Article
Chemistry, Analytical
Yangyang Bian, Matthew The, Piero Giansanti, Julia Mergner, Runsheng Zheng, Mathias Wilhelm, Alexander Boychenko, Bernhard Kuster
Summary: Acquiring proteomic data in a single-shot by microflow LC-MS/MS system allows for efficient and comprehensive analysis of proteins from various samples, with high reliability for samples with sufficient quantities. This method demonstrates high proteome coverage and quantitative accuracy, showing potential for further advancements in rapid chromatography and data independent acquisition approaches.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Liying Zhang, Shihan Qin, Sunv Tang, E. Shuai, Kailin Li, Jing Li, Wei Cai, Lei Sun, Hui Li
Summary: For the first time, this study systematically characterized the chemical constituents in Tojapride, identifying a total of 222 compounds, including 218 that were reported for the first time. This newly developed approach provides a new method for understanding the chemical constituents of Tojapride and can be extended to other traditional Chinese medicine compound research.
Article
Food Science & Technology
Enning Zhou, Qi Wang, Xiangxin Li, Dan Zhu, Qingsheng Niu, Qiangqiang Li, Liming Wu
Summary: Royal jelly, secreted by honeybees, is valued for its bioactive substances and its lipid composition is influenced by the plant source of bee pollen and feeding time. Lipidomic analyses of royal jelly produced by honeybees fed with different sources of bee pollen (BP-Am and BP-Pa) were conducted using UPLC-Q-Exactive Orbitrap mass spectrometry. The results showed differences in phospholipid and fatty acid contents between royal jelly produced by honeybees fed BP-Am and BP-Pa. The study also revealed temporal variations in lipid compounds with a decrease after single-pollen feeding began, followed by a gradual increase and a decrease again after 30 days of feeding. The study provides guidance for the production of high-quality royal jelly.
Article
Biochemical Research Methods
Sachin Patil, Jeffrey Rohrer
Summary: Characterization of galactosyl oligosaccharides (GOS) is important due to their beneficial effects on digestive and immune health. High performance anion exchange chromatography with pulsed amperometric detection (HPAE-PAD) is a widely used method for GOS characterization, combined with Orbitrap mass spectrometry for in-depth information on GOS composition.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2021)
Article
Chemistry, Analytical
Kailin Li, Mingjuan Liu, Min Zhang, Qing Li, Kaiquan Yu, Jiaxin Li, Zichao Shang, Wei Cai
Summary: In this research, a method combining ultra-high-performance liquid chromatography and mass spectrometry was used to detect the active metabolites of diacerein in rat plasma. A total of 32 metabolites were identified, among which 31 were newly discovered. The metabolites showed various reactions in the body, and two metabolites, M21 and M1, showed strong affinity with IL-1 receptors, indicating their potential as active metabolites of diacerein.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2023)
Article
Chemistry, Applied
Rui Li, Yalin Zhou, Yajun Xu
Summary: In this study, UPLC-QE-HF-MS was used to detect human milk oligosaccharides, bovine milk oligosaccharides, goat milk oligosaccharides, and rat milk oligosaccharides. The four milk oligosaccharides showed significant differences in number and composition. Rat milk oligosaccharides were found to contain 14 neutral and 3 acidic oligosaccharides for the first time. The composition and abundances of rat milk oligosaccharides were more similar to human milk oligosaccharides, suggesting their potential use as models in biological/biomedical studies. Bovine milk oligosaccharides and goat milk oligosaccharides could have applications in medical and functional foods as promising bioactive molecules.
Article
Food Science & Technology
Dong Zhang, Xu Guo, Qian Wang, Luyao Zhao, Qincai Sun, Xiaoliang Duan, Yanping Cao, Hui Sun
Summary: The lipid profile of peanut oil at different roasting levels was comprehensively analyzed in this study, revealing that dark roasting severely damaged the cell membrane, while both light and dark roasting resulted in darker oil color and increased acid value. Additionally, peroxide value, conjugated dienes, and oxidized fatty acids showed different trends during roasting, and phospholipids were significantly affected as well. This study provides valuable information for peanut oil processing.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Food Science & Technology
Madhushri S. Varunjikar, Ikram Belghit, Jennifer Gjerde, Magnus Palmblad, Eystein Oveland, Josef D. Rasinger
Summary: Untargeted proteomics plays a significant role in the analysis of composition and authenticity of mixed food and feed products. In this study, a new analytical flow tandem mass spectrometry method was developed for the analysis of insect meal. The results obtained from comparing the data with previous studies showed that the newly established method is effective in differentiating insect species and identifying novel markers for targeted MS analyses.
