Article
Biochemical Research Methods
Stefan Loroch, Dominik Kopczynski, Adriana C. Schneider, Cornelia Schumbrutzki, Ingo Feldmann, Eleftherios Panagiotidis, Yvonne Reinders, Roman Sakson, Fiorella A. Solari, Alicia Vening, Frauke Swieringa, Johan W. M. Heemskerk, Maria Grandoch, Thomas Dandekar, Albert Sickmann
Summary: This study introduces a novel strategy for positive-pressure 96-well filter-aided sample preparation (PF96), which significantly increases throughput and demonstrates high reproducibility. The study confirms the excellent reproducibility and stability of PF96 at the protein level, as well as its compatibility with nanoLC-MS instrumentation. This method has promising applications in biomedical and clinical research.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Plant Sciences
Tatiana Leonova, Christian Ihling, Mohamad Saoud, Nadezhda Frolova, Robert Rennert, Ludger. A. A. Wessjohann, Andrej Frolov
Summary: Gel-free LC-based shotgun proteomics is considered the gold standard for proteome analysis. However, sample preparation methods greatly impact the accuracy and reliability of protein quantification. Detergents have been used to improve sample preparation efficiency, but they can disrupt chromatographic separation and ionization. Filter-aided sample preparation (FASP) is a method that can overcome these limitations. The applicability of FASP in plants and its compatibility with plant-specific protein isolation methods have not been confirmed. This study evaluated the potential of FASP in quantitative analysis of pea seed and Arabidopsis leaf proteomes and compared it to conventional FASP-based digestion methods.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Dimitrios Baltzis, George Z. Tsogas, Constantinos K. Zacharis, Paraskevas D. Tzanavaras
Summary: A high-throughput fluorimetric assay for histidine was developed using a 96-well plates platform. The method detects histidine in human urine samples using a smartphone after illumination under UV light without the need for instruments. The results were in good agreement with an HPLC corroborative method, and the assay showed minimal interference from other substances in urine.
Article
Chemistry, Analytical
Joshua J. Coon, Laura K. Muehlbauer, Annie Jen, Yunyun Zhu, Yuchen He, Evgenia Shishkova, Katherine A. Overmyer
Summary: Multi-omics analysis is a powerful and increasingly used method to understand complex biological systems. However, the sample preparation process for multi-omics is time-consuming and wasteful. We propose a simple and efficient method, called BAMM, which saves time and achieves comparable results to existing methods.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Adam H. Szmelter, Giulia Venturini, Rana J. Abbed, Manny O. Acheampong, David T. Eddington
Summary: High blood pressure is the primary risk factor for heart disease. Current methods to replicate physiological pressures in vitro are limited. We introduce a high-throughput hydrostatic pressure exposure system that can replicate real patients' blood pressures and other medically-relevant pressures.
Article
Chemistry, Analytical
Changding Wang, Xiang Wang, Chen Li, Xiaohui Xu, Weichun Ye, Guoyu Qiu, Degui Wang
Summary: The study demonstrates the successful preparation of uniform and stable Ag mirror films on polydopamine-coated well plates for SERS detection using 96-well technology. The high-quality Ag mirror films showed excellent performance in terms of sensitivity, reproducibility, and stability. They were effectively used to quantify organic dyes and small molecules in environmental water samples and urine matrix, with satisfactory sensitivity and recovery.
Article
Multidisciplinary Sciences
Yan Chen, Jennifer Gin, Ying Wang, Markus J. de Raad, Stephen R. Tan, Nathan D. Hillson, Trent J. Northen, Paul Adams, Christopher Petzold, Faiz ul-Hassan Nasim
Summary: Plate-based proteomic sample preparation is a useful method for processing a large number of samples in the biotechnology field. It can be applied to various microbes and does not require desalting column cleanup. The protocol provides a cost-effective and environmentally-friendly option and takes approximately 30 minutes to extract protein from 96 samples. It is suitable for rapid and low-variance sample preparation of hundreds of samples.
