Review
Biochemical Research Methods
Qiuqin Zhou, Annabelle Fueloep, Carsten Hopf
Summary: MALDI-MSI is a rapidly growing technique for visualizing the distribution of biomolecules in tissue sections, with challenges such as sensitivity and specificity. Recent developments in small organic MALDI matrices and on-tissue chemical derivatization reagents play a crucial role in improving image quality and expanding application areas.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Review
Chemistry, Analytical
Paulina Kobylis, Piotr Stepnowski, Magda Caban
Summary: Ionic liquid matrices (ILMs) are introduced as alternatives to crystal matrices for MALDI MS analysis almost 20 years ago. They have advantages such as high homogeneity, reproducibility, reducing background, and enabling quantitative analysis. However, despite various synthesized ILMs, there are few reports on quantitative analysis using ILMs, and there is a lack of guidelines for selecting ILMs for specific tasks.
MICROCHEMICAL JOURNAL
(2021)
Review
Chemistry, Multidisciplinary
Zhi Qiao, Franziska Lissel
Summary: Researchers have overcome challenges in analyzing low molecular weight compounds using MALDI MS by adjusting sample preparation strategies and developing new matrices. These new matrices not only have high absorption and ionization efficiency, but also ensure vacuum stability and do not produce interfering signals in the low m/z region.
CHEMISTRY-AN ASIAN JOURNAL
(2021)
Review
Materials Science, Multidisciplinary
Manale Noun, Rayane Akoumeh, Imane Abbas
Summary: Mass spectrometry imaging (MSI) is a powerful technique that can reveal the spatial distribution of atomic and molecular ions on the surfaces of biological samples. MALDI-TOF and TOF-SIMS, two commonly used MSI techniques, have witnessed significant advancements in studying cells and tissue sections due to their high resolution, sensitivity, precision, and chemical specificity. This article briefly discusses the principles and sampling methods of MALDI-TOF and TOF-SIMS, while highlighting their importance as diagnostic tools and robust analytical techniques in the medicinal, pharmaceutical, and toxicology fields through representative published studies.
MICROSCOPY AND MICROANALYSIS
(2022)
Article
Biochemistry & Molecular Biology
Vanna Denti, Maria K. Andersen, Andrew Smith, Anna Mary Bofin, Anna Nordborg, Fulvio Magni, Siver Andreas Moestue, Marco Giampa
Summary: The study successfully investigated lipid alterations in patient-derived xenograft of breast cancer using MALDI MSI technology, confirming the technical reliability and effectiveness of the method. This research provides strong support for the establishment of a MALDI MSI-based workflow.
Article
Chemistry, Analytical
Margaux Fresnais, Juergen Burhenne, Walter E. Haefeli, Remi Longuespee
Summary: Desorption/ionization (DI) methods are crucial for rapid and sensitive drug quantification from solid samples. Validating these methods requires careful consideration of the specific characteristics of DI approaches compared to traditional LC-MS methods.
ANALYTICAL CHEMISTRY
(2021)
Review
Chemistry, Analytical
Quan He, Cuirong Sun, Jian Liu, Yuanjiang Pan
Summary: This article discusses the role of matrix-assisted laser desorption/ionization mass spectrometry imaging in cancer drug development and therapy, emphasizing its importance in revealing drug distribution and metabolism.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Margaux Fresnais, Esra Yildirim, Seda Karabulut, Dirk Jaeger, Inka Zoernig, Julia Benzel, Kristian W. Pajtler, Stefan M. Pfister, Jurgen Burhenne, Walter E. Haefeli, Remi Longuespee
Summary: Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been underutilized in therapeutic drug monitoring due to the complexity of ionization processes. Successful development of MALDI-MS methods requires consideration of matrix-analyte compatibility, matrix crystallization properties, and MS instrumentation. Controlling key parameters, addressing unresolved issues, and considering future perspectives are essential for establishing MALDI-MS as a universal method for drug monitoring.
Article
Food Science & Technology
Sandrine Livet, Sylvia Worbs, Herve Volland, Stephanie Simon, Martin B. Dorner, Francois Fenaille, Brigitte G. Dorner, Francois Becher
Summary: The study developed a MALDI-TOF mass spectrometry approach for fast and sensitive detection of abrin in food samples, providing a new method for analyzing the toxin.
