Article
Biochemical Research Methods
Guangju Ge, Qiming Zheng, Zeyu Sun, Huan Wang, Huailan Wang, Keyi Ren, Haiyang Wu, Shibin Zhu, Gonghui Li
Summary: Changes in proteomic profiles can reflect the underlying biological mechanisms during the development of urosepsis after UUTEL, leading to the discovery of diagnostic biomarkers for early detection. A diagnostic model composed of three proteins (LBP, CLU, and VCAM1) can achieve high accuracy in early detection (2 hours postoperatively) with an ROC curve area of 0.921.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Analytical
Francis Berthias, Hayden A. Thurman, Gayani Wijegunawardena, Haifan Wu, Alexandre A. Shvartsburg, Ole N. Jensen
Summary: Advances in proteomics have shown the ubiquity and biological importance of diverse proteoforms. The ability to separate and analyze intact isomeric proteoforms is crucial for understanding their functions. A novel technique using trapped IMS was demonstrated to achieve baseline resolution of isomeric proteoforms, opening new avenues in proteomics and epigenetics.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Alessandra Olianas, Giulia Guadalupi, Tiziana Cabras, Cristina Contini, Simone Serrao, Federica Iavarone, Massimo Castagnola, Irene Messana, Simona Onali, Luchino Chessa, Giacomo Diaz, Barbara Manconi
Summary: Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) are autoimmune liver diseases with chronic inflammation and fibrosis. Saliva has potential as a diagnostic tool. Proteomics is emerging as a field for personalized medicine.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Jake A. Melby, Kyle A. Brown, Zachery R. Gregorich, David S. Roberts, Emily A. Chapman, Lauren E. Ehlers, Zhan Gao, Eli J. Larson, Yutong Jin, Justin R. Lopez, Jared Hartung, Yanlong Zhu, Sean J. McIlwain, Daojing Wang, Wei Guo, Gary M. Diffee, Ying Ge
Summary: Single-cell proteomics is a powerful method to study cellular heterogeneity and functional networks. However, it faces challenges in analyzing proteoforms from genetic mutations, alternative splicing, and post-translational modifications. In this study, a sensitive top-down proteomics method was developed to analyze proteoforms from single muscle fibers. The study identified heterogeneity in large proteoforms and a relationship between sarcomeric proteoforms and muscle fiber types.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemical Research Methods
James M. Fulcher, Aman Makaju, Ronald J. Moore, Mowei Zhou, David A. Bennett, Philip L. De Jager, Wei-Jun Qian, Ljiljana Pasa-Tolic, Vladislav A. Petyuk
Summary: The study focused on how to improve the depth of top-down proteomics (TDP) using high-field asymmetric waveform ion mobility spectrometry (FAIMS), enhancing protein coverage in Alzheimer's disease brain tissue samples and identifying amyloid beta proteoforms associated with Alzheimer's disease.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Jan Leipert, Philipp T. Kaulich, Max K. Steinbach, Britta Steer, Konrad Winkels, Christine Blurton, Matthias Leippe, Andreas Tholey
Summary: Researchers have developed a sample preparation method based on protein aggregation and acidic elution, allowing for sensitive protein identification analysis of single nematodes on a digital microfluidics device. Compared to in-tube sample preparation, this method increases proteoform identifications by 46%. Label-free quantification also reveals changes in proteoform abundance that cannot be distinguished by bottom-up proteomics. This workflow facilitates proteoform-focused analysis on limited availability samples.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Tanja Habeck, Edvaldo Vasconcelos Soares Maciel, Kevin Kretschmer, Frederik Lermyte
Summary: In recent years, top-down mass spectrometry has been widely used to study proteoforms, with the goal of improving sequence coverage. This study investigated the effects of two high-boiling solvents, DMSO and propylene carbonate, on the top-down fragmentation patterns of two different proteins. The results revealed reproducible differences in the fragmentation patterns in the presence of these additives, potentially due to the selective formation of different protonation site isomers. The presence of additives often led to higher sequence coverage, and combining datasets from different solution conditions further increased cleavage coverage.