Article
Biochemistry & Molecular Biology
Sanja Milkovska-Stamenova, Michele Woelk, Ralf Hoffmann
Summary: Sample preparation is a critical step in proteomics, affecting protein and peptide identification and quantification. Different approaches have varying advantages and disadvantages, with FASP being more time efficient but less reproducible quantitatively. Prior protein precipitation improved quantification in FASP.
Article
Biochemical Research Methods
Marica Grossegesse, Paula Leupold, Joerg Doellinger, Lars Schaade, Andreas Nitsche
Summary: This study tested five different proteomics lysis buffers for their inactivation capacity of coronaviruses, with results showing that at room temperature, SDS, SDC, and TFA successfully inactivated both coronaviruses, while GdmCl and urea resulted in partially incomplete inactivation.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Polymer Science
Malene Moller Jorgensen, Jenni Kathrine Sloth, Rikke Baek
Summary: The study on extracellular vesicles (EVs) emphasizes the importance of optimization experiments when characterizing EVs in a clinical setting. Factors such as storage conditions and additives have a significant impact on the results of EV Array analysis.
Article
Chemistry, Analytical
Fujia Wang, Tim Veth, Marije Kuipers, Maarten Altelaar, Kelly E. Stecker
Summary: A successful mass spectrometry-based phosphoproteomics analysis relies on effective sample preparation strategies. The performance of the S-Trap protocol for phosphoproteomics studies is unclear, and the addition of phosphoric acid (PA) in the existing protocol is detrimental to downstream phosphopeptide enrichment. This study systematically evaluates the performance of the S-Trap digestion for proteomics and phosphoproteomics, and demonstrates that an optimized S-Trap approach, with trifluoroacetic acid substituted for PA, is a simple and effective method for phosphoproteomics sample preparation.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Andrew P. Burns, Ya-Qin Zhang, Tuan Xu, Zhengxi Wei, Qin Yao, Yuhong Fang, Valeriu Cebotaru, Menghang Xia, Matthew D. Hall, Ruili Huang, Anton Simeonov, Christopher A. LeClair, Dingyin Tao
Summary: The development of a highly automated universal sample preparation platform has significantly improved the efficiency of proteomics sample preparation, enabling high-throughput extraction and analysis of proteins from various human cell types. This platform demonstrates excellent digestion efficiency, reproducibility, and universality in quantifying target proteins, showcasing its potential for clinical research.
ANALYTICAL CHEMISTRY
(2021)
Review
Spectroscopy
Qin Fu, Christopher I. Murray, Oleg A. Karpov, Jennifer E. Van Eyk
Summary: Sample preparation for mass spectrometry-based proteomics is time-consuming and prone to analytical errors, especially the proteolytic digestion step. Automated liquid handling workstations offer a reliable solution for sample processing, with diligent assessment of sample type, protocol design, reagents, and incubation conditions improving speed and consistency. Automated sample preparation facilitates increased throughput and reproducible quantitation of biomarker candidates, which is essential for processing large patient cohorts to validate potential clinical applications.
MASS SPECTROMETRY REVIEWS
(2023)
Article
Cell & Tissue Engineering
Alexandra Muntiu, Andrea Papait, Federica Vincenzoni, Alberto Vitali, Wanda Lattanzi, Pietro Romele, Anna Cargnoni, Antonietta Silini, Ornella Parolini, Claudia Desiderio
Summary: This study characterized the protein composition of the hAMSCs secretome using the FASP digestion and LC-MS approach. Gene ontology classification and functional protein interaction analysis were performed on the data using bioinformatics tools.
STEM CELL RESEARCH & THERAPY
(2023)
Review
Biochemistry & Molecular Biology
Van-An Duong, Hookeun Lee
Summary: Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomics is a powerful technique for analyzing cellular, tissue, and fluid proteomes. While LC-MS/MS and data analysis techniques have been well-developed, sample preparation remains a challenging and laborious process. In this review, various methods for sample preparation in proteomics, as well as devices and methods for integrating different steps of sample preparation and peptide fractionation, are outlined and discussed.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Geriatrics & Gerontology
Yanbao Yu, Harinder Singh, Keehwan Kwon, Tamara Tsitrin, Joann Petrini, Karen E. Nelson, Rembert Pieper
Summary: The study found that in the age range of 70 to 82, individuals with chronic illnesses have impaired immune function, which may indicate unhealthy aging. People with lower quantities of nine cytokines in the blood plasma are more likely to experience healthy aging.