Article
Chemistry, Analytical
Xu Jing, Dong Pingping, Cui Yifang, Li Huajian, Jiang Shan, Wang Yong, Zhang Jiayu
Summary: This study established a rapid profiling and identification method for dihydromyricetin metabolites in rats and revealed the biotransformation pathways. A total of 49 metabolites were identified, providing a foundation for understanding the action mechanism of dihydromyricetin and other compounds in traditional Chinese medicines or natural plants.
JOURNAL OF SEPARATION SCIENCE
(2022)
Article
Plant Sciences
Lian Zhu, Sheng-jun Ma, Ming-juan Liu, Kai-lin Li, E. Shuai, Zi-ming Wang, Sha-ni Li, Sheng-lan Zhang, Wei Cai
Summary: An analytical method based on affinity ultrafiltration coupled with UHPLC-Q-Exactive Orbitrap mass spectrometry was established to rapidly screen and identify estrogen receptor ligands from Arnebiae Radix extract. Molecular docking and surface plasmon resonance experiments were conducted to investigate the bindings and affinities of the ligands with estrogen receptor alpha and estrogen receptor beta. The study demonstrated the potential bioactive components and possible mechanisms of action of Arnebiae Radix, as well as providing a basis for quality control of this traditional Chinese medicine.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Jingwen Zhang, Junning Liu, Yuheng Wang, Yong Wang, Ruiqin Yang, Xinyang Zhou
Summary: Since neonicotinoid insecticides are widely used worldwide, a rapid and sensitive method for determining these insecticides in human whole blood was developed. The method optimized the extraction solvent, salting-out agent, and adsorbent in the QuEChERS method. The separation and quantification were achieved using an Agilent EC18 column and Q Exactive orbitrap high-resolution mass spectrometry. The method showed good linearity, low detection and quantitation limits, and satisfactory recoveries and precision. It was successfully applied to a real case of neonicotinoid insecticide poisoning, demonstrating its feasibility for forensic analysis and environmental monitoring.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)
Article
Medicine, Research & Experimental
Silin Shi, Kailin Li, Jie Peng, Jian Li, Lilan Luo, Mingjuan Liu, Yuqi Chen, Ziye Xiang, Pei Xiong, Lianghong Liu, Wei Cai
Summary: A study on the chemical constituents and biological activities of Kadsua coccinea leaves reveals the presence of various compounds and significant antioxidant and anti-inflammatory properties.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Biochemical Research Methods
Elizabeth A. Mojica, Dietmar Kultz
Summary: This study developed a workflow for analyzing histone post-translational modifications (PTMs) in nonmodel organisms, and validated it in Mozambique tilapia. By using mass spectrometry methods, 214 biologically relevant histone PTMs were reliably quantified. The study found that 91.59% of histone PTMs were tissue-dependent. The developed workflow and tools are now publicly available for investigating the influence of environmental stress on histone PTMs in nonmodel organisms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Ahmad Jalloh, Antwoine Flowers, Charles Hudson, Dale Chaput, Jennifer Guergues, Stanley M. Stevens, Paula C. Bickford
Summary: Research indicates that microglial activity is a central factor in aging-related dysfunction, with protein signaling cascades playing a key role in altering microglial function. Polyphenols may offer a means of addressing age-related decline, highlighting their potential therapeutic role in age-associated dysfunction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Valeriy I. I. Postoenko, Leyla A. A. Garibova, Lev I. I. Levitsky, Julia A. A. Bubis, Mikhail V. V. Gorshkov, Mark V. V. Ivanov
Summary: One of the key steps in DDA proteomics is detecting peptide isotopic clusters and matching them to MS/MS-based peptide identifications. IQMMA is an integrated solution that combines multiple untargeted peptide feature detection algorithms to provide the most probable intensity values for the MS/MS-based identifications.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Cardiac & Cardiovascular Systems
Fiona Doig, Zhen Qi Lu, Susan Smith, Rishendran Naidoo
Summary: In patients undergoing CABG and mitral valve intervention for IMR, long-term mortality remains high. There was no difference in short- or long-term mortality between repair and replacement although recurrence of at least moderate mitral regurgitation was significantly higher with mitral valve repair.
