ryan D. Morin, Gregg B. Morin, Gian Luca Negri
Summary: PeptideRanger is a tool that efficiently detects and quantifies low abundance proteins by identifying peptides with suitable physiochemical properties for mass spectrometry analysis. It is a flexible and extensively annotated R package that can be customized to prioritize and filter peptides based on selected properties.
JOURNAL OF PROTEOME RESEARCH
(2023)