Article
Cardiac & Cardiovascular Systems
Yi-Han Lin, Maryann P. Platt, Ryan P. Gilley, David Brown, Peter H. Dube, Yanbao Yu, Norberto Gonzalez-Juarbe
Summary: This study found significant alterations in the cardiac proteome and phosphoproteome after pulmonary influenza infection, with viral particles persisting in the heart. Inhibition of necroptosis or prevention of mitochondrial damage may be potential therapeutic interventions to reduce cardiac damage during influenza infections.
CIRCULATION RESEARCH
(2021)
Review
Immunology
Patricia M. Sikorski, Alessandra G. Commodaro, Michael E. Grigg
Summary: Toxoplasma's infection competence relies on its ability to inactivate the host complement system. By recruiting host regulatory proteins and limiting complement activation on its surface, Toxoplasma can shield itself from immediate lysis while still maintaining biological effector functions of complement products that stimulate protective immunity. This balance ultimately controls parasite burden systemically but can lead to exacerbated immune responses locally, impacting host survival and transmissibility.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Virology
Angelene M. Cantwell, Harinder Singh, Maryann Platt, Yanbao Yu, Yi-Han Lin, Yuji Ikeno, Gene Hubbard, Yan Xiang, Norberto Gonzalez-Juarbe, Peter H. Dube
Summary: The study reports a Syrian hamster model that develops severe COVID-19-like disease, showing dynamic innate immune responses and immune pathologies consistent with severe human disease. Using an integrated multiorgan analysis, changes in gene transcription and protein expression over the course of infection were evaluated to provide a kinetic overview of host responses to infection. The model will be valuable for understanding the pathogenesis of severe COVID-19 and testing interventions.
JOURNAL OF VIROLOGY
(2021)
Article
Immunology
Milkessa HaileMariam, Yanbao Yu, Harinder Singh, Takele Teklu, Biniam Wondale, Adane Worku, Aboma Zewude, Stephanie Mounaud, Tamara Tsitrin, Mengistu Legesse, Ameni Gobena, Rembert Pieper
Summary: The differential diagnosis of tuberculosis (TB) and latent TB infection (LTBI) is crucial in high TB burden countries. Diagnostic tests for LTBI rely on immune cell stimulation and measurements of interferon-gamma concentrations. The study identified potential sputum diagnostic biomarkers, such as differentially abundant proteins, that could aid in distinguishing TB disease states.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Medicine, General & Internal
Yanbao Yu, Harinder Singh, Tamara Tsitrin, Shiferaw Bekele, Yi-Han Lin, Patricia Sikorski, Kelvin J. Moncera, Manolito G. Torralba, Lisa Morrow, Randall Wolcott, Karen E. Nelson, Rembert Pieper
Summary: Biofilms composed of multiple microorganisms on indwelling urethral catheters can cause chronic infections. Bacteria in catheter biofilms are mainly Enterobacteriaceae species, and systemic antibiotic treatments may lead to microbial community perturbations. Proteomic analysis can provide insights into the mechanisms of infection caused by certain bacteria.
FRONTIERS IN MEDICINE
(2021)
Article
Microbiology
Maryann P. Platt, Yi-Han Lin, Rosana Wiscovitch-Russo, Yanbao Yu, Norberto Gonzalez-Juarbe
Summary: It has long been recognized that the combination of influenza and bacterial infections can lead to severe cardiac damage. This study provides the first in vivo evidence that influenza infection promotes the infiltration of Streptococcus pneumoniae into the heart, causing necrotic damage and proteomic remodeling.
