Article
Chemistry, Applied
Junfu Ji, Xinyu Liu, Xiaosong Hu, Fang Chen, Christoph Bueschl, Rainer Schuhmacher, Andrew L. Waterhouse, Lingjun Ma
Summary: This study successfully identified quinone reaction products in wine using a stable-isotope labelling approach combined with high-resolution mass spectrometry. Different nucleophiles were found to react in white wines and red wines.
Article
Pharmacology & Pharmacy
Sabrina Wohlfart, Michael Kilian, Philip Storck, Thomas Gutsmann, Klaus Brandenburg, Walter Mier
Summary: A novel method for precise quantification of Pep19-2.5 in biological samples has been developed in this study, which is crucial for the treatment of sepsis. The method utilizes mass spectrometry and labeled amino acid residues to reliably quantify the peptide content.
Article
Biochemical Research Methods
Jing Dong, Anthony Duchesne, Andrew N. Bayne, Nguyen-Vi Mohamed, Wei Yi, Meghna Mathur, Carol X. Q. Chen, Zhipeng You, Narges Abdian, Lorne Taylor, Edward A. Fon, Thomas M. Durcan, Jean-Francois Trempe
Summary: Patient-derived organoids from induced pluripotent stem cells provide a model for studying human diseases. The researchers developed a workflow to extract proteins from brain organoids, measure protein turnover, and analyze differences between genotypes. This method accurately characterized the half-lives of multiple proteins in midbrain organoids.
Review
Chemistry, Analytical
Di Yu, Lina Zhou, Xinyu Liu, Guowang Xu
Summary: The introduction of stable isotope labeling (SIL) technology has become a routine tool for functional metabolomics studies and allows for a deeper understanding of dynamic metabolic regulation in organisms. Mass spectrometry (MS) techniques have shown great vitality in this field by utilizing the different mass spectrometric characteristics between endogenous metabolites and their isotope-labeling forms. Recent advances in MS-based stable isotope-resolved metabolomics (SIRM) methods have expanded the breadth and depth of SIRM research by improving sample pretreatment, MS analysis, and data analysis. This review describes the recent progress of SIRM methods, summarizes their applications in metabolite identification, accurate quantification, and metabolic flux analysis, and discusses current limitations and challenges.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Sunkyu Choi, Atilio Reyes Romero, Fathima Mashood, Neha Goswami, Lotfi Chouchane, Frank Schmidt
Summary: Protein turnover, the balance between protein synthesis and degradation, is essential for cellular protein homeostasis. This study aimed to analyze protein turnover in adipocytes using time-dependent SILAC labeling. The results revealed associations between protein half-lives and various cellular processes, including energy metabolism, RNA splicing, and Golgi complex. These findings contribute to a better understanding of adipocyte proteome dynamics and protein homeostasis maintenance.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Environmental Sciences
Marisa A. Wirth, Lars Longwitz, Marion Kanwischer, Peter Gros, Peter Leinweber, Thomas Werner
Summary: Stable isotope labeling of pollutants is important for studying their environmental fate. A synthetic pathway to the labeled metabolite AMPA-N-15 was developed for the commonly used herbicide glyphosate, enabling its accurate detection and quantitation in soil extracts. The newly developed analysis concepts will facilitate future research on the environmental behavior of glyphosate.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Review
Spectroscopy
Xiaobo Tian, Hjalmar P. Permentier, Rainer Bischoff
Summary: This article summarizes the advances in liquid chromatography and mass spectrometry in proteome quantification approaches, focusing on the principles, benefits, and limitations of chemical isotope labeling-based methods. It also discusses the potential and limitations of multiplex isotope labeling approaches for data-independent acquisition mode.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Biochemical Research Methods
Sunkyu Choi, Rudolf Engelke, Neha Goswami, Frank Schmidt
Summary: This study used SILAC-based proteomic profiling to investigate the effects of metformin on 3T3-L1 adipocytes. The results showed that metformin not only affects glucose and lipid metabolism, but also has an impact on protein folding, endoplasmic reticulum stress, negative regulation of appetite, and one-carbon folate metabolism in adipocytes.
Review
Biochemistry & Molecular Biology
Rocco J. Rotello, Timothy D. Veenstra
Summary: In the era of genomics research, mass spectrometry has become a vital tool for quantitatively comparing proteins within cells and organisms, despite the complexity of identifying quantitative changes in proteomes due to their dynamic nature and limitations in technology coverage. The combined development of sample preparation and MS methods has enabled the quantitation of thousands of proteins obtained from cells and organisms.
CURRENT PROTEIN & PEPTIDE SCIENCE
(2021)
Article
Marine & Freshwater Biology
Eric Bollinger, Jochen P. Zubrod, Marco Konschak, Ralf Schulz, Mirco Bundschuh
Summary: Stable isotope analysis is an important technique in food web ecology, but its effectiveness can be unclear in complex systems. The use of heavy isotope tracers has been suggested as a way to enhance the utility of stable isotope analysis, but this study found that labeling could potentially affect isotopic fractionation and bias conclusions. While the physiological and activity levels of organisms in autotrophy-based and detritus-based aquatic food webs were not significantly affected by labeling, the study supported the isotopic redundancy hypothesis, which suggests that metabolic processes can be altered by discrete quantum mechanical states.
