Article
Biochemical Research Methods
Nhu Q. Vu, Hsu-Ching Yen, Lauren Fields, Weifeng Cao, Lingjun Li
Summary: Neuropeptides play important regulatory roles in biochemical, physiological, and behavioral processes. This study introduces HyPep, a novel database searching tool that utilizes sequence homology searching for neuropeptide identification. The performance of HyPep was optimized and compared with a commercial database searching software, PEAKS DB, using LC-MS/MS measurements. HyPep identified more neuropeptides than PEAKS DB at a 1% false discovery rate and both programs had a false match rate of 2%. The report also highlights how HyPep can aid in the discovery of novel neuropeptides.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Michael C. Yoon, Janneca Ames, Charles Mosier, Zhenze Jiang, Sonia Podvin, Anthony J. O'Donoghue, Vivian Hook
Summary: This study analyzed the proteases involved in neuropeptide processing using peptide profiling, and found that cathepsin L and cathepsin V cleave at the N-terminal side and between dibasic residues, while PC1/3 and PC2 cleave at the C-terminal side of a few peptide substrates. Cathepsin L showed the highest specific activity.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Claudia Neves Correa, Louise Oliveira Fiametti, Gabriel Marques de Barros, Leandro Mantovani de Castro
Summary: This study identified 1080 peptides in the gills of the seahorse H. reidi using fast heat inactivation of proteases and liquid chromatography coupled to mass spectrometry. Among these peptides, 1013 were present in all samples and 67 were identified in an additional LC-MS/MS run from an alkylated and reduced pool of samples. The majority of the identified peptides were fragments of the internal region of precursor proteins, including ribosomal proteins, histones, and hemoglobin, and some fragments from moronecidin-like protein with antimicrobial activity were also found.
Article
Chemistry, Analytical
Junxian Li, Xiang Lv, Bingxv Li, Lina Liu, Chengli Yu, Haibo Cheng, Jing Zhou, Yuyu Zhu, Hongyue Ma
Summary: In this study, high-resolution mass spectrometry-based peptidomics platforms were used to identify and analyze peptides in Cinobufacini. Specific peptides were discovered using a gel- and HLB-based separation and purification system, and confirmed through target parallel reaction monitoring mode. This mapping provides important peptide information for the quality control of Bufo bufo gargarizans skin and its preparation.
JOURNAL OF SEPARATION SCIENCE
(2022)
Review
Biochemical Research Methods
Rachel E. Foreman, Amy L. George, Frank Reimann, Fiona M. Gribble, Richard G. Kay
Summary: Improvements in LC and MS instrumentation have enhanced proteomic and metabolomic analysis, but there has been less focus on detecting and quantifying small bioactive peptides. It is important to preserve the structure of processed peptide products to prevent misidentification and consider the stability of peptides in biological matrices when developing methods to study them. Bioinformatic analysis of peptidomics data sets should include specific post-translational modifications critical for the function of bioactive peptides.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Cell Biology
Marlies K. R. Peeters, Geert Baggerman, Ralf Gabriels, Elise Pepermans, Gerben Menschaert, Kurt Boonen
Summary: Bioactive peptides play crucial roles in various biological processes. However, peptides originating from small open reading frames with unique expression patterns face challenges in full characterization. This study introduces a proteogenomics methodology and machine learning tools to improve identification of potential bioactive peptides in the mouse brain, enhancing understanding of the neuropeptidome.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Nhu Q. Vu, Kellen DeLaney, Lingjun Li
Summary: Neuropeptides are important endogenous peptides in the nervous system regulating physiological functions, and investigating their dysregulation is crucial for understanding their role in diseases. Mass spectrometry, especially mass spectrometry imaging (MSI), is a powerful tool for global profiling multiple neuropeptides simultaneously. Recent advancements in MSI sample preparation and instrumentation have shown improvements in neuropeptide detection, signal to noise ratio, and spatial resolution, indicating potential for clinical applications.