Review
Spectroscopy
Khalil Mallah, Kazem Zibara, Coline Kerbaj, Ali Eid, Nour Khoshman, Zahraa Ousseily, Abir Kobeissy, Tristan Cardon, Dasa Cizkova, Firas Kobeissy, Isabelle Fournier, Michel Salzet
Summary: Traumatic brain injury (TBI) is a major public health concern worldwide, and the use of proteomic and lipidomic platforms has broadened our understanding of TBI-related mechanisms and neuropathological complications. This study provides an updated overview of spatially resolved microproteomics and microlipidomics approaches guided by mass spectrometry imaging in TBI studies and discusses their applications in neurotrauma research. The accurate and precise techniques of microproteomic sampling, such as laser capture microdissection, parafilm assisted microdissection, and liquid microjunction extraction, are evaluated. The potential of lipid profiling, particularly in phospholipid metabolism and proinflammatory molecules, is highlighted.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Biology
Antonella Raffo-Romero, Soulaimane Aboulouard, Emmanuel Bouchaert, Agata Rybicka, Dominique Tierny, Nawale Hajjaji, Isabelle Fournier, Michel Salzet, Marie Duhamel
Summary: Developing a robust canine mammary tumor model in the form of tumoroids has been achieved, which can replicate the diversity and heterogeneity of tumors. Canine tumoroids are a reliable drug screening model and can be cryopreserved to create a biobank.
Article
Multidisciplinary Sciences
Diego Fernando Garcia-del Rio, Tristan Cardon, Sven Eyckerman, Isabelle Fournier, Amelie Bonnefond, Kris Gevaert, Michel Salzet
Summary: Scientists used subcellular fractionation to increase information about alternative proteins (AltProts) and facilitate the detection of protein-protein interactions. A total of 112 unique AltProts were identified, with 16 identified crosslinks between AltProts and referenced proteins (RefProts). The study of the interactome and localization of AltProts reveals the importance of the ghost proteome.
Article
Cell Biology
Alice Capuz, Sylvain Osien, Melodie Anne Karnoub, Soulaimane Aboulouard, Estelle Laurent, Etienne Coyaud, Antonella Raffo-Romero, Marie Duhamel, Amelie Bonnefond, Mehdi Derhourhi, Marco Trerotola, Ikram El Yazidi-Belkoura, David Devos, Monika Zilkova, Firas Kobeissy, Fabien Vanden Abeele, Isabelle Fournier, Dasa Cizkova, Franck Rodet, Michel Salzet
Summary: Using various omics analyses, we discovered that newborn rat astrocytes produce neural immunoglobulin chains with similarities to aberrant immunoglobulins found in cancers. The complete enzymatic V(D)J recombination complex was also found in astrocytes. In addition, we identified different immunoglobulin chains in adult rat astrocytes and primary astrocytes from human fetus. These neural IgGs play a role in astrocyte fate and interact with specific targets.
CELL DEATH & DISEASE
(2023)
Article
Oncology
Eric Leblanc, Fabrice Narducci, Gwenael Ferron, Audrey Mailliez, Jean-Yves Charvolin, El Hajj Houssein, Frederic Guyon, Virginie Fourchotte, Eric Lambaudie, Agathe Crouzet, Yves Fouche, Sebastien Gouy, Pierre Collinet, Frederic Caquant, Christophe Pomel, Francois Golfier, Veronique Vaini-Cowen, Isabelle Fournier, Michel Salzet, Emmanuelle Tresch, Alicia Probst, Anne-Sophie Lemaire, Marie-Cecile Le Deley, Delphine Hudry
Summary: A two-step approach of radical fimbriectomy followed by delayed oophorectomy appears to be a safe and well-tolerated method for reducing the risk of ovarian cancer in high-risk women, avoiding surgery-induced early menopause.
Article
Chemistry, Analytical
Khawla Seddiki, Frederic Precioso, Melissa Sanabria, Michel Salzet, Isabelle Fournier, Arnaud Droit
Summary: Liquid chromatography-mass spectrometry (LC-MS) is a powerful method for cell profiling in cancer research. However, the presence of noise, peak shifts, and high dimensionality of the data make early cancer diagnosis challenging. This study proposes an end-to-end deep learning methodology that addresses these challenges and preserves the potential of LC-MS data.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Dimitrios Diamantis, Antonios D. Tsiailanis, Christina Papaemmanouil, Maria-Christina Nika, Zoi Kanaki, Simona Golic Grdadolnik, Andrej Babic, Eleftherios Paraskevas Tzakos, Isabelle Fournier, Michel Salzet, Prem Prakash Kushwaha, Nikolaos S. Thomaidis, Theodoros Rampias, Eswar Shankar, Serdar Karakurt, Sanjay Gupta, Andreas G. Tzakos
Summary: A novel prodrug approach was developed to inhibit cancer progression by targeting alkaline phosphatase (ALP) in the tumor microenvironment (TME). The prodrug, phospho-apigenin, increased the stability of apigenin and showed enhanced antiproliferative effect in malignant cells with elevated ALP levels compared to apigenin alone. In vivo experiments also demonstrated its significant tumor growth suppression.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Correction
Cell Biology
Alice Capuz, Sylvain Osien, Tristan Cardon, Melodie Anne Karnoub, Soulaimane Aboulouard, Antonella Raffo-Romero, Marie Duhamel, Dasa Cizkova, Marco Trerotola, David Devos, Firas Kobeissy, F. Vanden Abeele, Amelie Bonnefond, Isabelle Fournier, Franck Rodet, Michel Salzet
CELL DEATH & DISEASE
(2023)
Article
Cell Biology
Alice Capuz, Sylvain Osien, Tristan Cardon, Melodie Anne Karnoub, Soulaimane Aboulouard, Antonella Raffo-Romero, Marie Duhamel, Dasa Cizkova, Marco Trerotola, David Devos, Firas Kobeissy, Fabien van den Abelle, Amelie Bonnefond, Isabelle Fournier, Franck Rodet, Michel Salzet
Summary: The dogma of one gene, one protein is outdated as cells use alternative splicing, alternative translation initiation sites, and alternative termination sites to generate multiple protein isoforms. Recent studies have shown that some non-coding RNAs can actually be translated into proteins. This article presents a longitudinal proteomic study on rat spinal cord injury (SCI) and identifies a plethora of newly predicted protein hits. Among these proteins, one with high homology to immunoglobulin Kappa variable light chains, named Heimdall, is expressed in astrocytes and may play a role in regulating their fate.