Article
Chemistry, Analytical
Yue Sun, Yu Liang, Chao Wang, Baofeng Zhao, Zhen Liang, Xiaodan Zhang, Yukui Zhang, Lihua Zhang
Summary: Comprehensive characterization of membrane proteins at the level of proteoforms in complex biological samples by top-down mass spectrometry (MS) is of vital importance in revealing their precise functions. However, severe peak broadening in the separation of hydrophobic membrane proteins, caused by resistance to mass transfer and strong adsorption on separation materials, leads to MS spectra overlap and signal suppression, which makes against the in-depth research on membrane proteoforms.
ANALYTICAL CHEMISTRY
(2023)
Article
Oncology
Yanhong Liu, Lan Gao, Yanru Fan, Rufei Ma, Yunxia An, Guanghui Chen, Yan Xie
Summary: Potential protein biomarkers and mechanism of venous thromboembolism (VTE) in non-small cell lung cancer (NSCLC) patients were identified through proteomics research. A total of 280 differentially expressed proteins were found, and 5 proteins (SAA1, S100A8, LBP, HP and LDHB) showed significant changes between VTE and non-VTE patients. These results suggest that these proteins may be used for diagnosing VTE in NSCLC patients.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Francesca Scebba, Stefano Salvadori, Silvia Cateni, Paola Mantellini, Francesca Carozzi, Simonetta Bisanzi, Cristina Sani, Marzia Robotti, Ivana Barravecchia, Francesca Martella, Valentina Colla, Debora Angeloni
Summary: Ovarian cancer (OC) is a deadly gynecological cancer, and early diagnosis is crucial for a cure. Currently, a reliable screening method for early detection of OC is lacking. In this study, saliva samples were analyzed using proteomics to identify candidate biomarkers for OC. The results show that saliva is an informative test fluid for early detection of OC.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Jared B. Shaw, Dale A. Cooper-Shepherd, Darren Hewitt, Jason L. Wildgoose, Joseph S. Beckman, James Langridge, Valery G. Voinov
Summary: This study demonstrates the utility of combining electron capture dissociation (ECD) with high-resolution cyclic ion mobility spectrometry (cIMS) to greatly enhance top-down protein characterization capabilities.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Zach Rolfs, Lloyd M. Smith
Summary: A significant portion of unidentified fragment ion intensity in top-down proteomics is believed to come from internal fragment ions, which contain neither protein terminus. The computational complexity of internal fragment ions has historically limited their application to low-complexity samples, but the implementation of internal fragment ion functionality in MetaMorpheus allows for proteome-wide annotation of these ions, leading to disambiguation of proteoforms and increased identification accuracy. MetaMorpheus demonstrated success in disambiguating previously unclear proteoforms and improving proteoform-spectrum matches in mammalian cell lysates.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Geoffrey Yuet Mun Wong, Connie Diakos, Thomas J. Hugh, Mark P. Molloy
Summary: Colorectal liver metastases (CRLM) are a major cause of death in patients with metastatic colorectal cancer (CRC). Liver resection is the main treatment for select patients with CRLM, but effective treatment remains challenging due to high rates of recurrence. Genomic profiling has improved our understanding of CRC, but the functional context at the protein level is not well-established. Proteomic biomarkers are being explored for predicting CRLM and recurrence. This review aims to rationalize the proteomic complexity of CRC and explore the potential applications of proteomic biomarkers in CRLM.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Katherine A. Graham, Charles F. Lawlor, Nicholas B. Borotto
Summary: Mass spectrometry-based proteomics workflows are widely used but often result in complex mass spectra. Ion mobility spectrometry (IMS) can separate ions based on their mass and size-to-charge ratios, providing a solution to this problem. This study characterizes a new method to dissociate intact protein ions in a trapped ion mobility spectrometry (TIMS) device, enabling easy identification of similar product ions. The results show that collisional activation within a TIMS device can dissociate protein ions up to 66 kDa and that the size of the ion population significantly affects fragmentation efficiency. Additionally, comparing collisional activation modes, CIDtims in TIMS improves annotation of overlapping fragment ions and enhances sequence coverage.