HEART LUNG AND CIRCULATION
(2021)
Editorial Material
Cardiac & Cardiovascular Systems
Robert Bentley, Sunil Jit R. J. Logantha, Parveen Sharma, Richard R. Rainbow, Gregory Y. H. Lip
CARDIOVASCULAR RESEARCH
(2021)
Article
Multidisciplinary Sciences
Deborah Wenk, Vladimir Ignatchenko, Andrew Macklin, Harald Huebner, Peter Gmeiner, Dorothee Weikert, Monika Pischetsrieder, Thomas Kislinger
Summary: The study found that biased and balanced dopamine D-2 receptor agonists and antagonists can impact the global protein expression in cells, with antagonists affecting exocytosis and peroxisome function, while balanced agonists leading to downregulation of proteins involved in synaptic signaling.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Andres Di Paolo, Joaquina Farias, Joaquin Garat, Andrew Macklin, Vladimir Ignatchenko, Thomas Kislinger, Jose Sotelo Silveira
Summary: In this study, proteomic analysis was used to investigate axons in adult rat sciatic nerves, revealing an increase in ribosomal proteins after injury and newly synthesized axonal proteins. The results suggest that proteomics profiling is an effective method for interrogating axons, and that ribosomal proteins may play an important role during injury.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Multidisciplinary Sciences
Farshad Nassiri, Jeff Liu, Vikas Patil, Yasin Mamatjan, Justin Z. Wang, Rupert Hugh-White, Andrew M. Macklin, Shahbaz Khan, Olivia Singh, Shirin Karimi, Rosario I. Corona, Lydia Y. Liu, Caroline Y. Chen, Ankur Chakravarthy, Qingxia Wei, Bharati Mehani, Suganth Suppiah, Andrew Gao, Adriana M. Workewych, Ghazaleh Tabatabai, Paul C. Boutros, Gary D. Bader, Daniel D. de Carvalho, Thomas Kislinger, Kenneth Aldape, Gelareh Zadeh
Summary: Meningiomas, the most common primary intracranial tumor in adults, often require surgery due to lack of effective medical therapies. This study introduced four consensus molecular groups of meningioma, which accurately predicted clinical outcomes and informed therapeutic options. Single-cell RNA sequencing revealed inter-individual variations in meningioma biology, highlighting the importance of molecular classification in guiding treatment strategies.
Review
Urology & Nephrology
Amanda Khoo, Lydia Y. Liu, Julius O. Nyalwidhe, O. John Semmes, Danny Vesprini, Michelle R. Downes, Paul C. Boutros, Stanley K. Liu, Thomas Kislinger
Summary: Prostate cancer patients urgently need biomarkers to improve risk stratification, as current clinical prognostic tools are not accurate enough. Mass spectrometry technologies enable systematic discovery and validation of protein-based biomarkers in relevant fluids. Existing protein biomarkers for diagnosis, prognosis, and relapse-monitoring in localized prostate cancer are predominantly centered around PSA and its variants.
NATURE REVIEWS UROLOGY
(2021)
Article
Biochemical Research Methods
Natalie Kurganovs, Hanzhi Wang, Xiaoyong Huang, Vladimir Ignatchenko, Andrew Macklin, Shahbaz Khan, Michelle R. Downes, Paul C. Boutros, Stanley K. Liu, Thomas Kislinger
Summary: Proteomic analysis of DU145 prostate cancer cells revealed over 400 differentially expressed proteins in radiation resistant cell lines, with enrichment in pathways such as epithelial to mesenchymal transition, glycolysis, and hypoxia. The cell surface protein CD44 was identified as a potential therapeutic target in the glycolysis and epithelial to mesenchymal transition pathways among the radiation resistant protein candidates.
PROTEOMICS CLINICAL APPLICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Barbara T. Grunwald, Antoine Devisme, Geoffroy Andrieux, Foram Vyas, Kazeera Aliar, Curtis W. McCloskey, Andrew Macklin, Gun Ho Jang, Robert Denroche, Joan Miguel Romero, Prashant Bavi, Peter Bronsert, Faiyaz Notta, Grainne O'Kane, Julie Wilson, Jennifer Knox, Laura Tamblyn, Molly Udaskin, Nikolina Radulovich, Sandra E. Fischer, Melanie Boerries, Steven Gallinger, Thomas Kislinger, Rama Khokha
Summary: Through large-scale integration of histology-guided regional multiOMICs with clinical data and patient-derived preclinical models, we identified distinct subTMEs in the human pancreatic tumor microenvironment (TME) that are linked to tumor immunity, subtypes, differentiation, and treatment response. Reactive subTMEs rich in coordinated fibroblast communities were immune hot, while matrix-rich deserted subTMEs harbored fewer activated fibroblasts but showed chemoprotective features. These subTMEs originated in fibroblast differentiation trajectories and produced patient-specific heterogeneity tightly linked to malignant biology.
Article
Pharmacology & Pharmacy
Peter Kilfoil, Shuyun Lily Feng, Asser Bassyouni, Tiffany Lee, Derek Leishman, Dingzhou Li, David J. MacEwan, Parveen Sharma, Eric D. Watt, Stephen Jenkinson
Summary: This study examined the ability of hIPSC-CM model to predict clinically observed effects of various compounds on electrocardiogram endpoints. Measurements were taken acutely and chronically to capture responses from compounds with slow onset kinetics. The study showed high predictivity in defining TdP risk and correlation between QRS prolongation risk and an increase in action potential rise-time.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2021)
Article
Oncology
Jeffrey A. Zuccato, Vikas Patil, Sheila Mansouri, Jeffrey C. Liu, Farshad Nassiri, Yasin Mamatjan, Ankur Chakravarthy, Shirin Karimi, Joao Paulo Almeida, Anne-Laure Bernat, Mohammed Hasen, Olivia Singh, Shahbaz Khan, Thomas Kislinger, Namita Sinha, Sebastien Froelich, Homa Adle-Biassette, Kenneth D. Aldape, Daniel D. De Carvalho, Gelareh Zadeh
Summary: This study identifies prognostic epigenetic chordoma subtypes using plasma methylomes and may transform patient management by balancing treatment aggressiveness with patient risk according to prognosis. Plasma methylomes can distinguish chordomas from other clinical diagnoses and accurately classify tumors based on plasma methylation data.
