Article
Chemistry, Analytical
Ludwig R. Sinn, Sven H. Giese, Marchel Stuiver, Juri Rappsilber
Summary: Ion-mobility spectrometry has the potential to solve analytically challenging research questions by adding an extra separation dimension to liquid chromatography-mass spectrometry. By using machine learning, the understanding of field asymmetric waveform ion-mobility spectrometry for the analysis of cross-linked peptides has been deepened and ideal compensation voltages correlating with chromatography fraction number have been identified.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Chih-Hsiang Chang, Darien Yeung, Victor Spicer, Kosuke Ogata, Oleg Krokhin, Yasushi Ishihama
Summary: The study investigates the impact of peptide amino acid sequence on collision cross section values (CCS); ion mobility is mainly affected by the peptide's ability to solvate positively charged sites; the positioning of amino acid residues, as well as helical propensity and hydrophobicity, play important roles in the formation of extended structures.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Roelant Hilgers, Sin Yong Teng, Anamarija Bris, Aleksandr Y. Pereverzev, Paul White, Jeroen J. Jansen, Jana Roithova
Summary: This study introduces a simple and rapid method for determining enantioselectivities based on mass spectrometry. By using ion mobility separation and delayed reactant labeling experiments, the method can link mass spectra with reaction kinetics to predict the enantioselectivity of the overall reaction.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemical Research Methods
Kevin Brown Chandler, Daniel E. Marrero Roche, Robert Sackstein
Summary: Bottom-up nLC-MS/MS-based glycoprotein mass spectrometry workflows face challenges due to suppression of hydrophilic glycopeptide ions by more abundant non-glycosylated peptides. This study investigates the use of high-field asymmetric waveform ion mobility spectrometry (FAIMS) for orthogonal separation of non-glycosylated peptides and glycopeptides, and evaluates its impact on glycopeptide assignment confidence. The optimized FAIMS conditions for human alpha-1-acid glycoprotein (AGP) tryptic N-glycopeptide ions transmission and analysis are documented. These optimized methods increase the number of unique glycopeptide identifications and the confidence of glycopeptide assignments.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Applied
Haixia Zhang, Randy W. Purves, Thomas D. Warkentin, Albert Vandenberg
Summary: Faba bean seeds are a rich source of proteins and levodopa, but the presence of vicine and convicine limits its consumption. A quantification method using FAIMS and QqQ was previously reported, and a similar method with commercial instruments was developed. Both methods provided accurate measurements and recovery, but the commercial method had a lower limit of quantification and a wider linear range. The results showed that levodopa levels in faba bean were genotype dependent, but not directly correlated with vicine or convicine levels.
Article
Chemistry, Analytical
Serina Fukui, Eiji Sugiyama, Hajime Mizuno, Iwao Sakane, Daiki Asakawa, Kazumi Saikusa, Yuki Nishiya, Yuri Amano, Kentaro Takahara, Daisuke Higo, Toshimasa Toyo'oka, Kenichiro Todoroki
Summary: A rapid method for separating dl-2-hydroxyglutaric acid using a single analytical instrument was presented, demonstrating potential for clinical analysis. This method is more efficient and effective compared to traditional methods, showing promise for future applications in clinical settings.
JOURNAL OF SEPARATION SCIENCE
(2021)
Article
Biochemical Research Methods
Frantisek Malinka, Ashkan Zareie, Jan Prochazka, Radislav Sedlacek, Vendula Novosadova
Summary: Aligning and combining individually preprocessed batches in large-scale multi-batch experiments is a challenging task. We present two methods and demonstrate that retention order swaps are not rare in untargeted LC-MS data.
Article
Chemistry, Multidisciplinary
Karen E. Butler, Yoshihiko Takinami, Adam Rainczuk, Erin S. Baker, Blaine R. Roberts
Summary: Native mass spectrometry combined with IMS-MS technology can be used to study the tertiary and quaternary structure of proteins, validate other structural determination methods, and provide more comprehensive structural information.
