Article
Biochemical Research Methods
Masato Taoka, Kota Kamei, Akiko Kashima, Yuko Nobe, Takahiro Takekiyo, Takamasa Uekita, Tohru Ichimura
Summary: Many ion channels and receptor proteins are potential targets for new drugs. This study presents a novel proteomic sample preparation platform that allows for the processing of sub-microgram level starting materials using an ionic liquid-based sample preparation strategy and an in-StageTip technique. This approach enables the rapid solubilization and analysis of integral membrane proteins from human samples, surpassing the performance of conventional methods.
ANALYTICAL BIOCHEMISTRY
(2023)
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: In this study, native mass spectrometry (MS) and fast photochemical oxidation of peptides (FPOP) were used to investigate the interactions between the antibiotic daptomycin and different lipid bilayer nanodiscs. The results showed that daptomycin incorporates randomly into bilayers and has stronger interactions with rigid membranes. Pore formation may occur in fluid membranes, exposing daptomycin to oxidation. These findings demonstrate the complementarity of native MS, FPOP, and membrane conductance experiments in understanding antibiotic peptide-membrane interactions.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Harvey E. Johnston, Kranthikumar Yadav, Joanna M. Kirkpatrick, George S. Biggs, David Oxley, Holger B. Kramer, Rahul S. Samant
Summary: Complete and reproducible extraction of protein is crucial for proteome analysis. Solvent precipitation SP3 (SP4) is proposed as an alternative method, which captures protein aggregates by centrifugation instead of magnetism. SP4 provides equivalent or higher protein yields and improved reproducibility. It also recovers more low-solubility and transmembrane proteins, offering higher recovery rates.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Corinne A. Lutomski, Tarick J. El-Baba, Joshua D. Hinkle, Idlir Liko, Jack L. Bennett, Neha V. Kalmankar, Andrew Dolan, Carla Kirschbaum, Kim Greis, Leonhard H. Urner, Parth Kapoor, Hsin-Yung Yen, Kevin Pagel, Christopher Mullen, John E. P. Syka, Carol V. Robinson
Summary: By using an infrared laser in a high-pressure linear ion trap, researchers were able to remove detergent micelles and obtain good sequence coverage for membrane proteins and their complexes through top-down mass spectrometry.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Analytical
Joao Raul Belinato, Vinicius Ricardo Acquaro, Luciana Teresa Dias Cappelini, Fabio Augusto
Summary: The interest in bioactive compounds from microorganisms has increased since the first discovery, with microorganisms being a key source of biomolecules with diverse applications. While conventional sample preparation techniques are still widely used, microextraction techniques show promise in overcoming limitations and promoting a deeper understanding of complex systems and the discovery of new molecules.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Noortje de Haan, Ming Song, Oliver C. Grant, Zilu Ye, Fawzi Khoder Agha, Mikkel Koed Moller Aasted, Robert J. Woods, Sergey Y. Vakhrushev, Hans H. Wandall
Summary: Cell surface glycans play a crucial role in cell communication, adhesion, and migration. However, obtaining specific information about the structures of glycoproteins on the cell surface remains a challenge. In this study, we developed a new method to analyze the N-glycoprotein forms expressed on the cell surface, allowing us to study their functional role in cell processes.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Fujia Wang, Tim Veth, Marije Kuipers, Maarten Altelaar, Kelly E. Stecker
Summary: A successful mass spectrometry-based phosphoproteomics analysis relies on effective sample preparation strategies. The performance of the S-Trap protocol for phosphoproteomics studies is unclear, and the addition of phosphoric acid (PA) in the existing protocol is detrimental to downstream phosphopeptide enrichment. This study systematically evaluates the performance of the S-Trap digestion for proteomics and phosphoproteomics, and demonstrates that an optimized S-Trap approach, with trifluoroacetic acid substituted for PA, is a simple and effective method for phosphoproteomics sample preparation.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Fenglin Shen, Yueting Xiong, Lei Zhang, Hengchao Li, Huanhuan Zhao, Xiaohui Liu, Pengyuan Yang
Summary: A new rapid and simple sample preparation method was developed for serum proteomic studies, allowing for efficient identification of multiple proteins in under 2 hours. This method has the potential to accelerate biomarker discovery and clinical application in serum protein research.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Runsheng Zheng, Natalia Govorukhina, Tabiwang N. Arrey, Christopher Pynn, Ate van der Zee, Gyorgy Marko-Varga, Rainer Bischoff, Alexander Boychenko