Article
Oncology
Mathieu Seyfrid, William Thomas Maich, Vaseem Muhammad Shaikh, Nazanin Tatari, Deepak Upreti, Deween Piyasena, Minomi Subapanditha, Neil Savage, Dillon McKenna, Nicholas Mikolajewicz, Hong Han, Chirayu Chokshi, Laura Kuhlmann, Amanda Khoo, Sabra Khalid Salim, Blessing Archibong-Bassey, William Gwynne, Kevin Brown, Nadeem Murtaza, David Bakhshinyan, Parvez Vora, Chitra Venugopal, Jason Moffat, Thomas Kislinger, Sheila Singh
Summary: This study identifies CD70 as a potential therapeutic target for recurrent glioblastoma stem cells (CSCs). Targeting CD70 with CAR-T therapy significantly improves prognosis in animal models and the CD70/CD27 axis may provide a viable polytherapeutic avenue for targeting both glioblastoma and its tumor immune microenvironment.
JOURNAL FOR IMMUNOTHERAPY OF CANCER
(2022)
Article
Cell Biology
Vanessa L. Correll, Joseph J. Otto, Cristina M. Risi, Brian P. Main, Paul C. Boutros, Thomas Kislinger, Vitold E. Galkin, Julius O. Nyalwidhe, O. John Semmes, Lifang Yang
Summary: Isolation and analysis of extracellular vesicles (EVs) from urine samples is a common strategy for studying vesicle biology and biomarker discovery. However, standard EV isolation methods often co-isolate protein contaminants and high levels of uromodulin (THP) in urine can reduce EV yield. In this study, a modified isolation method was developed to improve EV isolation and enrich prostate cancer-associated EV-resident proteins.
JOURNAL OF EXTRACELLULAR VESICLES
(2022)
Article
Biochemical Research Methods
Laura Kuhlmann, Meinusha Govindarajan, Salvador Mejia-Guerrero, Vladimir Ignatchenko, Lydia Y. Liu, Barbara T. Grunwald, Jennifer Cruickshank, Hal Berman, Rama Khokha, Thomas Kislinger
Summary: This study identified a previously undescribed TNBC-enriched cell surface protein, PLXNB3, through N-glycoproteome analysis, and demonstrated its crucial role in the growth, invasion, and migration of TNBC cells.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Meinusha Govindarajan, Vladimir Ignatchenko, Laurie Ailles, Thomas Kislinger
Summary: The tumor microenvironment, particularly cancer-associated fibroblasts (CAFs), plays a crucial role in the progression of high-grade serous ovarian cancer (HGSC). In this study, we used mass-spectrometry to analyze the proteomes of HGSC patient-derived CAFs and compared them with the epithelial component of HGSC, aiming to understand their tumor-promoting characteristics. By integrating our data with primary tissue data, we identified a proteomic signature of HGSC CAFs and discovered several novel CAF proteins that have prognostic value in an independent HGSC patient cohort. This study provides the first MS-based global proteomic characterization of CAFs in HGSC and emphasizes the clinical significance of HGSC CAFs.
Article
Endocrinology & Metabolism
Mathepan Jeya Mahendralingam, Hyeyeon Kim, Curtis William McCloskey, Kazeera Aliar, Alison Elisabeth Casey, Pirashaanthy Tharmapalan, Davide Pellacani, Vladimir Ignatchenko, Mar Garcia-Valero, Luis Palomero, Ankit Sinha, Jennifer Cruickshank, Ronak Shetty, Ravi N. Vellanki, Marianne Koritzinsky, Vid Stambolic, Mina Alam, Aaron David Schimmer, Hal Kenneth Berman, Connie J. Eaves, Miquel Angel Pujana, Thomas Kislinger, Rama Khokha
Summary: Cancer cells adapt their metabolic network from the tissue of origin. Normal mammary cells exhibit diverse metabolic programs, with basal cells enriched in glycolysis and luminal progenitors in oxidative phosphorylation. Targeting these metabolic vulnerabilities in mammary progenitors could potentially advance breast cancer therapy, as breast cancer subtypes retain metabolic features of their putative cell of origin.
