Article
Food Science & Technology
Xuening Yu, Shijie Dou, Xiaoyang Liu, Fawen Yin, Deyang Li, Pengfei Jiang, Dayong Zhou
Summary: This study developed a new zinc supplement delivery system that showed stability and absorption in gastrointestinal environments. The system had a high zinc ion release rate and slow-release effects, resulting in better zinc absorption.
Article
Food Science & Technology
Jorge Parodi, Hector Herrera, Rodrigo Sanchez, Brian Effer
Summary: This study proposes a proteolysis system to indirectly assess the quality of protein in salmonid diets. By using an artificial gastric solution and conducting experiments, the source and quality of protein can be evaluated, providing support for nutrition studies.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Food Science & Technology
Kangyi Zhang, Qingyu Wen, Yufei Wang, Tianqi Li, Bin Nie, Yu Zhang
Summary: In this study, the in vitro digestion process of green wheat protein (GWP) was simulated to explore its digestibility. The protein was mainly digested by trypsin and the digestion process led to changes in particle size and structure. The peptide lengths were relatively dispersed and the molecular weight of the digestion products varied. Sensitizing peptide sequence of wheat protein was detected in the final digestion products of GWP.
FOOD SCIENCE & NUTRITION
(2022)
Article
Biochemical Research Methods
Neil A. McCracken, Sarah A. Peck Justice, Aruna B. Wijeratne, Amber L. Mosley
Summary: The study introduces a user-friendly analysis of the melt shift calculation workflow and quantitatively assesses the impact of key steps in the analysis workflow on the final output list of stabilized and destabilized proteins. It also presents a more optimized analysis workflow, illustrating the importance of selected calculation steps on the final list of reported proteins of interest in a study. The development of the R based program Inflect offers a valuable resource for the research community to analyze data from TPP and CETSA experiments.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Analytical
Philip J. Jakubec, Alan A. Doucette
Summary: An improved transmembrane electrophoresis device has been developed in this study for rapid depletion of sodium dodecyl sulfate (SDS), achieving a final concentration of less than 5 ppm with high analyte recovery. The device was successfully utilized in a detergent-based proteomic workflow, demonstrating significant protein recovery and increasing the number of identifications.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Qingce Zang, Manjiangcuo Wang, Ying Zhu, Lingzhi Wang, Zhigang Luo, Xin Li, Jiuming He, Ruiping Zhang, Zeper Abliz
Summary: The study developed a novel hydrogel-assisted chemical derivatization approach for enhanced visualization of inaccessible molecules in biological tissues and successfully detected and visualized unusual carbonyl metabolites in rat brain, kidney, and liver tissue. The methodology provides a new approach to enhance chemical labeling for in situ tissue submetabolome profiling and improve understanding of the molecular histology and complex metabolism of biological tissues.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Maxwell C. McCabe, Lauren R. Schmitt, Ryan C. Hill, Monika Dzieciatkowska, Mark Maslanka, Willeke F. Daamen, Toin H. van Kuppevelt, Danique J. Hof, Kirk C. Hansen
Summary: The study reveals the challenge of identifying proteins in the extracellular matrix but demonstrates a significant improvement through optimized extraction methods. Different approaches to ECM extraction were explored in the research, providing insights for better evaluation of ECM proteins.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Food Science & Technology
Bianca Chima, Paul Mathews, Scott Morgan, Sarah A. Johnson, Charlene B. Van Buiten
Summary: Polyphenols are beneficial to human health, but their intake is low in the United States due to the low consumption of fruits and vegetables. Dairy foods such as milk and yogurt can increase the bioavailability of polyphenols through protein-polyphenol interactions. The study compared whey, pea, and hemp proteins for their ability to form complexes with polyphenols from blueberries. The results showed that pea and hemp proteins had stronger binding affinities with blueberry polyphenols than whey. The pH of the solution was found to play a role in protein-polyphenol complex formation.