FRONTIERS IN CHEMISTRY
(2021)
Review
Chemistry, Analytical
Daniel G. Delafield, Gaoyuan Lu, Cameron J. Kaminsky, Lingjun Li
Summary: Mass spectrometry-based biomolecular analyses have become popular in research settings. Gas phase ion separation techniques provide a fourth dimension of analysis, enabling rapid characterization and high throughput profiling. This review highlights the latest developments and applications of high-end ion-mobility enabled instruments and their advantages for biomolecular research.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Zeng Hong-Da, Du Xiao-Xia, Pan Jia-Kai, Wang Yi-Fei, Chen Zhen-Cheng, Li Hua
Summary: A hollow needle-ring ion source was proposed in this study to improve the resolving power and sensitivity of FAIMS systems by introducing helium and argon gases. The experiment showed that helium was more effective than argon in enhancing both parameters, and a mixture of three gases resulted in multiple ion peaks in the FAIMS spectrum.
CHINESE JOURNAL OF ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
David S. Roberts, Morgan Mann, Jake A. Melby, Eli J. Larson, Yanlong Zhu, Allan R. Brasier, Song Jin, Ying Ge
Summary: Researchers have successfully elucidated the complete structure of newly discovered O-glycans on the S protein regional-binding domain (SR-BD) of the SARS-CoV-2 virus through a hybrid mass spectrometry approach. This method can provide insights into the interactions between the virus and host cells, laying a foundation for understanding the functional roles of O-glycans in SARS-CoV-2 and other glycoproteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Chemistry, Analytical
Li Shan, Chen Zhen, Chang-Jie Liu, Jin Jiao, Wang Han, Hu Jun, Ma He, Jia-Liang Shi, Ren Qian, Yu-Peng Cheng, You-Jiang Liu, Chi-Lai Chen
Summary: This study proposed a Nafion-FAIMS technology for rapid detection of hydrogen sulfide gas under ambient humidity. The results showed that this method had high stability and recognition ability, and it was suitable for mixture detection. The method exhibited high linearity and low detection limit in the concentration range of H2S.
CHINESE JOURNAL OF ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Wojciech Fabianowski, Miroslaw Maziejuk, Monika Szyposzynska, Monika Wisnik-Sawka
Summary: The article presents a technique of differential ion mobility spectrometry (DMS) for the detection and identification of volatile organic compounds (VOCs) from various categories. It analyzes the possibility of mixture identification using only the DMS spectrometer and provides several examples. The article also discusses the analysis of different compounds, their mechanisms of fragmentation, influence on effective ion temperature, and high electric field intensity.
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
Biology
Phasit Charoenkwan, Nalini Schaduangrat, Pietro Lio, Mohammad Ali Moni, Balachandran Manavalan, Watshara Shoombuatong
Summary: This study proposes a novel computational approach, NEPTUNE, for the accurate and large-scale identification of Tumor Homing Peptides (THPs) from sequence information. The results demonstrate that NEPTUNE achieves superior performance in THP prediction and improves interpretability using the SHapley additive explanations method.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Chemistry, Physical
Anna L. Simmonds, Andrea F. Lopez-Clavijo, Peter J. Winn, David H. Russell, Iain B. Styles, Helen J. Cooper
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Biochemical Research Methods
Oliver J. Hale, Emma K. Sisley, Rian L. Griffiths, Iain B. Styles, Helen J. Cooper
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2020)
Article
Multidisciplinary Sciences
Jana Havlikova, Robin C. May, Iain B. Styles, Helen J. Cooper
SCIENTIFIC REPORTS
(2020)
Article
Chemistry, Analytical
Oliver J. Hale, Helen J. Cooper
Summary: By utilizing nanospray-desorption electrospray ionization (nano-DESI), native mass spectrometry imaging (native MSI) has achieved significant improvements in resolution compared to native LESA MSI, allowing for more precise imaging. This technique can also be used for location-targeted proteomic analysis directly from tissues.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Jana Havlikova, Robin C. May, Iain B. Styles, Helen J. Cooper
Summary: The ESKAPE pathogens were successfully identified using liquid extraction surface analysis mass spectrometry (LESA MS), with a identification success rate of 79%.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Physics, Atomic, Molecular & Chemical
Oliver J. Hale, James W. Hughes, Helen J. Cooper