Article
Biochemistry & Molecular Biology
Alessandro Marrone, Daniele La Russa, Laura Barberio, Maria Stella Murfuni, Marco Gaspari, Daniela Pellegrino
Summary: Investigating the early changes in post mortem protein degradation can lead to the discovery of new PMI specific biomarkers, which could potentially serve as a reliable method for PMI determination.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Analytical
Yu Feng, Bingming Chen, Qinying Yu, Xuefei Zhong, Dustin C. Frost, Chrysanthy Ikonomidou, Lingjun Li
ANALYTICAL CHEMISTRY
(2019)
Article
Hematology
Elspeth M. Beauchamp, Sameem M. Abedin, Sara G. Radecki, Mariafausta Fischietti, Ahmet Dirim Arslan, Gavin T. Blyth, Angela Yang, Connor Lantz, Alissa Nelson, Young Ah Goo, Imo Akpan, Elizabeth A. Eklund, Olga Frankfurt, Eleanor N. Fish, Paul M. Thomas, Jessica K. Altman, Leonidas C. Platanias
Article
Obstetrics & Gynecology
Jamie Limjoco, Lucyna Zawadzki, Meghan Belden, Jens Eickhoff, Chrysanthy Ikonomidou
JOURNAL OF MATERNAL-FETAL & NEONATAL MEDICINE
(2020)
Article
Neurosciences
Ivan M. Rosado-Mendez, Kevin K. Noguchi, Laura Castaneda-Martinez, George Kirvassilis, Sophie H. Wang, Francesca Manzella, Brant S. Swiney, Kobe Masuoka, Saverio Capuano, Kevin G. Brunner, Kristin Crosno, Quinton W. Guerrero, Hayley Whitson, Ansgar Brambrink, Heather S. Simmons, Andres F. Mejia, James A. Zagzebski, Timothy J. Hall, Chrysanthy Ikonomidou
NEUROBIOLOGY OF DISEASE
(2019)
Article
Neurosciences
Chrysanthy Ikonomidou, George Kirvassilis, Brant S. Swiney, Sophie H. Wang, Jacob N. Huffman, Sasha L. Williams, Kobe Masuoka, Saverio Capuano, Kevin R. Brunner, Kristin Crosno, Heather S. Simmons, Andres F. Mejia, Christopher A. Turski, Ansgar Brambrink, Kevin K. Noguchi
NEUROBIOLOGY OF DISEASE
(2019)
Article
Biochemical Research Methods
Qinying Yu, Xiaofang Zhong, Bingming Chen, Yu Feng, Min Ma, Carol A. Diamond, Julie S. Voeller, Miriam Kim, Kenneth B. DeSantes, Christian M. Capitini, Neha J. Patel, Margo L. Hoover-Regan, Michael J. Burke, Kimberly Janko, Diane M. Puccetti, Chrysanthy Ikonomidou, Lingjun Li
JOURNAL OF PROTEOME RESEARCH
(2020)
Article
Acoustics
Laura Castaneda-Martinez, Kevin K. Noguchi, I. Chrysanthy Ikonomidou, James A. Zagzebski, Timothy J. Hall, Ivan M. Rosado-Mendez
ULTRASOUND IN MEDICINE AND BIOLOGY
(2020)
Review
Oncology
Chrysanthy Ikonomidou
Summary: In childhood leukemia, the involvement of the central nervous system (CNS) is a major cause of treatment failures. Analysis of cerebrospinal fluid is crucial for detecting CNS leukemia. Treatments for childhood leukemia can adversely affect the developing brain, leading to neurocognitive deficits. This review highlights the utility of cerebrospinal fluid biomarkers in tracking both CNS disease and neurotoxicity of treatments in childhood leukemias.
Article
Neurosciences
Kevin K. Noguchi, Nicole A. Fuhler, Sophie H. Wang, Saverio Capuano, Kevin R. Brunner, Shreya Larson, Kristin Crosno, Heather A. Simmons, Andres F. Mejia, Lauren D. Martin, Gregory A. Dissen, Ansgar Brambrink, Chrysanthy Ikonomidou
Summary: Barbiturates and benzodiazepines show extensive toxicity in the developing brain, leading to apoptosis of neurons and oligodendrocytes. Neurodegenerative effects become more severe with longer exposure duration, spreading trans-synaptically. Further exploration is needed to understand the impact of these sequelae on neurocognitive outcomes and the brain connectome.