Article
Biochemical Research Methods
Stephanie Biedka, Brigitte F. Schmidt, Nolan M. Frey, Sarah M. Boothman, Jonathan S. Minden, Amber Lucas
Summary: This study presents a new protein sample preparation method, ProMTag, which enables whole proteome capture, cleanup, and release of intact proteins, as well as generation of peptides for downstream analysis. The ProMTag workflow yields high percentages for both intact proteins and proteome digests, making it a versatile and high-quality approach for proteome sample preparation.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Maria Ryaboshapkina, Kevin Saitoski, Ghaith M. Hamza, Andrew F. Jarnuczak, Severine Pechberty, Claire Berthault, Kaushik Sengupta, Christina Rye Underwood, Shalini Andersson, Raphael Scharfmann
Summary: In this study, the representativeness of EndoC-beta H1 cells as a translational human beta cell model was verified through omics analysis. The secretome of EndoC-beta H1 cells was characterized, revealing similarities and differences compared to human beta cells and insulinomas. The study also identified a high proportion of extracellular vesicle proteins in the secretome of EndoC-beta H1 cells. These findings provide valuable insights into the secretion regulation of human beta cells and warrant further investigation.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Food Science & Technology
Yuhan Chen, Hanzhi Jing, Shanbai Xiong, Anne Manyande, Hongying Du
Summary: This study compared the differences in digestion between fat-removed pork and grass carp. The results showed that grass carp was more easily digested, with a higher degree of hydrolysis, smaller protein particle size, and greater release of oligopeptides and amino acids. The degradation of protein structure during gastric digestion was more pronounced in pork than in grass carp. The antioxidant properties of the digestive fluids from the two types of meat varied in different assays, but TCA-soluble peptides, random coil content, and particle size significantly influenced both types. These findings provide new insights into protein structure and antioxidant properties in meat digestion, contributing to the understanding of the nutritional value of pork and grass carp.
Article
Biochemical Research Methods
Pedro H. M. Torres, Artur D. Rossi, Tom L. Blundell
Summary: Recent advances in gene sequencing technologies and protein structure knowledge have enabled the construction of proteome-scale databases. However, most biological processes involve oligomerization, which is often not represented in current protein model databases. To address this issue, ProtCHOIR was developed to automatically generate homo-oligomeric structures, providing detailed information for input proteins and output complexes.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
L. Sunil, Prakruthi Appaiah, Asha Martin, Prasanna Vasu
Summary: Through a combination of experimental data and theoretical modeling, a protein enriched with branched-chain amino acids was successfully designed and confirmed to be easily digestible and non-allergenic, offering a potential supplementary approach for the treatment of chronic liver diseases.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Plant Sciences
Liang Chai, Haojie Li, Xiaoguang Zhao, Cheng Cui, Benchuan Zheng, Ka Zhang, Jun Jiang, Jinfang Zhang, Liangcai Jiang
Summary: In this study, we compared the genomes, transcriptomes, and proteomes of the rapeseed lines zws-ms and zws-217, finding genes that may be associated with the multi-silique trait, such as BnaA09g05900D encoding an MADS-box protein. We also identified differentially accumulated proteins related to homologous recombination and mismatch repair pathways. This study provides insights into the mechanism of multi-pistil flower formation, which can facilitate future research on rapeseed production.
Article
Chemistry, Analytical
Kunning Lin, Jin Xu, Huige Guo, Yunlong Huo, Yuanbiao Zhang
Summary: A flow injection analysis (FIA) method was established for the spectrophotometric determination of total dissolved nitrogen (TDN) in natural waters. The method, which uses an on-line ultraviolet digester and vanadium chloride reductant, showed accurate and reliable results with high potential for field or monitoring applications. Recovery rate from natural water samples was between 87.0 and 104.4%, and the method was validated using certified reference materials.