Summary: In this study, the integration of travelling wave ion mobility spectrometry (TWIMS) into native nanoDESI MSI workflow was demonstrated, showing improved specificity in ion images by allowing subtraction of chemical noise and enabling the calculation of collision cross sections for protein structure. Results presented ion images and collision cross sections for a variety of proteins and protein assemblies with molecular weights up to 42.6 kDa, showing good agreement with experimental and literature-derived values.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2021)
Article
Chemistry, Multidisciplinary
Emma K. Sisley, Oliver J. Hale, Iain B. Styles, Helen J. Cooper
Summary: This study demonstrates the use of mass spectrometry imaging to map the noncovalent interactions of proteins in the tissue environment of rat brain. By directly identifying proteins from tissue using nanospray-desorption electrospray ionization, the spatial distributions of ligand-bound and metal-bound proteins were mapped. Additionally, the nature of the ligand was confirmed through multiple rounds of tandem mass spectrometry. The study also identified several natively monomeric proteins displaying distinct spatial distributions.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Editorial Material
Biochemical Research Methods
Helen J. Cooper, Aneika C. Leney
Article
Chemistry, Analytical
Oliver J. Hale, James W. Hughes, Emma K. Sisley, Helen J. Cooper
Summary: This study demonstrates the detection and identification of a range of intact endogenous protein assemblies with various stoichiometries from different tissue types using multiple NAMS techniques, showing a greater than twofold increase in accessible molecular weight. Additionally, spatial distributions of protein assemblies up to 94 kDa were mapped in brain and kidney by nanospray desorption electrospray ionization (nano-DESI) mass spectrometry imaging.
ANALYTICAL CHEMISTRY
(2022)
Article
Dentistry, Oral Surgery & Medicine
Melissa M. Grant, John J. Taylor, Katrin Jaedicke, Andrew Creese, Catherine Gowland, Bernard Burke, Khawla Doudin, Upen Patel, Paul Weston, Michael Milward, Susan M. Bissett, Helen J. Cooper, Gerben Kooijman, Amir Rmaile, Marko de Jager, Philip M. Preshaw, Iain L. C. Chapple
Summary: Differential protein biomarkers in saliva and gingival crevicular fluid can be used to objectively distinguish between periodontal health and disease states.
JOURNAL OF CLINICAL PERIODONTOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Eva Illes-Toth, Oliver J. Hale, James W. Hughes, Nicole Strittmatter, Jonathan Rose, Ben Clayton, Rebecca Sargeant, Stewart Jones, Andreas Dannhorn, Richard J. A. Goodwin, Helen J. Cooper
Summary: This study demonstrates for the first time the in situ mass spectrometry analysis of a non-covalent protein-drug complex formed in vivo, and provides a direct route for target-drug characterization in early stage drug discovery by spatial mapping across liver tissue.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Oliver J. Hale, Helen J. Cooper
Summary: This study demonstrates a mass spectrometry analysis method for the direct analysis of intact oligomeric membrane proteins from tissue. By characterizing protein assembly directly from sheep eye lens sections without sample pre-treatment, our approach allows for simultaneous analysis of soluble protein assemblies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biochemical Research Methods
Eva Illes-Toth, Christopher J. Stubbs, Emma K. Sisley, Jeddidiah Bellamy-Carter, Anna L. Simmonds, Todd H. Mize, Iain B. Styles, Richard J. A. Goodwin, Helen J. Cooper
Summary: Liquid extraction surface analysis coupled with native mass spectrometry was used to quantitatively analyze protein-ligand interactions. The results showed good consistency when both protein and ligand were present in the sample.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Chemistry, Multidisciplinary
Emma K. Sisley, Oliver J. Hale, James W. Hughes, Helen J. Cooper
Summary: Native ambient mass spectrometry allows for in situ analysis of proteins in tissue, providing both structural and spatial information. This study demonstrates the analysis of membrane proteins using this technique, including integral membrane proteins and membrane-associated proteins. The results show that a washing protocol can effectively remove soluble proteins without disrupting the spatial distribution of the membrane proteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Chemistry, Multidisciplinary
Yuying Du, Robin C. May, Helen J. Cooper
Summary: In this study, we demonstrated that intact non-covalent protein complexes can be directly detected from bacterial colonies growing on agar by combining electroporation with native ambient mass spectrometry. Homodimers HdeA and HdeB, as well as the 50 kDa Mn-bound superoxide dismutase homodimer, were identified, along with some previously undetected monomeric proteins.
CHEMICAL COMMUNICATIONS
(2022)