Article
Chemistry, Multidisciplinary
Daniele Ubbiali, Marta Fratini, Lolita Piersimoni, Christian H. Ihling, Marc Kipping, Ingo Heilmann, Claudio Iacobucci, Andrea Sinz
Summary: The conformational ensemble of alpha-synuclein shifts during liquid-liquid phase separation, and a novel mass spectrometry-based approach is established to solve open questions in LLPS structural biology.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Analytical
Virginia K. James, James D. Sanders, Konstantin Aizikov, Kyle L. Fort, Dmitry Grinfeld, Alexander Makarov, Jennifer S. Brodbelt
Summary: Measurement of collision cross section (CCS) is a parameter reflecting the size and shape of an ion and provides structural information beyond molecular mass alone. Previously, isolation of individual charge states was required for CCS analysis, limiting throughput. In this study, CCSs were determined from commonly available mass spectra files using an Orbitrap mass spectrometer, allowing for simultaneous estimation of CCS for multiple charge states and expanding the applicability of this method.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Carter Lantz, Jaybree Lopez, Andrew K. Goring, Muhammad A. Zenaidee, Karl Biggs, Julian P. Whitelegge, Rachel R. Ogorzalek Loo, Frank-Gerrit Klarner, Thomas Schrader, Gal Bitan, Joseph A. Loo
Summary: This study investigates the interaction between CLR01 and different proteoforms of alpha-synuclein and how it affects the structure of alpha-synuclein. The results show that CLR01 can bind to various proteoforms of alpha-synuclein and alter its ability to bind other ligands. Additionally, CLR01 compacts the structure of alpha-synuclein, suggesting a mechanism for halting the formation of oligomers and fibrils associated with neurodegenerative diseases.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Biochemistry & Molecular Biology
Jijing Wang, Sergey Rodin, Amir Ata Saei, Xuepei Zhang, Roman A. Zubarev
Summary: This article discusses the nonenzymatic reaction of ammonia loss from (L)-asparaginyls in proteins and presents experimental evidence supporting the possibility of a full repair reaction. If confirmed, the true repair of (L)-asparaginyl deamidation could potentially prevent aging and neurodegenerative diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
M. Andrasi, G. Vishwakarma, R. Szabo, C. Nagy, A. Gaspar
Summary: The applicability of capillary zone electrophoresis (CZE) was studied for the separation of different recombinant human insulins and their deamidated isoforms. CZE demonstrated high resolving power, separating insulin isoforms with small differences in mass and shape. Humulin, glargine, and glulisine were selected for study due to their similar sequences and chemical parameters, and the deamidation processes were influenced by minor differences in their amino acid sequences. The use of a basic pH background electrolyte enabled not only the separation of different types of insulin but also the separation of deamidated protein forms even in a bare fused silica capillary. The LOD values for UV and ESI-MS detection ranged from 0.6-0.93 mg/L and 2.17-4.37 mg/L, respectively. Deamidation was minimal at temperatures between -20 to -80 degrees C but accelerated above +5 degrees C. Acidified samples incubated for a month at room temperature showed varying levels of deamidation for different insulins.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Biochemical Research Methods
Jacob W. McCabe, Benjamin J. Jones, Thomas E. Walker, Robert L. Schrader, Adam P. Huntley, Jixing Lyu, Nathan M. Hoffman, Gordon A. Anderson, Peter T. A. Reilly, Arthur Laganowsky, Vicki H. Wysocki, David H. Russell
Summary: This study presents a digital-waveform dual-quadrupole mass spectrometer to improve the performance of a drift tube FT-IMS high-resolution Orbitrap mass spectrometer in studying large proteins and protein complexes. The dual-quadrupole analyzer allows for low-energy collisional activation of ions and precise mass selection using digital-waveform technology, enhancing the capabilities of the instrument at a lower cost compared to traditional RF drivers.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Elvin R. Cabrera, Brian H. Clowers
Summary: By casting ion population's mobility information in the frequency domain, time-dispersive ion mobility techniques can now be compatible with slower mass analyzers like ion traps. Recent progress has been made in maximizing the efficiency of Fourier transform ion mobility-mass spectrometry (FT-IM-MS) experiments, but the intersection between practical implementation considerations and theoretical limits of traditional signal processing techniques needs to be further explored. The importance of avoiding signal aliasing due to undersampling signals, along with evaluating limitations imposed by experimental parameters, is crucial for successful Fourier-based multiplexing experiments.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Analytical
Dan B. Kristensen, Martin Orgaard, Trine M. Sloth, Gerard Comamala, Pernille F. Jensen
