Article
Chemistry, Analytical
Na Wu, Lingyi Jiao, Matthias Butikofer, Zhihui Zeng, Renato Zenobi
Summary: This study successfully utilized commercially available purified proteins as internal standards for high-mass MALDI-MS analysis, achieving absolute quantification of various high-mass analytes. By systematically evaluating four sample deposition methods and using a sandwich deposition method with saturated sinapinic acid, robust quantitative analysis by high-mass MALDI-MS was performed. Furthermore, combining this quantitative strategy with chemical cross-linking allowed for evaluation of the affinity of protein-protein interactions, providing dissociation constants between 10 nM and 5 mu M for the protein complexes formed.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Applied
Jeremy Manheim, Mingxiang Lin, John Kong, Mirlinda Biba, Ping Zhuang
Summary: This study successfully differentiated and quantified isomeric pneumococcal polysaccharides using a partial chemical degradation mass spectrometry approach. The results demonstrated high precision and robustness of this method.
CARBOHYDRATE POLYMERS
(2022)
Article
Chemistry, Analytical
Wassim Gabriel, Matthew The, Daniel P. Zolg, Florian P. Bayer, Omar Shouman, Ludwig Lautenbacher, Karsten Schnatbaum, Johannes Zerweck, Tobias Knaute, Bernard Delanghe, Andreas Huhmer, Holger Wenschuh, Ulf Reimer, Guillaume Medard, Bernhard Kuster, Mathias Wilhelm
Summary: The accurate prediction of fragment ion intensities and retention time for peptides has been a topic of significant interest, particularly for unlabeled peptides. In this study, a comprehensive resource of synthetic TMT-labeled peptides was generated as part of the ProteomeTools project, and the deep learning model Prosit was extended to accurately predict the retention time and fragment ion intensities of TMT-labeled peptides with high accuracy.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Frederic Dewez, Edwin De Pauw, Ron M. A. Heeren, Benjamin Balluff
Summary: The multilabel approach in quantitative mass spectrometry imaging provides more accurate quantitation compared to a single-label approach, particularly when the target compound is unevenly distributed at a wide concentration range in the tissue.
ANALYTICAL CHEMISTRY
(2021)
Article
Plant Sciences
Wiebke Hanke, Julian Patt, Judith Alenfelder, Jan H. Voss, Mitja M. Zdouc, Stefan Kehraus, Jung Bong Kim, Goran Grujicic, Vigneshwaran Namasivayam, Raphael Reher, Christa E. Mueller, Evi Kostenis, Max Cruesemann, Gabriele M. Koenig
Summary: This study investigated and compared the metabolomes of two FR producers using feature-based molecular networking, leading to the discovery of 30 previously unknown FR derivatives, with one-third being unique to C. vaccinii. A novel FR derivative, FR-6, was isolated and confirmed to effectively suppress G(q) signaling. This work demonstrates the power of molecular networking in guiding the discovery of novel G(q)-inhibiting FR derivatives.
JOURNAL OF NATURAL PRODUCTS
(2021)
Article
Biochemical Research Methods
Christine C. Ghetu, Richard P. Scott, Glenn Wilson, Rachel Liu-May, Kim A. Anderson
Summary: An expanded analytical method was introduced to distinguish between sources of PAHs, with the addition of alkylated series and evaluation of forensic ratios accurately predicting the sources of PAHs.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Sule Yilmaz, Florian Busch, Nagarjuna Nagaraj, Juergen Cox
Summary: Researchers have developed a novel computational proteomics workflow called MaxLynx for analyzing cross-linking combined with mass spectrometry (XL-MS) data, which has shown better performance in testing.
ANALYTICAL CHEMISTRY
(2022)
Review
Biochemical Research Methods
Zainab Noor, Seong Beom Ahn, Mark S. Baker, Shoba Ranganathan, Abidali Mohamedali
Summary: Accurate protein identification is crucial in proteomics, with mass spectrometry being the primary technique used. Understanding data generation and parameters used in computational tools is essential for proper protein identification. Bioinformatics and computational methodologies are also important for validating protein identification in proteomics.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Alejandro Heres, Marta Gallego, Leticia Mora, Fidel Toldra
Summary: Reducing salt in meat products can affect the natural mechanisms of proteolysis, leading to changes in texture and flavor. This study quantified the presence of dipeptides in low-salt Spanish dry-cured ham using mass spectrometry. The results showed a correlation between these dipeptides and taste attributes, as well as potential health benefits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Medical Laboratory Technology
Shin Aleks, Connolly Shawn, Little Randie, Kabytaev Kuanysh
Summary: This study developed an assay for absolute quantitation of glycated albumin based on isotope dilution liquid chromatography-mass spectrometry. The method showed good analytical performance with a linear correlation between LC-MS/MS and Lucica method. This approach allows simultaneous quantitation of glycated and non-glycated peptides.