AQUATIC TOXICOLOGY
(2023)
Article
Chemistry, Analytical
Xi-Ling Li, Yuxuan Li, Shuyun Xiao, Qingsong Li, Chengqiang Han, Danyang Liu, Tengfei Cui, Xiyang Rao, Kenichiro Todoroki, Guang Yang, Jun Zhe Min
Summary: Acute myocardial infarction (AMI) is a serious threat to human life, but clinical biomarkers often have limited sensitivity and specificity. Therefore, it is important to screen novel glycan biomarkers with high sensitivity and specificity for the prevention and treatment of AMI. In this study, a new method using UHPLC-Q-Orbitrap HRMS with d0/d5-BOTC probe labeling was established to screen glycan biomarkers in the serum of AMI patients. Several glycan expressions were found to be significantly different between AMI patients and healthy volunteers. H4N6SA, H5N4FSA, and H4N6F2 showed high accuracy and specificity and may serve as potential glycan biomarkers for AMI diagnosis and treatment monitoring.
ANALYTICA CHIMICA ACTA
(2023)
Review
Biochemistry & Molecular Biology
Ekaterina Mikhailovna Stakhneva, Evgeniia Vitalievna Striukova, Yulia Igorevna Ragino
Summary: Proteomic studies play a crucial role in investigating atherosclerotic cardiovascular diseases, identifying potential biomarkers, and offering novel diagnostic approaches.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Mogjiborahman Salek, Jonas D. Foerster, Wolf-Dieter Lehmann, Angelika B. Riemer
Summary: In mass spectrometry-based proteomics, heavy internal standards are used for validating target peptide detections and calibrating peptide quantitation. However, contamination in heavy labelled synthetic peptides may compromise the detection and quantitation of low abundant cellular peptides. It is important to establish guidelines to prevent false-positive identifications of endogenous light peptides and errors in their quantitation from biological samples.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Review
Oncology
Arada Vinaiphat, Jee Keem Low, Kheng Wei Yeoh, Wee Joo Chng, Siu Kwan Sze
Summary: Cancer, as a major contributor to global chronic disease burden, is closely related to low-oxygen stress. Traditional proteomic approaches have been used to study cancer mechanisms associated with oxygen deprivation, but clinical therapeutic outcomes have been limited. Therefore, the development of new strategies and technologies is crucial for multi-target drug discovery.
FRONTIERS IN ONCOLOGY
(2021)
Article
Geochemistry & Geophysics
Ren T. C. Marquez, Francois L. H. Tissot
Summary: The double spike (DS) technique is crucial for high-precision and high-accuracy mass-dependent isotope fractionations. The recently developed cosmo software package addresses the need to optimize DS measurements for small samples with mass-independent anomalies, allowing for a wider range of sample types and measurement scenarios.
Article
Multidisciplinary Sciences
Rotem Katzir, Ibrahim H. Polat, Michal Harel, Shir Katz, Carles Foguet, Vitaly A. Selivanov, Philippe Sabatier, Marta Cascante, Tamar Geiger, Eytan Ruppin
SCIENTIFIC REPORTS
(2019)
Article
Oncology
Hadar Brand, Georgina D. Barnabas, Stav Sapoznik, Keren Bahar-Shany, Yair Pozniak, Yuval Yung, Ariel Hourvitz, Tamar Geiger, Jasmine Jacob-Hirsch, Keren Levanon
Editorial Material
Biochemistry & Molecular Biology
Gali Yanovich-Arad, Tamar Geiger
Article
Multidisciplinary Sciences
Yael Elbaz-Alon, Yuting Guo, Nadav Segev, Michal Harel, Daniel E. Quinnell, Tamar Geiger, Ori Avinoam, Dong Li, Jodi Nunnari
NATURE COMMUNICATIONS
(2020)
Article
Biochemistry & Molecular Biology
Anjana Shenoy, Nishanth Belugali Nataraj, Gili Perry, Fabricio Loayza Puch, Remco Nagel, Irina Marin, Nora Balint, Noa Bossel, Anya Pavlovsky, Iris Barshack, Bella Kaufman, Reuven Agami, Yosef Yarden, Maya Dadiani, Tamar Geiger
MOLECULAR SYSTEMS BIOLOGY
(2020)
Article
Cell Biology
Dvir Shechter, Michal Harel, Abhishek Mukherjee, Leonel M. Sagredo, David Loven, Elad Prinz, Shimrit Avraham, Veronique Orian-Rousseau, Tamar Geiger, Yuval Shaked, Haguy Wolfenson
Correction
Biology
Lee Shaashua, Anabel Eckerling, Boaz Israeli, Gali Yanovich, Ella Rosenne, Suzana Fichman-Horn, Ido Ben Zvi, Liat Sorski, Rita Haldar, Ronit Satchi-Fainaro, Tamar Geiger, Erica K. Sloan, Shamgar Ben-Eliyahu
Article
Oncology
Georgina D. Barnabas, Joo Sang Lee, Tamar Shami, Michal Harel, Lir Beck, Michael Selitrennik, Livnat Jerby-Arnon, Neta Erez, Eytan Ruppin, Tamar Geiger
Summary: This study highlights the crucial role of IDH2 in triple-negative breast cancer (TNBC) and HER2, and demonstrates its oncogenic effects in cell proliferation, glycolysis, and other metabolic processes. PHGDH and PSAT1 are identified as synthetic dosage lethal (SDL) partners of IDH2, and their knockout shows the essentiality in IDH2-high cells. Clinical findings suggest that patients with IDH2-high/PHGDH-low tumors have longer survival, and PHGDH inhibitors show effectiveness in treating IDH2-high cells.