MICROCHEMICAL JOURNAL
(2021)
Article
Chemistry, Analytical
Gregory W. Vandergrift, William Kew, Jessica K. Lukowski, Arunima Bhattacharjee, Andrey Liyu, Elizabeth A. Shank, Ljiljana Pasa-Tolic, Venkateshkumar Prabhakaran, Christopher R. Anderton
Summary: This study combines nanospray desorption electrospray ionization mass spectrometry with 21T FTICR MS, enabling high-resolution and accurate ambient sampling and imaging. By conducting experiments on biological samples and imaging rat brain tissue, isotopic fine structure (IFS) information can be obtained, providing further confidence in molecular annotation.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Elvin R. Cabrera, Brian H. Clowers
Summary: This study describes a method of modulating the ion gates of ion mobility spectrometry using a discrete stepwise function, achieving synchronization between the generated frequencies and the scan rate of the linear ion trap. This method eliminates the ambiguity of assigning the ion current derived from a single modulation frequency and maintains high levels of precision across different combinations.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2022)
Article
Multidisciplinary Sciences
Sung-Hwan Cho, Katalin Toth, Daewon Kim, Phuc H Vo, Chung-Ho Lin, Pubudu P. Handakumbura, Albert Rivas Ubach, Sterling Evans, Ljiljana Pasa-Tolic, Gary Stacey
Summary: The mevalonate pathway is crucial for cellular processes in both animals and plants. In plants, it affects growth, development, and response to stress. The interaction between mevalonate kinase and extracellular ATP receptor P2K1, with phosphorylation impacting plant metabolism, emphasizes the significance of purinergic signaling and the role of eATP in influencing plant metabolic pathways.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Jesse W. Wilson, Aivett Bilbao, Juan Wang, Yen-Chen Liao, Dusan Velickovic, Roza Wojcik, Marta Passamonti, Rui Zhao, Andrea F. G. Gargano, Vincent R. Gerbasi, Ljiljana Pasa-Tolicprime, Scott E. Baker, Mowei Zhou
Summary: SARS-CoV-2 cellular infection is mediated by heavily glycosylated spike protein. Recombinant spike protein and receptor-binding domain (RBD) play important roles in seropositivity assays and potential vaccines against viral infection. Liquid chromatography coupled to mass spectrometry is used to characterize post-translational modifications, including glycosylation. The HILIC top-down MS platform shows great potential in resolving heterogeneous glycoproteins for quality control applications.
ANALYTICAL CHEMISTRY
(2022)
Review
Microbiology
Noah W. Sokol, Eric Slessarev, Gianna L. Marschmann, Alexa Nicolas, Steven J. Blazewicz, Eoin L. Brodie, Mary K. Firestone, Megan M. Foley, Rachel Hestrin, Bruce A. Hungate, Benjamin J. Koch, Bram W. Stone, Matthew B. Sullivan, Olivier Zablocki, Jennifer Pett-Ridge
Summary: Soil microorganisms play a critical role in global biogeochemical cycles, and their metabolic functions are influenced by ecological interactions and the surrounding environment. Understanding microbial life and death can help predict soil biogeochemical dynamics.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Cell Biology
Miriam Pasquini, Nicolas Grosjean, Kim K. Hixson, Carrie D. Nicora, Estella F. Yee, Mary Lipton, Ian K. Blaby, John D. Haley, Crysten E. Blaby-Haas
Summary: The evolution of zinc as a protein cofactor altered the functional landscape of biology, but dependency on zinc also created an Achilles' heel, necessitating adaptive mechanisms to ensure zinc availability to proteins. Evidence for a conserved family of putative metal transferases was presented, which interact with zinc-dependent proteins. In vitro experiments showed that these transferases can transfer zinc or cobalt to apo-proteins.
Article
Biochemistry & Molecular Biology
Jongmin Woo, Geremy C. Clair, Sarah M. Williams, Song Feng, Chia-Feng Tsai, Ronald J. Moore, William B. Chrisler, Richard D. Smith, Ryan T. Kelly, Ljiljana Pasa-Tolic, Charles Ansong, Ying Zhu
Summary: Single-cell proteomics (scProteomics) is a powerful tool for studying cell functions in complex biological systems. However, current methods face challenges in identifying and quantifying low-abundance proteins accurately. In this study, we present a method called transferring identification based on FAIMS filtering (TIFF), which combines ion mobility-enhanced mass spectrometry acquisition and peptide identification to improve the sensitivity and accuracy of label-free scProteomics. By filtering out singly charged ions, the TIFF method extends the ion accumulation times for peptide ions. Peptide identities are determined using a three-dimensional MS1 feature matching approach. Using TIFF, we achieved unbiased proteome analysis of over 1,700 proteins in single HeLa cells, with more than 1,100 proteins consistently identified. We also applied the TIFF method to study time-dependent proteome changes in single murine macrophage cells during lipopolysaccharide stimulation.
Article
Chemistry, Analytical
Zackary R. Kinlein, Gordon A. Anderson, Brian H. Clowers
Summary: This paper presents a simplified platform for lossless ion manipulation using traveling wave structures. Technological innovations and methodologies are introduced to simplify the experimentation process and accelerate the prototyping. The efficacy of the platform is demonstrated through various experiments, showing the potential to expand the adoption of this technique.
