Article
Immunology
Guo-ning Zhang, Ying-jia Xu, Lei Jin
Summary: This study aimed to identify differential expression of peptides associated with ankylosing spondylitis (AS) patients using LC-MS/MS analysis. Bioinformatics analysis indicated that these differentially expressed peptides might be associated with MHC class I protein binding and pathogenic Escherichia coli infection pathways, which might further affect the progression of AS. Three differentially expressed peptides were identified that could significantly promote the proliferation of fibroblasts in AS patients.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Mabel Deladem Tettey, Federico Rojas, Keith R. Matthews
Summary: This study identifies secreted peptidases released by trypanosomes and systematically assesses their role in stumpy formation in vivo. The results demonstrate the dominance of oligopeptidase B and metallocarboxypeptidase 1 in quorum sensing.
NATURE COMMUNICATIONS
(2022)
Article
Food Science & Technology
Yu-Ping Huang, Randall C. Robinson, Fernanda Furlan Goncalves Dias, Juliana Maria Leite Nobrega de Moura Bell, Daniela Barile
Summary: This study evaluated different SPE approaches and found that mixed-mode SPE is more suitable than conventional reverse-phase SPE in improving LC-MS/MS analysis of both oligosaccharides and peptides simultaneously.
Article
Pharmacology & Pharmacy
Ju-Hsuan Huang, Nhung Thi Phuong Nong, Jue-Liang Hsu
Summary: In this study, a combination of ACE pre-incubation, LC-MS, and stable-isotope labeling was used for efficient screening of ACE's exogenous substrates from milk hydrolysate. 31 substrates were identified, and their activities were confirmed using synthetic peptides. The study also revealed the protective effects of AYFYPELFR and HLPLPLLQSW against ACE-mediated hydrolysis of Ang-I, suggesting their potential as substrate-type inhibitors.
Article
Chemistry, Analytical
Amelie Descamps, Kevin Van der Borght, Anton De Spiegeleer, Evelien Wynendaelea, Bart De Spiegeleer
Summary: To improve the translation of peptidomic research, it is crucial to detect peptides at low levels in biofluids. This study investigates often neglected parts of the analytical process and proposes novel approaches for sample collection, preparation, chromatography, and MS detection. The recommendations provided will enhance the reliability of peptidomics bio-analytics.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2023)
Article
Multidisciplinary Sciences
Andrew R. Castle, Sang-Gyun Kang, Ghazaleh Eskandari-Sedighi, Serene Wohlgemuth, My-Anh Nguyen, Daniel J. Drucker, Erin E. Mulvihill, David Westaway
Summary: In prion infections, the cellular prion protein (PrPC) can convert to pathogenic conformations (PrPSc) and bind toxic oligomers formed by amyloid-beta alpha-synuclein and tau. β-Endoproteolysis of PrPC into N- and C-terminal fragments (N2 and C2) is of interest, but the proteolytic mechanism remains unconfirmed. A recent study identified S9B peptidase subfamily membrane proteins as potential β-cleavage candidates for PrPC.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biochemistry & Molecular Biology
Wendell Albuquerque, Parviz Ghezellou, Kwang-Zin Lee, Quintus Schneider, Phillip Gross, Tobias Kessel, Bodunrin Omokungbe, Bernhard Spengler, Andreas Vilcinskas, Holger Zorn, Martin Gand
Summary: In this study, the researchers used model wine haze proteins and confirmed that peptidases from Drosophila suzukii larvae can degrade the proteins under acidic conditions. The combination of mass spectrometry and protein modeling allowed for the visualization of cleavage sites. This research provides a valuable screening tool for finding optimal peptidases for wine clarification processes.