CURRENT PROTEIN & PEPTIDE SCIENCE
(2021)
Review
Biochemistry & Molecular Biology
Besnik Muqaku, Patrick Oeckl
Summary: Mass spectrometry is an important technique for analyzing biomolecules, especially in the field of neurodegenerative diseases where peptidomics analysis of cerebrospinal fluid samples has played a crucial role.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cardiac & Cardiovascular Systems
Shenglong Zhao, Chenghong Yin, Yanhong Zhai, Zhaoxia Jia, Shaofei Su, Yifan Lu, Lanlan Meng, Chunbo Li, Xiang Liu, Yuting Cong, Youran Li, Ying Liu, Lu Chen, Jing Wang, Zhengwen Xu, Yuanyuan Zheng, Zhi Sun, Ruben Y. Luo, Xiaobo Yu, He S. Yang, Xiaowei Liu, Zhen Zhao, Zheng Cao
Summary: The study identified and validated a novel three-peptide biomarker panel predictive for preeclampsia in pregnant women using peptidomics. The levels of three peptides (FGA-1033.4, ITIH4-2026.9, ITIH4-2051.1) showed significant differences between PE-positive and PE-negative groups, with an AUC of 0.985 and 0.923 in the discovery and validation cohorts respectively.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2022)
Article
Biochemical Research Methods
Pawel Marciniak, Joanna Pacholska-Bogalska, Lapo Ragionieri
Summary: This study analyzed the neuropeptidomes of two closely related tenebrionid beetles, Tenebrio molitor and Zophobas atratus, providing a basis for further functional studies and the design of environmentally friendly peptidomimetics. The identification of numerous neuropeptides and protein hormones precursors in these beetles will be useful for optimizing production programs and could potentially lead to the development of new biopesticides.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Alejandro Heres, Marta Gallego, Leticia Mora, Fidel Toldra
Summary: Reducing salt in meat products can affect the natural mechanisms of proteolysis, leading to changes in texture and flavor. This study quantified the presence of dipeptides in low-salt Spanish dry-cured ham using mass spectrometry. The results showed a correlation between these dipeptides and taste attributes, as well as potential health benefits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Immunology
Chun-Xue Zhou, Min Gao, Bing Han, Hua Cong, Xing-Quan Zhu, Huai-Yu Zhou
Summary: Our study utilized a label-free peptidomics approach to identify over 2,700 endogenous peptides in the brains of hosts infected with Toxoplasma gondii. Quantitative analysis revealed hundreds of differentially expressed peptides during acute and chronic infection stages. Functional analysis suggested these peptides play roles in cellular processes and come from cell parts.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Chemistry, Applied
Olivia Ogilvie, Sarah Roberts, Kevin Sutton, Nigel Larsen, Juliet Gerrard, Laura Domigan
Summary: The study investigated the impact of adding different concentrations of mTG to bread on gluten structure, digestibility, and immunogenic peptides. The results showed that the addition of mTG did not affect the deamidation state and digestibility of immunogenic peptides, indicating that mTG addition does not produce activated gluten peptides.
Editorial Material
Biochemistry & Molecular Biology
James W. Checco
Summary: Peptidomics is an underutilized method that uses mass spectrometry to identify and measure endogenous peptides, which play crucial biological roles and have potential as biomarkers. This article serves as a brief introduction to peptidomics, aiming to raise awareness and encourage its application among researchers interested in studying endogenous peptides.
ACS CHEMICAL NEUROSCIENCE
(2023)
Article
Chemistry, Analytical
Eduardo A. De la Toba, Sara E. Bell, Elena Romanova, Jonathan Sweedler
Summary: Neuropeptides play important roles in physiological processes and diseases. Mass spectrometry has become a powerful tool for quantitatively measuring neuropeptides, but there are challenges to overcome. This review provides an overview of mass spectrometry-based measurement approaches for neuropeptides and discusses techniques to address the challenges.
ANNUAL REVIEW OF ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Michal Aleksander Ciach, Blazej Miasojedow, Grzegorz Skoraczynski, Szymon Majewski, Michal Startek, Dirk Valkenborg, Anna Gambin
Summary: This study developed a linear regression algorithm based on the Wasserstein distance, improving the estimation accuracy of mass spectra data and reducing the preprocessing requirements for spectra. Experimental results showed that this method effectively handles measurement inaccuracies occurring in real experiments.