CLINICA CHIMICA ACTA
(2021)
Article
Plant Sciences
Yuki Hayashi, Yohei Takahashi, Kohei Fukatsu, Yasuomi Tada, Koji Takahashi, Keiko Kuwata, Takamasa Suzuki, Toshinori Kinoshita
Summary: In guard-cell protoplasts (GCPs) from Vicia faba, an unknown 61 kDa protein is phosphorylated by ABA-activated protein kinase, which binds to 14-3-3 protein in a phosphorylation-dependent manner. ABA-dependent phosphorylated proteins known as AKSs were identified in Arabidopsis thaliana GCPs, but the identity of the 61 kDa protein in Vicia GCPs as an AKS was uncertain. Mass spectrometry analysis revealed several AKS isoforms (VfAKSs) in V. faba, with the 61 kDa protein being identified as VfAKS1, showing the importance of phosphorylation in response to ABA. Co-immunoprecipitation studies also identified interactions between 14-3-3 protein and orthologs of AtABCG40 and CHC1 in guard cells.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Biochemical Research Methods
Vilmos Kertesz, John F. Cahill
Summary: Mass spectrometry has become the primary tool for routine quantitative analysis of biomolecules, and is increasingly used to reveal the spatial distribution of proteins, metabolites, and pharmaceuticals in tissue. However, most spatially resolved MS measurements are qualitative due to potential biases. As demand for quantitative MS imaging and profiling data increases in pharmacological and clinical fields, various technologies now exist to provide different levels of spatial and quantitative information.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Minmin Li, Yuting Xiong, Yuchen Cao, Chen Zhang, Yuting Li, Hanwen Ning, Fan Liu, Han Zhou, Xiaonong Li, Xianlong Ye, Yue Pang, Jiaming Zhang, Xinmiao Liang, Guangyan Qing
Summary: The structural complexity of glycans poses a significant challenge to existing analytical methods. In this study, the authors use a glycan derivatization strategy and nanopore sensing to identify glycan isomers, glycans with varying chain lengths, and distinct branched glycans. The structural complexity of glycans arises from the diversities in composition, linage, configuration, and branching, making structural analysis complicated.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Eduardo A. De la Toba, Sara E. Bell, Elena Romanova, Jonathan Sweedler
Summary: Neuropeptides play important roles in physiological processes and diseases. Mass spectrometry has become a powerful tool for quantitatively measuring neuropeptides, but there are challenges to overcome. This review provides an overview of mass spectrometry-based measurement approaches for neuropeptides and discusses techniques to address the challenges.
ANNUAL REVIEW OF ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Goksu Ozcelikay, Ahmet Cetinkaya, Esen Bellur Atici, Sibel A. Ozkan
Summary: In this study, an electroanalytical quantification method for sugammadex was developed using molecular imprinting via the electropolymerization technique. The EP-MIP(SUG)/SPAuE sensor exhibited high sensitivity and specificity/selectivity, as demonstrated by its ability to detect sugammadex in biological fluids and differentiate it from similar molecules. The EP-MIP(SUG)/SPAuE sensor showed good analytical performance and validation parameters according to ICH guidelines, making it a promising tool for quantitative analysis of sugammadex in various samples.
ANALYTICAL METHODS
(2023)
Article
Biochemical Research Methods
Guadalupe Espadas, Julia Morales-Sanfrutos, Rebeca Medina, Morghan C. Lucas, Eva Maria Novoa, Eduard Sabido
Summary: The article presents a new analytical method for the identification and quantification of modified ribonucleosides. The method combines mixed-mode nano-flow liquid chromatography column with high-and low-collision energy data-independent mass spectrometry, allowing the identification of various modified nucleosides in biological matrices.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Biochemistry & Molecular Biology
Neus Mestre-Farras, Santiago Guerrero, Nadine Bley, Ezequiel Rivero, Olga Coll, Eva Borras, Eduard Sabido, Alberto Indacochea, Carlos Casillas-Serra, Aino Jarvelin, Baldomero Oliva, Alfredo Castello, Stefan Huettelmaier, Fatima Gebauer
Summary: In this study, the melanoma RBPome was characterized using RNA interactome capture (RIC), leading to the discovery of novel RBPs involved in melanoma progression. Functional validation revealed unexpected roles of RBPs in melanoma malignancy. PDIA6, an ER-lumen chaperone, was identified as one of the RBPs involved in metastatic progression and its RNA-binding activity was found to be required for its tumorigenic properties. These findings demonstrate the potential of RIC technologies in uncovering novel vulnerabilities of cancer cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Ecology
Xavier Grau-Bove, Cristina Navarrete, Cristina Chiva, Thomas Pribasnig, Meritxell Anto, Guifre Torruella, Luis Javier Galindo, Bernd Franz Lang, David Moreira, Purificacion Lopez-Garcia, Inaki Ruiz-Trillo, Christa Schleper, Eduard Sabido, Arnau Sebe-Pedros
Summary: This study combines comparative proteomics and genomics analysis to explore the evolutionary history of eukaryotic chromatin in archaea and eukaryotes. The research reveals the existence of histone post-translational modifications in archaea, though they are scarce compared to the highly conserved and abundant marks found in eukaryotes. The study also suggests that chromatin-associated catalytic functions have pre-eukaryotic origins, while histone mark readers and chaperones are innovations in eukaryotes.