Summary: This study compares 1D-nanoLC-MS with an automated online-2D high-pH RP x low pH RP separation method for deep proteome profiling, demonstrating that the new method can increase peptide and protein identifications without the need for extra sample handling. Serum sample preparation related changes were revealed, which should be taken into account when planning multicentric biomarker discovery and validation studies.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
John B. Coulton, James L. Edwards
Summary: The sample preparation technique described in the study involves online filter-assisted electroporation-based cell lysis and chilled organic solvent extraction for rapid preparation of metabolomic samples from suspended cells. By using isotopically labeled internal standards and C-13-glucose labeling experiments, the method ensures enzymatic quenching and successful incorporation of C-13 into organic acid metabolites. Analysis by nano-reverse-phase liquid chromatography-mass spectrometry (nano-RP-LC-MS) demonstrates the effectiveness of the technique in studying metabolites such as itaconate.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Yen -Chen Liao, James M. Fulcher, David J. Degnan, Sarah M. Williams, Lisa M. Bramer, Dusan Velickovic, Kevin J. Zemaitis, Marija Velickovic, Ryan L. Sontag, Ronald J. Moore, Ljiljana Pasa-Tolic, Ying Zhu, Mowei Zhou
Summary: Conventional proteomic approaches cannot accurately measure signals from sub-populations of cells, while recent developments in bottom-up proteomics enable spatial mapping of cellular heterogeneity. However, bottom-up proteomics cannot define and quantify intact forms of proteins capturing genetic variations and posttranslational modifications. A spatially resolved top-down proteomics (TDP) platform is described, which allows direct identification and quantitation of proteoforms from tissue sections. This platform consists of a nanodroplet processing system for sample preparation and a laser capture microdissection-based cell isolation system. The improved sample preparation method enhances the coverage of nuclear proteins. The TDP platform has potential for biomarker discovery at the proteoform level from small tissue sections.
MOLECULAR & CELLULAR PROTEOMICS
(2023)
Article
Chemistry, Analytical
Durga Devi Khanal, Sajad Tasharofi, Mohammadmehdi Azizi, Morteza G. Khaledi
Summary: The new supramolecular biphasic systems containing fluoroalcohol-induced coacervates (FAiC) offer concomitant fractionation and high solubilizing power for proteins, especially membrane proteins, leading to enrichment of low-abundance proteins. When used in bottom-up proteomics workflow, these systems significantly increase coverage of the whole proteome, various subproteomes, post-translationally modified proteins, and low-abundance proteins compared to conventional methodologies, with a particular impact on integral membrane proteins and proteins with alpha-helices.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Tanja Bien, Sebastian Bessler, Klaus Dreisewerd, Jens Soltwisch
Summary: Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has the potential to visualize the spatial distribution of biomolecules in cell cultures and tissue sections with high resolution, but sample preparation is crucial. A study found that a robust sample preparation protocol can preserve cell morphology and molecular integrity, contributing to the study of cell-to-cell heterogeneities at a molecular level. Advancements in single-cell MALDI imaging could benefit from these protocols.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Lianlian Ma, Qingrong Xie, Mingyi Du, Yudi Huang, Yingying Chen, Dong Chen, Yizhu Xu, Hanhong Xu, Xinzhou Wu, Zhibin Yin
Summary: This study systematically investigated the optimized sample preparation conditions for insects and model organisms in mass spectrometry imaging (MSI), providing guidelines for MSI analysis and expanding its potential in life sciences and environmental sciences.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Multidisciplinary
Andres Machuca, Estefania Garcia-Calvo, Daniela S. Anunciacao, Jose L. Luque-Garcia
CHEMISTRY-A EUROPEAN JOURNAL
(2020)
Article
Microbiology
Hector Estevez, Ainhoa Palacios, David Gil, Juan Anguita, Maria Vallet-Regi, Blanca Gonzalez, Rafael Prados-Rosales, Jose L. Luque-Garcia
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Gastroenterology & Hepatology
Leyre Mestre, Francisco J. Carrillo-Salinas, Ana Feliu, Miriam Mecha, Graciela Alonso, Carmen Espejo, Laura Calvo-Barreiro, Jose L. Luque-Garcia, Hector Estevez, Luisa Maria Villar, Carmen Guaza
Article
Environmental Sciences
E. Garcia-Calvo, P. Cabezas-Sanchez, J. L. Luque-Garcia
Summary: The widespread use of quantum dots has led to potential emerging contaminants, necessitating evaluation of their potential toxicity and impact. Studies have shown that CdSe/ZnS quantum dots induce hypoxia and ROS generation in hepatic cells, leading to apoptosis through the TDP-43 pathway, as well as causing serious neural and developmental problems in developing organisms.