Article
Food Science & Technology
Santiaga Maria Vivanco-Maroto, Marta Santos-Hernandez, Javier Sanchon, Gianluca Picariello, Isidra Recio, Beatriz Miralles
Summary: This study evaluated the use of enzymes from the brush border membrane (BBM) in simulated gastrointestinal digestion of milk proteins. The use of BBM resulted in additional cleavages and a decrease in the number of identified peptides. Comparing the simulated gastrointestinal digests with human digests, BBM did not significantly change the peptide profile but allowed the identification of peptides found in human digests. Additionally, the study evaluated the transepithelial transport of resistant peptides and found that the nature of the peptide ends was important for the transport rate.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Microbiology
Nikita Alkin, Yakov Dunaevsky, Elena Elpidina, Galina Beljakova, Valeria Tereshchenkova, Irina Filippova, Mikhail Belozersky
Summary: Proline-specific peptidases (PSP) are essential for processing fungal toxins, pheromones, and intracellular signaling, with potential applications in biotechnology. In silico analysis of PSP homologs in 42 species of higher fungi revealed characteristic homologs from various kingdoms and families of peptidases. Phylogenetic analysis suggested a duplication of ancestral DPP4 into transmembrane and secreted versions, predating the split of ascomycete and basidiomycete lineages. Comparative biochemical analysis showed the activity and stability of DPP4 under alkaline conditions and high salt concentrations in alkaliphilic and alkali-tolerant fungal strains.
Article
Chemistry, Analytical
Xuefei Zhong, Shruti Nayak, Lili Guo, Shivkumar Raidas, Yunlong Zhao, Rachel Weiss, Matthew Andisik, Chinnasamy Elango, Giane Sumner, Susan C. Irvin, Michael A. Partridge, Hong Yan, Sook E. Yen, Haibo Qiu, Yuan Mao, Albert Torri, Ning Li
Summary: REGEN-COV, a cocktail of two human monoclonal antibodies, has shown promising results in reducing SARS-CoV-2 viral load in COVID-19 patients. A liquid chromatography-mass spectrometry method was developed for the determination of REGEN-COV concentrations in serum samples from patients participating in clinical trials. The concentrations measured by this method were comparable to those measured by a validated immunoassay.
ANALYTICAL CHEMISTRY
(2021)
Review
Biochemical Research Methods
Zheng Zhang, Yujie Li, Wenqian Yuan, Zhiwei Wang, Cuihong Wan
Summary: Short open reading frames (sORFs) have the potential to encode proteins, leading to a new research focus in proteomics. Mass spectrometry (MS) is a significant tool for directly detecting the sequence of sORF encoded peptides (SEPs), but the low abundance and short sequences of SEPs present challenges in detection.
Article
Microbiology
Katharina Bersching, Thomas Michna, Stefan Tenzer, Stefan Jacob
Summary: The dynamic interplay of signaling networks in cellular processes is characterized by reversible protein phosphorylation. Quantitative phospho-peptidomics has become a powerful platform for comprehensively analyzing the phosphorylation profile of living organisms. However, the presence of missing values in experimental procedures remains a major problem, reducing confidence in subsequent bioinformatic processing. By using data independent acquisition (DIA) in a filamentous fungus model organism, we were able to increase data completeness while maintaining data quality, providing a refined methodology for investigating signaling processes in filamentous fungi.
Article
Chemistry, Analytical
Alan B. Moran, Richard A. Gardner, Manfred Wuhrer, Guinevere S. M. Lageveen-Kammeijer, Daniel I. R. Spencer
Summary: Sialic acids play diverse biological roles and linkage-specific analysis is important in glycomic studies. The combination of procainamide fluorescent labeling with sialic acid linkage-specific derivatization is presented, which allows for unambiguous assignment of sialic acid linkages and separation of sialylated isomers.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Philipp T. Kaulich, Liam Cassidy, Juergen Bartel, Ruth A. Schmitz, Andreas Tholey
Summary: The use of multiple proteases in GeLC-MS/MS analysis can improve the identification and sequence coverage of small proteins and SEPs. Combining data from various proteases helped identify more small proteins and SEPs, enhancing their molecular characterization capabilities.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Agronomy
Archis Pandya, Bjorn Thiele, Andres Zurita-Silva, Bjorn Usadel, Fabio Fiorani
Summary: The study evaluated saponin content and their corresponding sapogenins in 114 different quinoa accessions, showing considerable variability in saponin content in quinoa. Approximately 75% of the genotypes were classified as low-saponin content lines, which is promising for current and future quinoa breeding programs. Additionally, twelve saponins of the oleanane type were identified, including a previously unreported compound, contributing to the valorization of genetic resources for quinoa.