NATURE ECOLOGY & EVOLUTION
(2022)
Article
Biochemical Research Methods
Melisa Gualdron-Lopez, Miriam Diaz-Varela, Gigliola Zanghi, Iris Aparici-Herraiz, Ryan W. J. Steel, Carola Schafer, Pol Cusco, Vorada Chuenchob, Niwat Kangwangransan, Zachary P. Billman, Tayla M. Olsen, Juan R. Gonzalez, Wanlapa Roobsoong, Jetsumon Sattabongkot, Sean C. Murphy, Sebastian A. Mikolajczak, Eva Borras, Eduard Sabido, Carmen Fernandez-Becerra, Erika L. Flannery, Stefan H. Kappe, Hernando A. del Portillo
Summary: This study identified parasite and human proteins associated with extracellular vesicles (EVs) secreted from in vivo infections exclusively containing hypnozoites. This provides a foundation for understanding the biological features of hypnozoite infection and identifying associated biomarkers.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemical Research Methods
Devon Kohler, Maanasa Kaza, Cristina Pasi, Ting Huang, Mateusz Staniak, Dhaval Mohandas, Eduard Sabido, Meena Choi, Olga Vitek
Summary: Liquid chromatography coupled with bottom-up mass spectrometry (LC-MS/MS)-based proteomics is a versatile technology for identifying and quantifying proteins in complex biological mixtures. To make the statistical methods in MSstats accessible to users with limited programming and statistical background, an R-Shiny graphical user interface (GUI) called MSstatsShiny has been created, providing a point and click analysis pipeline applicable to a wide variety of proteomics experimental types.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Medicine, Research & Experimental
Melissa Bradbury, Eva Borras, Marta Vilar, Josep Castellvi, Jose Luis Sanchez-Iglesias, Assumpcio Perez-Benavente, Antonio Gil-Moreno, Anna Santamaria, Eduard Sabido
Summary: A new strategy has been established in this study, combining molecular and clinical parameters to predict the response to first-line treatment in high-grade serous carcinoma (HGSC) patients at the time of diagnosis. This strategy can improve therapeutic decision-making and assess alternative treatment strategies, contributing to the advancement of patient outcomes and personalized care for HGSC patients.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Multidisciplinary Sciences
Lea Maitre, Mariona Bustamante, Carles Hernandez-Ferrer, Denise Thiel, Chung-Ho E. Lau, Alexandros Siskos, Marta Vives-Usano, Carlos Ruiz-Arenas, Dolors Pelegri-Siso, Oliver Robinson, Dan Mason, John Wright, Solene Cadiou, Remy Slama, Barbara Heude, Maribel Casas, Jordi Sunyer, Eleni Z. Papadopoulou, Kristine B. Gutzkow, Sandra Andrusaityte, Regina Grazuleviciene, Marina Vafeiadi, Leda Chatzi, Amrit K. Sakhi, Cathrine Thomsen, Ibon Tamayo, Mark Nieuwenhuijsen, Jose Urquiza, Eva Borras, Eduard Sabido, Ines Quintela, Angel Carracedo, Xavier Estivill, Muireann Coen, Juan R. Gonzalez, Hector C. Keun, Martine Vrijheid
Summary: Environmental exposures during early life have a significant impact on lifelong health, but the molecular effects underlying these exposures are poorly understood. In the HELIX project, researchers investigate the associations between individual exposomes and multi-omics profiles in a cohort of 1301 mother-child pairs. The findings reveal potential biological responses and sources of exposure, with pregnancy exposures primarily affecting child DNA methylation changes and childhood exposures affecting features across multiple omics layers, such as the serum metabolome.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
Mireia Ortega, Ilario De Toma, Alvaro Fernandez-Blanco, Anna Calderon, Lucia Barahona, Ramon Trullas, Eduard Sabido, Mara Dierssen
Summary: This study found that Dyrk1A overexpression affects oxidative phosphorylation and mitochondrial function in the cerebellum, and the EGCG in green tea extract can partially restore these changes.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Biology
Evelyn Andrades, Agusti Toll, Gustavo Deza, Sonia Segura, Ramon Gimeno, Guadalupe Espadas, Eduard Sabido, Noemi Haro, Oscar Pozo, Marta Bodalo, Paloma Torres, Ramon M. Pujol, Inmaculada Hernandez-Munoz
Summary: This study analyzed the role of extracellular matrix and intravascular non-coding small RNAs in the metastasis of cutaneous squamous cell carcinoma (cSCC). The study found that metastatic cSCCs showed reduced expression of small nucleolar RNAs and progressive loss of Dyskerin, which triggered disruption of lipid metabolism and acquisition of metastatic traits. Treatment of Dyskerin-depleted cells with Shimastatin, an inhibitor of the mevalonate pathway, blocked the expression of proteins related to epithelial-to-mesenchymal transition. These findings highlight the importance of mevalonate metabolism in cSCC metastasis and suggest potential therapeutic approaches.