Article
Food Science & Technology
Estefania Garcia-Calvo, Andres Machuca, Cristina Nerin, Noelia Rosales-Conrado, Daniela S. Anunciacao, Jose L. Luque-Garcia
FOOD AND CHEMICAL TOXICOLOGY
(2020)
Article
Multidisciplinary Sciences
Silvia Perez-Perez, Maria Inmaculada Dominguez-Mozo, Aitana Alonso-Gomez, Silvia Medina, Noelia Villarrubia, Jose Ignacio Fernandez-Velasco, Maria Angel Garcia-Martinez, Estefania Garcia-Calvo, Hector Estevez, Lucienne Costa-Frossard, Jose C. Alvarez-Cermeno, Jose L. Luque-Garcia, Rafael Arroyo, Luisa M. Villar, Roberto Alvarez-Lafuente
Article
Pharmacology & Pharmacy
Hector Estevez, Estefania Garcia-Calvo, Jose Rivera-Torres, Maria Vallet-Regi, Blanca Gonzalez, Jose L. Luque-Garcia
Summary: The study identified new targets and pathways related to the antitumor mechanisms of chitosan-stabilized Se nanoparticles (Ch-SeNPs) through a global transcriptome analysis, confirming alterations in the cell cycle and effects on tumor suppressors. Additionally, the antioxidant properties and ability of Ch-SeNPs to induce senescence were demonstrated.
Article
Pharmacology & Pharmacy
Andres Machuca, Estefania Garcia-Calvo, Daniela S. Anunciacao, Jose L. Luque-Garcia
Summary: Rhodium nanoparticles have been described as promising photosensitizers due to their low toxicity in the absence of near-infrared irradiation, but high cytotoxicity when irradiated. The multi-omics approach in this study revealed that these nanoparticles promote apoptosis by affecting the energy machinery of tumor cells and blocking beta-oxidation, leading to accumulation of free fatty acids and decrease in ATP, ADP and NAD+ levels.
Article
Chemistry, Multidisciplinary
Guillermo Aragoneses-Cazorla, M. Pilar Buendia-Nacarino, Maria L. Mena, Jose L. Luque-Garcia
Summary: Silver nanoparticles (AgNPs) are widely used, but their potential toxicity has raised concerns. This study combines metabolomics and transcriptomics to investigate the molecular mechanisms of toxicity induced by 10 nm AgNPs. The results show that AgNPs affect cellular antioxidant defense and energy metabolism.
Article
Chemistry, Analytical
Guillermo Aragoneses-Cazorla, Maria Vallet-Regi, Ma. Milagros Gomez-Gomez, Blanca Gonzalez, Jose L. Luque-Garcia
Summary: A combination of transcriptomics and metabolomics was used to study the mechanisms behind the antitumor action of a nanosystem called Ag@MSNs-Tf. Transcriptomics analysis was done using gene microarrays and RT-qPCR, while metabolomics analysis was done using high-resolution mass spectrometry. This multiomics approach revealed the impact of the nanosystem on various molecular pathways, including glycolysis, the pentose phosphate pathway, oxidative phosphorylation, and fatty acid synthesis.
Editorial Material
Biology
Jose L. Luque-Garcia, Rafael Prados-Rosales
Article
Chemistry, Inorganic & Nuclear
Guillermo Aragoneses-Cazorla, Juana Serrano-Lopez, Ines Martinez-Alfonzo, Maria Vallet-Regi, Blanca Gonzalez, Jose L. Luque-Garcia
Summary: The study developed a novel nanosystem for targeted cancer therapy, demonstrating selective internalization and cytotoxic potential in cancer cells without activating monocytes or inducing platelet aggregation, supporting its potential future clinical applicability.
INORGANIC CHEMISTRY FRONTIERS
(2021)
Meeting Abstract
Clinical Neurology
S. Perez-Perez, J. P. Cuello, M. Martinez-Gines, B. Pardo-Rodriguez, J. M. Garcia-Dominguez, M. I. Dominguez-Mozo, A. Lozano-Ros, M. A. Garcia-Martinez, Y. Higueras, E. Garcia-Calvo, A. Meldana-Rivera, H. Estevez, H. Goicochea-Briceno, A. Tejeda-Velarde, J. I. Fernandez-Velasco, S. Medina, J. L. Luque-Garcia, R. Arroyo, L. M. Villar, R. Alvarez-Lafuente
MULTIPLE SCLEROSIS JOURNAL
(2019)