Article
Oncology
Lir Beck, Michal Harel, Shun Yu, Ettai Markovits, Ben Boursi, Gal Markel, Tamar Geiger
Summary: The study identified associations between the proteomic profiles of metastatic melanoma patients and clinical information such as survival and immunotherapy response, particularly highlighting the correlation between lung metastases and better immunotherapy response. Analysis of BRAF status and treatment history provided insights into the impact on immunotherapy response and suggested potential for improved treatment efficacy through combination therapy.
CLINICAL CANCER RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Sapir Schlam-Babayov, Ariel Bensimon, Michal Harel, Tamar Geiger, Ruedi Aebersold, Yael Ziv, Yosef Shiloh
Summary: This study conducted a comprehensive phosphoproteomic analysis in human wild-type and A-T cells to reveal the fine-tuned dynamics and relationships between PIKKs in the response to genotoxic stress. The results highlight the complex interactions among ATM, ATR, and DNA-PK in the DDR.
Article
Biochemistry & Molecular Biology
Hagai Marmor-Kollet, Aviad Siany, Nancy Kedersha, Naama Knafo, Natalia Rivkin, Yehuda M. Danino, Thomas G. Moens, Tsviya Olender, Daoud Sheban, Nir Cohen, Tali Dadosh, Yoseph Addadi, Revital Ravid, Chen Eitan, Beata Toth Cohen, Sarah Hofmann, Claire L. Riggs, Vivek M. Advani, Adrian Higginbottom, Johnathan Cooper-Knock, Jacob H. Hanna, Yifat Merbl, Ludo Van den Bosch, Paul Anderson, Pavel Ivanov, Tamar Geiger, Eran Hornstein
Article
Multidisciplinary Sciences
Osnat Bartok, Abhijeet Pataskar, Remco Nagel, Maarja Laos, Eden Goldfarb, Deborah Hayoun, Ronen Levy, Pierre-Rene Korner, Inger Z. M. Kreuger, Julien Champagne, Esther A. Zaal, Onno B. Bleijerveld, Xinyao Huang, Juliana Kenski, Jennifer Wargo, Alexander Brandis, Yishai Levin, Orel Mizrahi, Michal Alon, Sacha Lebon, Weiwen Yang, Morten M. Nielsen, Noam Stern-Ginossar, Maarten Altelaar, Celia R. Berkers, Tamar Geiger, Daniel S. Peeper, Johanna Olweus, Yardena Samuels, Reuven Agami
Article
Biochemistry & Molecular Biology
Elee Shimshoni, Idan Adir, Ran Afik, Inna Solomonov, Anjana Shenoy, Miri Adler, Luca Puricelli, Fabio Sabino, Simonas Savickas, Odelia Mouhadeb, Nathan Gluck, Sigal Fishman, Lael Werner, Tomer-Meir Salame, Dror S. Shouval, Chen Varol, Ulrich auf dem Keller, Alessandro Podesta, Tamar Geiger, Paolo Milani, Uri Alon, Irit Sagi
Summary: This study investigates the extracellular-matrix dynamics during the onset of inflammatory bowel diseases, revealing a unique matrix signature in the colon even before the appearance of clinical symptoms. The presence of a pre-symptomatic matrix mediated by immune cells carrying remodeling enzymes was found, suggesting its relevance to a wide range of diseases, both chronic and acute.
Article
Biology
Lee Shaashua, Anabel Eckerling, Boaz Israeli, Gali Yanovich, Ella Rosenne, Suzana Fichman-Horn, Ido Ben Zvi, Liat Sorski, Rita Haldar, Ronit Satchi-Fainaro, Tamar Geiger, Erica K. Sloan, Shamgar Ben-Eliyahu
Article
Biochemistry & Molecular Biology
Saleh Khawaled, Giovanni Nigita, Rosario Distefano, Sara Oster, Sung-Suk Suh, Yoav Smith, Abed Khalaileh, Yong Peng, Carlo M. Croce, Tamar Geiger, Victoria L. Seewaldt, Rami Aqeilan
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2020)