CELL DEATH & DISEASE
(2023)
Article
Biochemical Research Methods
Diego Fernando Garcia-del Rio, Isabelle Fournier, Tristan Cardon, Michel Salzet
Summary: This study presents a protocol for identifying human subcellular AltProts and deciphering their interactions using cross-linking mass spectrometry. The protocol includes steps for cell culture, in cellulo cross-linking, subcellular extraction, and sequential digestion, as well as liquid chromatography-tandem mass spectrometry and cross-link data analyses. The implementation of this workflow allows for the non-targeted identification of signaling pathways involving AltProts.
Review
Oncology
Andreas Bikfalvi, Cristine Alves da Costa, Tony Avril, Jean-Vianney Barnier, Luc Bauchet, Lucie Brisson, Pierre Francois Cartron, Helene Castel, Eric Chevet, Herve Chneiweiss, Anne Clavreul, Bruno Constantin, Valerie Coronas, Thomas Daubon, Monique Dontenwill, Francois Ducray, Natacha Entz-Werle, Dominique Figarella-Branger, Isabelle Fournier, Jean-Sebastien Frenel, Mathieu Gabut, Thierry Galli, Julie Gavard, Gilles Huberfeld, Jean-Philippe Hugnot, Ahmed Idbaih, Marie-Pierre Junier, Thomas Mathivet, Philippe Menei, David Meyronet, Celine Mirjolet, Fabrice Morin, Jean Mosser, Elisabeth Cohen-Jonathan Moyal, Veronique Rousseau, Michel Salzet, Marc Sanson, Giorgio Seano, Emeline Tabouret, Aurelie Tchoghandjian, Laurent Turchi, Francois M. Vallette, Somya Vats, Maite Verreault, Thierry Virolle
Summary: Glioblastoma (GBM) is a highly lethal brain tumor, and recent studies have emphasized the importance of the tumor microenvironment (TME) as a therapeutic target. However, a comprehensive understanding of the different cellular and molecular components involved in the GBM TME and their interactions is still needed for the development of more effective treatments. This review presents a comprehensive report on the GBM TME, combining the contributions of researchers and physicians in France, and provides a holistic view of the subject by describing the specific features of the GBM TME at the cellular, molecular, and therapeutic levels.
Article
Endocrinology & Metabolism
Lise Folon, Morgane Baron, Benedicte Toussaint, Emmanuel Vaillant, Mathilde Boissel, Victoria Scherrer, Helene Loiselle, Audrey Leloire, Alaa Badreddine, Beverley Balkau, Guillaume Charpentier, Sylvia Franc, Michel Marre, Soulaimane Aboulouard, Michel Salzet, Mickael Canouil, Mehdi Derhourhi, Philippe Froguel, Amelie Bonnefond
Summary: Rare biallelic pathogenic mutations in PCSK1 cause early-onset obesity and other endocrinopathies. Functional genomic study shows that rare heterozygous variants of PCSK1 can also impact obesity risk.