NEUROBIOLOGY OF DISEASE
(2021)
Article
Cell Biology
Cara J. Westmark, Mikolaj J. Filon, Patricia Maina, Lauren Steinberg, Chrysanthy Ikonomidou, Pamela R. Westmark
Summary: Mice fed soy-based diets have increased weight gain and altered behavior. Soy protein-based diets may contribute to obesity and exacerbation of neurological phenotypes in developmental disabilities.
Article
Pediatrics
Emma A. Simpson, Catarina Saiote, Ellen Sutter, Daniel H. Lench, Chrysanthy Ikonomidou, Melissa A. Villegas, Bernadette T. Gillick
Summary: This study investigates the feasibility, safety, and tolerability of at-home active transcranial direct current stimulation in children with cerebral palsy. The findings will provide the opportunity for larger clinical trials exploring efficacy and illuminate the potential of remotely monitored tDCS in combination with rehabilitation interventions as a means of pediatric neurorehabilitation.
Article
Neurosciences
Chrysanthy Ikonomidou, Sophie H. Wang, Nicole A. Fuhler, Shreya Larson, Saverio Capuano, Kevin R. Brunner, Kristin Crosno, Heather A. Simmons, Andres F. Mejia, Kevin K. Noguchi
Summary: Exposure to a combination of phenobarbital and midazolam for 24 hours in neonatal macaques causes widespread apoptosis, and mild hypothermia does not protect against this effect.
NEUROBIOLOGY OF DISEASE
(2022)
Article
Clinical Neurology
Ricki Colman, Peter Pierre, Julie Adriansjach, Kristin Crosno, Kevin K. Noguchi, Chrysanthy Ikonomidou
Summary: The study demonstrated that neonatal exposure to the antiseizure medications PbM can have long-lasting effects on behavior and cognition in nonhuman primates, with treated animals showing lower scores for environmental exploration and higher scores for locomotion and vocalizations compared with controls. Additionally, combined PbM and hypothermia resulted in lower scores for aggression and vigilance at 12 months.
ANNALS OF NEUROLOGY
(2023)
Article
Clinical Neurology
Eleonora Aronica, Devin K. Binder, Meinrad Drexel, Chrysanthy Ikonomidou, Shilpa D. Kadam, Guenther Sperk, Christian Steinhaeuser
Summary: This study discusses the importance of common data elements for preclinical epilepsy research and addresses neuropathological changes associated with seizures and epilepsy in rodent models. Detailed tables and case report forms are provided to aid in standardization and comparability of translational preclinical epilepsy research.
Article
Oncology
Qi Jin, Carlos A. Martinez, Kelly M. Arcipowski, Yixing Zhu, Blanca T. Gutierrez-Diaz, Kenneth K. Wang, Megan R. Johnson, Andrew G. Volk, Feng Wang, Jian Wu, Charles Grove, Hui Wang, Ivan Sokirniy, Paul M. Thomas, Young Ah Goo, Nebiyu A. Abshiru, Nobuko Hijiya, Sofie Peirs, Niels Vandamme, Geert Berx, Steven Goosens, Stacy A. Marshall, Emily J. Rendleman, Yoh-hei Takahashi, Lu Wang, Radhika Rawat, Elizabeth T. Bartom, Clayton K. Collings, Pieter Van Vlierberghe, Alexandros Strikoudis, Stephen Kelly, Beatrix Ueberheide, Christine Mantis, Irawati Kandela, Jean-Pierre Bourquin, Beat Bornhauser, Valentina Serafin, Silvia Bresolin, Maddalena Paganin, Benedetta Accordi, Giuseppe Basso, Neil L. Kelleher, Joseph Weinstock, Suresh Kumar, John D. Crispino, Ali Shilatifard, Panagiotis Ntziachristos
CLINICAL CANCER RESEARCH
(2019)