Article
Chemistry, Analytical
Matthew B. Kilgore, Dimitrios Platis, Timothy Lim, Samantha Isenberg, C. Austin Pickens, Carla Cuthbert, Konstantinos Petritis
Summary: First-tier MS-based newborn screening has high presumptive positive rates, which can be reduced by using second-tier LC-MS/MS screening assays. The multiplexed second-tier method using HILIC column and MS/MS system can detect multiple disorders simultaneously in dried blood spots.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Kevin J. Zemaitis, Mowei Zhou, Willia M. Kew, Ljiljana Pasa-Tolic
Summary: MALDI imaging enables the profiling of proteoforms at a near-cellular level, but identifying unknowns using only intact mass information remains a challenge. Supplementary methods, such as bottom-up and/or top-down proteomics, have been used to create experimental databases for accurate mass matching. This study demonstrates the feasibility of top-down analyses of isolated MALDI protein ions using 193 nm ultraviolet photodissociation, allowing for more comprehensive characterization of proteoforms in MALDI imaging applications.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Medical Laboratory Technology
C. Austin Pickens, Elya Courtney, Samantha L. Isenberg, Carla Cuthbert, Konstantinos Petritis
Summary: In this study, a new method for newborn screening was developed to identify pre-symptomatic homocystinuria (HCU) by measuring the levels of total homocysteine (tHcy) in first-tier screening. The method used selective derivatization techniques and flow injection analysis-tandem mass spectrometry (FIA-MS/MS) for accurate quantification of tHcy.
CLINICAL CHEMISTRY
(2023)
Article
Genetics & Heredity
Paul Dantonio, Norma P. P. Tavakoli, Brooke Migliore, Elizabeth McCown, Timothy Lim, Sunju Park, Michele Caggana, Katerina S. S. Kucera, Han Phan, Natalie Street, Konstantinos Petritis, Robert F. F. Vogt
Summary: Pilot studies for newborn bloodspot screening to detect Duchenne Muscular Dystrophy (DMD) are being conducted in the US and RTI International. The US CDC NSQAP provided DBS reference materials with different levels of CK-MM for these studies, and the results from each laboratory correlated well with the CK-MM levels. This set of reference materials allows quality assessment of CK-MM levels in both normal and DMD-affected newborns.
INTERNATIONAL JOURNAL OF NEONATAL SCREENING
(2023)
Article
Genetics & Heredity
M. Christine Dorley, George J. Dizikes, Charles Austin Pickens, Carla Cuthbert, Khaja Basheeruddin, Fizza Gulamali-Majid, Paul Hetterich, Amy Hietala, Ashley Kelsey, Tracy Klug, Barbara Lesko, Michelle Mills, Shawn Moloney, Partha Neogi, Joseph Orsini, Douglas Singer, Konstantinos Petritis
Summary: In newborn screening, false-negative results can lead to disability and death, while false-positive results cause parental anxiety and unnecessary follow-ups. Harmonization of enzyme activities for Pompe and MPS I across laboratories and testing methods has been proposed to minimize false-negative and false-positive results and correct for method differences. Although reasonable agreement was achieved through harmonization, the reporting of results still depends on the cutoffs set by each laboratory.
INTERNATIONAL JOURNAL OF NEONATAL SCREENING
(2023)
Article
Genetics & Heredity
Elya Courtney, C. Austin Pickens, Carla Cuthbert, Konstantinos Petritis
Summary: MPS-II is a lysosomal storage disorder caused by deficiency in iduronate 2-sulphatase (I2S) enzyme. Cold-induced water ACN phase separation (CIPS) was investigated to improve the detection of I2S products without detrimental effects on other analytes. Using CIPS in dried blood spots (DBS) represents a promising method for achieving cleaner sample extracts in a new 7-plex LSD screening panel.
INTERNATIONAL JOURNAL OF NEONATAL SCREENING
(2023)
Meeting Abstract
Biotechnology & Applied Microbiology
Swapna Kollu, Anusha Sairavi, Stephanie Thibert, Mowei Zhou, Xiao-Xin Sun, Mushui Dai, Ljiljana Pasa-Tolic, Hiroyuki Nakai