LANCET DIABETES & ENDOCRINOLOGY
(2023)
Article
Biochemical Research Methods
Saranya Krishnan, Shina Sasi, Preshobha Kodakkattumannil, Salima Al Senaani, Geetha Lekshmi, Martin Kottackal, Khaled M. A. Amiri
Summary: This study aimed to develop an efficient DNA extraction protocol suitable for diverse plant species and tissues. A reliable and consistent protocol was described for the extraction of high-quality DNA from difficult-to-extract plant species. The optimized protocol was successful in extracting high-quality DNA from various plant species and tissues, making it useful for genomic studies of recalcitrant plants.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Eisaku Hokazono, Saori Fukumoto, Takeshi Uchiumi, Susumu Osawa
Summary: This study proposes a method for detecting nucleic acid amplification using pyrophosphate, which requires only two reagents and an automated analyzer. The technique has high sensitivity and reproducibility, and can detect pyrophosphate within 10 minutes. Therefore, this method has the potential to be a new, rapid, and simple detection technique for amplified nucleic acids.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Drew S. Sowersby, L. Kevin Lewis
Summary: SURE electrophoresis is a new method for concentrating samples in gels, which allows efficient detection of highly dilute DNA samples. This approach generates single bands with enhanced signal intensities and minimal band broadening.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Hongyi Liang, Guoliang Yin, Guangxi Shi, Zhiyong Liu, Xiaofei Liu, Jingwei Li
Summary: The mechanism of Echinacoside (ECH) in treating breast cancer (BC) was explored through network pharmacology and experimental validation. It was found that ECH plays an important role in anti-BC by regulating the PI3K/AKT/HIF-1 alpha/VEGF signaling pathway, and it exhibits multi-target and multi-pathway effects.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Daniel S. Kantner, Emily Megill, Anna Bostwick, Vicky Yang, Carmen Bekeova, Alexandria Van Scoyk, Erin L. Seifert, Michael W. Deininger, Nathaniel W. Snyder
Summary: This study compared the results of different methods for measuring the amount of acetyl-Coenzyme A. The colorimetric ELISA kit did not produce interpretable results, while the fluorometric enzymatic kit showed comparable results to the LC-MS-based methods depending on the matrix and extraction conditions. LC-MS/MS and LC-HRMS methods produced well-aligned results, especially when using stable isotope-labeled internal standards.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Jingyan Xu, Hanying Tan, Xionghui Ma, Linjing Su, Zhi Zhang, Yuhao Xiong
Summary: This study investigates the co-catalytic capabilities of MoO3 nanosheets in enhancing the enzyme-like catalytic activity of a two-dimensional ultrathin Fe(III)-modified covalent triazine framework (Fe-CTF) under neutral pH conditions. The Fe-CTF/MoO3 co-catalytic system exhibits enzyme-mimicking activity and enables the development of a colorimetric method for glucose detection. Furthermore, a straightforward one-pot colorimetric method is established for screening XOD inhibitors.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Lichao Zhang, Kang Xiao, Xueting Wang, Liang Kong
Summary: A novel fusion technology was designed to identify FAD-binding sites, achieving the best results on two independent test datasets and outperforming existing methods significantly. The high performance and certainty of the method were demonstrated through statistical tests and cross-entropy loss analysis.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Abdulkadir Kilic, Mehmet Aslan, Abdulkadir Levent
Summary: This study developed a simple, rapid, sensitive, and selective voltammetric technique for the electrochemical characterization and detection of the highly risky drug Edoxaban. The optimized voltammetric method showed good analytical working range and was successfully applied to urine and tablet samples.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Su Hyun Kim, Nara Shin, Jong-Min Jeon, Jeong-Jun Yoon, Jeong Chan Joo, Hee Taek Kim, Shashi Kant Bhatia, Yung-Hun Yang
Summary: To address environmental issues caused by traditional plastics, bioplastics have gained attention as alternatives. Although bioplastics have better degradability, their degradation still takes longer than anticipated. This study proposes a novel screening method to identify bioplastic degraders faster, saving time and providing more quantitative data.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Irem Okman Kocoglu, Pinar Esra Erden, Esma Kilic
Summary: In this study, an electrochemical biosensor based on carbon nanofibers and ionic liquid modification was constructed for tyramine detection. The biosensor showed linear response, low detection limit, high sensitivity, and exhibited good reproducibility, stability, and anti-interference ability.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Liana U. Akhmetzianova, Timur M. Davletkulov, Assol R. Sakhabutdinova, Alexey Chemeris, Irek M. Gubaydullin, Ravil R. Garafutdinov
Summary: A new program called LAMPrimers iQ has been developed for high-quality LAMP primer design, and its advantages in providing higher specificity and reliable detection of viral RNA were validated using SARS-CoV-2 coronavirus RNA as a model target.
ANALYTICAL BIOCHEMISTRY
(2024)
Article
Biochemical Research Methods
Tommaso Pileri, Alberto Sinibaldi, Agostino Occhicone, Norbert Danz, Elena Giordani, Matteo Allegretti, Frank Sonntag, Peter Munzert, Patrizio Giacomini, Francesco Michelotti
Summary: This study developed a biosensing device based on one-dimensional photonic crystal to detect HER2 in breast cancer. The device combines label-free and fluorescence operation modes, allowing for real-time and accurate detection in less than 20 minutes. It offers a promising technique for combined label-free and fluorescence detection in disease diagnosis and therapeutic monitoring.
ANALYTICAL BIOCHEMISTRY
(2024)