Review
Immunology
Petric Kuballa, Whitney M. Nolte, Adam B. Castoreno, Ramnik J. Xavier
ANNUAL REVIEW OF IMMUNOLOGY, VOL 30
(2012)
Review
Biochemistry & Molecular Biology
Anna Mari Lone, Yun-Gon Kim, Alan Saghatelian
CURRENT OPINION IN CHEMICAL BIOLOGY
(2013)
Article
Biochemistry & Molecular Biology
Whitney M. Nolte, Jean-Philippe Fortin, Benjamin D. Stevens, Gary E. Aspnes, David A. Griffith, Lise R. Hoth, Roger B. Ruggeri, Alan M. Mathiowetz, Chris Limberakis, David Hepworth, Philip A. Carpino
NATURE CHEMICAL BIOLOGY
(2014)
Article
Biochemical Research Methods
Yun-Gon Kim, Anna Mari Lone, Alan Saghatelian
Article
Multidisciplinary Sciences
Anna Mari Lone, Mathias Leidl, Amanda K. McFedries, James W. Horner, John Creemers, Alan Saghatelian
Article
Multidisciplinary Sciences
Yun-Gon Kim, Anna Mari Lone, Whitney M. Nolte, Alan Saghatelian
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2012)
Review
Immunology
Anna Mari Lone, Kjetil Tasken
FRONTIERS IN IMMUNOLOGY
(2013)
Article
Chemistry, Medicinal
Whitney M. Nolte, Robert T. Tessman, Jennifer L. Goldman
MEDICINAL CHEMISTRY RESEARCH
(2020)
Article
Pharmacology & Pharmacy
Anna Mari Lone, Kjetil Tasken
Summary: PGE(2) plays a crucial role in regulating T cell signaling, with studies revealing its effects in different pathways and the crosstalk between signaling pathways triggered by the four distinct receptors.
MOLECULAR PHARMACOLOGY
(2021)
Article
Pharmacology & Pharmacy
Stephani L. Stancil, Whitney Nolte, Robin E. Pearce, Vincent S. Staggs, J. Steven Leeder
Summary: This study aimed to investigate the factors influencing the biotransformation of naltrexone. The results showed that there is significant variability in naltrexone biotransformation in both children and adults, and it is influenced by age, sex, and genetic variation.
DRUG METABOLISM AND DISPOSITION
(2022)
Article
Biochemistry & Molecular Biology
Anna M. Lone, Piero Giansanti, Marthe Jontvedt Jorgensen, Enio Gjerga, Aurelien Dugourd, Arjen Scholten, Julio Saez-Rodriguez, Albert J. R. Heck, Kjetil Tasken
Summary: This study comprehensively characterized PGE(2) signaling networks in different T cell subsets, identifying key signaling nodes and pathways. It revealed distinct signaling outputs in T cell subtypes, with strong signaling in EP2-stimulated CD8(+) cells. The study also highlighted the contribution of G protein-independent signaling and suggested potential functional predictions from observed phosphosite changes.
Article
Biochemical Research Methods
Robert T. Tessman, Whitney Nolte, Paul Toren, Kim Gibson, Linda Vu, Jennifer Goldman
Summary: A reliable method has been developed for the quantification of TMP and its metabolites in human plasma. The method achieves chromatographic separation in less than 8 minutes and utilizes mass spectrometry for detection.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2022)
Article
Medicine, Research & Experimental
Stephani L. Stancil, Michaela Voss, Whitney Nolte, John Tumberger, William Adelman, Susan Abdel-Rahman
Summary: This study evaluated the exposure to NTX in adolescents with eating disorders. The results showed that systemic exposure to NTX is highly variable in adolescents and is modulated, in part, by AKR1C4 genotype and food intake.
CTS-CLINICAL AND TRANSLATIONAL SCIENCE
(2022)
Article
Pharmacology & Pharmacy
Heather Eng, Raman Sharma, Thomas S. McDonald, David J. Edmonds, Jean-Philippe Fortin, Xianping Li, Benjamin D. Stevens, David A. Griffith, Chris Limberakis, Whitney M. Nolte, David A. Price, Margaret Jackson, Amit S. Kalgutkar
DRUG METABOLISM AND DISPOSITION
(2013)