LIFE SCIENCE ALLIANCE
(2023)
Article
Environmental Sciences
Lorenzo Fabbri, Ronan Garlantezec, Karine Audouze, Mariona Bustamante, Angel Carracedo, Leda Chatzi, Juan Ramon Gonzalez, Regina Grazuleviciene, Hector Keun, Chung-Ho E. Lau, Eduard Sabido, Alexandros P. Siskos, Remy Slama, Cathrine Thomsen, John Wright, Wen Lun Yuan, Maribel Casas, Martin Vrijheid, Lea Maitre
Summary: This study aimed to identify multi-omic signatures associated with childhood exposure to non-persistent endocrine disrupting chemicals (EDCs). By using a repeated sampling strategy and integrating multiple omics data, a total of 950 reproducible associations were found, including 23 direct associations between EDCs and omics. These associations can help us understand the effects of EDCs on neurological and metabolic outcomes.
ENVIRONMENT INTERNATIONAL
(2023)
Article
Plant Sciences
Silvia Proietti, Gaia Salvatore Falconieri, Laura Bertini, Alberto Pascale, Elisabetta Bizzarri, Julia Morales-Sanfrutos, Eduard Sabido, Michelina Ruocco, Maurilia M. Monti, Assunta Russo, Kinga Dziurka, Marcello Ceci, Francesco Loreto, Carla Caruso
Summary: This study reveals that the interaction between tomato and the beneficial fungus Beauveria bassiana leads to changes in molecular pathways, metabolism, growth and defense hormones, and can effectively prevent necrotrophic infection. These findings are important for understanding the beneficial role of B. bassiana in tomato plants.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Biochemical Research Methods
Devon Kohler, Mateusz Staniak, Tsung-Heng Tsai, Ting Huang, Nicholas Shulman, Oliver M. Bernhardt, Brendan X. MacLean, Alexey I. Nesvizhskii, Lukas Reiter, Eduard Sabido, Meena Choi, Olga Vitek
Summary: The MSstats R-Bioconductor family of packages, particularly the new version MSstats v4.0, is widely used for statistical analyses of quantitative proteomic experiments. It provides improved usability, versatility, and accuracy of statistical methodology, as well as better memory use and computation speed. Empirical comparisons have demonstrated the stronger performance and better usability of MSstats v4.0 compared to existing methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ivan Milenkovic, Helaine Graziele Santos Vieira, Morghan C. Lucas, Jorge Ruiz-Orera, Giannino Patone, Scott Kesteven, Jianxin Wu, Michael Feneley, Guadalupe Espadas, Eduard Sabido, Norbert Huebner, Sebastiaan van Heesch, Mirko Voelkers, Eva Maria Novoa
Summary: The study investigates the existence of ribosome heterogeneity and its potential impact on specialized ribosomes. Through analyzing a knockout mouse strain, the researchers find that the depletion of RPL3L leads to an up-regulation of RPL3, resulting in the formation of RPL3-containing ribosomes in cardiomyocytes. Additionally, they discover that RPL3L depletion increases interactions between ribosomes and mitochondria, leading to elevated ATP levels.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Analytical
Cristina Chiva, Zahra Elhamraoui, Amanda Sole, Marc Serret, Mathias Wilhelm, Eduard Sabido
Summary: Mass spectrometry coupled to liquid chromatography is a powerful technology for proteome quantification in biomedical samples. However, the identification of all potential peptides for a given protein is challenging, and proteomics experiments often focus on a subset of peptides for protein quantitation. This study evaluated the stability of human proteotypic peptides and developed a deep learning model to predict peptide stability from tryptic sequences, providing a valuable resource for peptide selection in proteome quantification experiments.
ANALYTICAL CHEMISTRY
(2023)