Article
Multidisciplinary Sciences
Rui Tian, Xin Feng, Long Wei, Daoguo Dai, Ying Ma, Haifeng Pan, Shengxiang Ge, Lang Bai, Chaomin Ke, Yanlin Liu, Lixin Lang, Shoujun Zhu, Haitao Sun, Yanbao Yu, Xiaoyuan Chen
Summary: The authors propose a strategy to modify protein coatings with biofunctional molecules, resulting in long-wavelength fluorophores for in vivo imaging. These modified albumin variants protect inserted dyes, enhance their brightness, and can be genetically edited to develop size-tunable complexes with precise pharmacokinetics. This approach widens the clinical application prospects for NIR-II fluorophores.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Maryann P. Platt, Yi-Han Lin, Trevor Penix, Rosana Wiscovitch-Russo, Isha Vashee, Chris A. Mares, Jason W. Rosch, Yanbao Yu, Norberto Gonzalez-Juarbe
Summary: This study demonstrates that IAV can directly modulate the biology of Streptococcus pneumoniae (Spn) without the requirement of host effectors, supporting the idea that inter-kingdom interactions between human viruses and commensal pathobionts can promote bacterial pathogenesis and microbiome dysbiosis.
Article
Multidisciplinary Sciences
David Scieszka, Yi-Han Lin, Weizhong Li, Saibyasachi Choudhury, Yanbao Yu, Marcelo Freire
Summary: This study developed a model to decode the human genome and proteome of neutrophil extracellular traps (NETs), and validated and analyzed the model using in vitro systems. The results provide new insights into the molecular and cellular pathways involved in NET formation.
Editorial Material
Biochemical Research Methods
Chong Kim, Magali Carcenac, Hua-Chen Chang, William McAuliffe, Moo-jin Suh
Article
Endocrinology & Metabolism
Yuan Gui, Yuanyuan Wang, Zachary Palanza, Jack L. Wang, Priya Gupta, Jianling Tao, Yi Qiao, Geneva Hargis, Donald L. Kreutzer, Sheldon I. Bastacky, Yanbao Yu, Yanlin Wang, Silvia Liu, Haiyan Fu, Dong Zhou
Summary: This study revealed the connection between cellular mechanics and metabolism in fibrotic kidneys. The inhibition of CNN2, an actin stabilizer, was found to protect kidney function and alleviate fibrosis by regulating fatty acid oxidation. The interaction between CNN2, ESR2, and PPARa was also shown to play a role in kidney fibrosis. These findings provide insights for developing therapeutic strategies for kidney fibrosis.
MOLECULAR METABOLISM
(2023)
Article
Plant Sciences
Mayla Daiane Corre Molinari, Renata Fuganti-Pagliarini, Yanbao Yu, Lilian Hasegawa Florentino, Liliane Marcia Mertz-Henning, Rayane Nunes Lima, Daniela Matias de Carvalho Bittencourt, Marcelo Oliveira Freire, Elibio Rech
Summary: This study explored the proteomic profile of soybean bran for the first time and identified protein targets that remain stable and bioactive during processing, providing valuable information for improving soybean protein quality and quantity.
Article
Multidisciplinary Sciences
Hyesun Jang, Saibyasachi Choudhury, Yanbao Yu, Benjamin L. Sievers, Terri Gelbart, Harinder Singh, Stephen A. Rawlings, Amy Proal, Gene S. Tan, Yu Qian, Davey Smith, Marcelo Freire
Summary: An increasing number of studies have shown that COVID-19 is associated with inflammatory sequelae, and this study characterized the immune and proteome responses in plasma and saliva samples from convalescent COVID-19 patients. The results showed robust antibody responses in both saliva and plasma samples, and persistent inflammatory patterns were observed in convalescent samples. This study also suggests that saliva could be a viable fluid for monitoring immune responses and related sequelae.
Article
Medicine, Research & Experimental
Yong Zhang, Haonan Yang, Yanbao Yu, Ying Zhang
Summary: Nanostructured devices and nanoparticles have greatly advanced precision healthcare, while mass spectrometry-based proteomics has become a powerful tool for disease identification and drug development. The combination of these two disciplines has expanded our knowledge about human health and disease, with the help of nanotechnology-assisted sample processing strategies and emerging nanotechnologies.