Summary: This article introduces an optimized and automated Multi-Attribute Method (MAM) workflow that reduces missed cleavages and chromatographic peak tailing and carryover of hydrophobic peptides. The impact of postdigest acidification and the importance of maintaining hydrophobic peptides in solution using strong chaotropic agents are also discussed. The findings highlight the significant increase in the solubility of hydrophobic peptides through oxidation, which can affect quantitation of oxidation levels in MAM workflows.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Elvin R. Cabrera, Brian H. Clowers
Summary: This study describes a method of modulating the ion gates of ion mobility spectrometry using a discrete stepwise function, achieving synchronization between the generated frequencies and the scan rate of the linear ion trap. This method eliminates the ambiguity of assigning the ion current derived from a single modulation frequency and maintains high levels of precision across different combinations.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Biology
Dinesh Kumar, Pawan Kumar, Kumar Vikram, Himmat Singh
Summary: The study investigates the bio-efficacy of Pimenta dioica leaf derived silver nanoparticles (Pd@AgNPs) against malaria, filarial, and dengue vectors. The synthesized Pd@AgNPs showed larvicidal activity against the larvae of Aedes aegypti, Anopheles stephensi, and Culex quinquefasciatus without affecting non-targeted organisms. The green synthesis of AgNPs offers an effective technique for mosquito control and other therapeutic applications.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2022)
Article
Chemistry, Physical
Oscar Palomino-Hernandez, Carlo Santambrogio, Giulia Rossetti, Claudio O. Fernandez, Rita Grandori, Paolo Carloni
Summary: Mass spectrometry and single molecule force microscopy are experimental techniques that provide structural information on intrinsically disordered proteins (IDPs). This study analyzed molecular dynamics simulation data and experimental results to describe the main conformational ensemble of human alpha synuclein (AS) and shed light on its intramolecular interactions and overall compactness.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Applied
Chongshan Yang, Dandan Duan, Chunwang Dong, Chuanxia Li, Guanglin Li, Yunhai Zhou, Yifan Gu, Yachao Liu, Chunjiang Zhao, Daming Dong
Summary: Aroma is crucial in assessing tea quality. Illegal traders often add essence to expired or substandard tea to enhance its aroma for greater profit. Conventional testing methods are time-consuming and costly, while near-infrared spectroscopy and machine vision can only detect powdered solid essences in tea. In this study, proton-transfer reaction mass spectrometry (PTR-MS) and Fourier-transform infrared spectroscopy (FTIR) were used to rapidly detect volatile organic compounds (VOCs) in tea samples adulterated with liquid essence, achieving high prediction accuracies of 0.941 and 0.957, respectively. The study discusses the different application scenarios of the two technologies based on their performance characteristics.
Article
Chemistry, Analytical
Ayako Takemori, Philipp T. Kaulich, Liam Cassidy, Nobuaki Takemori, Andreas Tholey
Summary: The combination of liquid chromatography (LC) and gas-phase separation by field-asymmetric ion mobility spectrometry (FAIMS) is a powerful proteoform separation system for top-down proteomics. In this study, an in-depth top-down proteomics workflow, GeLC-FAIMS-MS, was presented, which utilized a molecular-weight-based proteome fractionation approach using SDS-poly-acrylamide gel electrophoresis. The authors optimized the MS parameters for each gel band and compensating voltage (CV) to improve the identification of proteoforms. They also developed a simple and cost-effective method, combining the PEPPI protocol with an AnExSP method, for stain and SDS removal. Results showed that this method was better suited for low-molecular-weight proteoforms, while a methanol-chloroform-water (MCW)-based protocol showed advantages for higher-molecular-weight proteoforms.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Deseree J. Reid, Tapasyatanu Dash, Zhihan Wang, Craig A. Aspinwall, Michael T. Marty
Summary: Daptomycin is a cyclic lipopeptide antibiotic that interacts with lipid membranes in a non-specific manner. The interaction strength depends on membrane rigidity, with more rigid membranes showing stronger interactions. More fluid membranes may undergo pore formation to expose daptomycin to oxidation. These findings highlight the complementary use of native mass spectrometry, fast photochemical oxidation of peptides, and membrane conductance experiments in studying antibiotic-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Davide Tanasi, Annamaria Cucina, Vincenzo Cunsolo, Rosaria Saletti, Antonella Di Francesco, Enrico Greco, Salvatore Foti
Summary: Mass spectrometry has been successfully used to identify ancient proteins in bones and tissues, but the recovery and identification of archaeological protein residues from ceramic artifacts is challenging due to low protein levels and degradation. This study characterizes proteins extracted from pottery at the Maltese site of Bahrija, providing insights into the diet of the ancient community. The proteomic data confirms issues of contamination and complexity in identifying endogenous proteins in archaeological samples.