RAPID COMMUNICATIONS IN MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Joris Van Houtven, Jef Hooyberghs, Kris Laukens, Dirk Valkenborg
Summary: Data normalization is crucial for differential expression studies in omics, and the CONSTANd method offers a fast and effective solution for researchers in different omics contexts. Adoption of this method could facilitate data integration in multiomics experiments.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Chemistry, Analytical
Thijs Becker, Kaat Vandecasteele, Christos Chatzichristos, Wim Van Paesschen, Dirk Valkenborg, Sabine Van Huffel, Maarten De Vos
Summary: Research on wearable technology for EEG monitoring aims to improve seizure detection accuracy in epilepsy patients by using automated algorithms to assist neurologists in analyzing EEG data. The study shows that deferring some data for expert analysis can lead to nearly perfect detection sensitivity. Additionally, filtering out unreliable EEG segments based on trust scores can decrease false detection rates while maintaining stable detection sensitivity.
Article
Nutrition & Dietetics
Juliana A. S. Leite, Carlos A. Montoya, Simon M. Loveday, Evelyne Maes, Jane A. Mullaney, Warren C. McNabb, Nicole C. Roy
Summary: The study found that there are differences in non-specific protease activity in whey and casein fractions among different ruminant milk species. Specific thermal treatments could be utilized to retain better protease activity in all ruminant milk species.
FRONTIERS IN NUTRITION
(2021)
Article
Biochemistry & Molecular Biology
Joris Van Houtven, Bart Cuypers, Pieter Meysman, Jef Hooyberghs, Kris Laukens, Dirk Valkenborg
Summary: This study investigated the application of a normalization method called CONSTANd in transcriptomics and proposed an adjustment for joint analysis. The results showed that CONSTANd can efficiently process large datasets, reduce systematic bias, and quickly reveal the underlying biological structure.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Review
Physiology
Alejandro Correa Rojo, Dries Heylen, Jan Aerts, Olivier Thas, Jef Hooyberghs, Gokhan Ertaylan, Dirk Valkenborg
Summary: Quantitative proteomics, as a powerful technology complementing genetics, provides insights into the dynamic behavior of proteins. It has a wide range of applications in clinical diagnostics, treatment stratification, and drug discovery in precision medicine.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Annelies Agten, Piotr Prostko, Melvin Geubbelmans, Youzhong Liu, Thomas De Vijlder, Dirk Valkenborg
Summary: Structural modifications of DNA and RNA molecules are crucial in epigenetic and posttranscriptional regulation. Various MS and MS/MS-based tools are being developed for the analysis of nucleic acids. A modeling approach has been presented to predict the isotope distribution of DNA and RNA molecules based on their elemental composition.
Article
Food Science & Technology
Weijun Chen, Hoi Tung Chiu, Ziqian Feng, Evelyne Maes, Luca Serventi
Summary: Spray-drying and freeze-drying can extend shelf life and improve transportability of high-nutritional foods, but their effects on nutrition are unclear. Results show that spray-dried pea water has higher fiber content, while freeze-dried pea water has the opposite.
Article
Chemistry, Applied
Evelyne Maes, Santanu Deb-Choudhury, Stefan Clerens, Stephanie L. Davis, Michael G. Davis, Jennifer M. Marsh, Robert J. Willicut, Jolon M. Dyer
Summary: The study utilized high-resolution mass spectrometry to analyze redox proteomic profiling in human hair, revealing an increase in redox-related modifications with higher levels of thermal and alkaline insults. Site-specific modifications within proteins, particularly an increase in cysteic acid modifications, were observed in samples subjected to more extreme insults. This information could potentially be used to develop strategies for mitigating or repairing hair protein damage caused by environmental or hair treatment-related insults.
INTERNATIONAL JOURNAL OF COSMETIC SCIENCE
(2022)
Article
Food Science & Technology
Yangfan Ye, Evelyne Maes, Santanu Deb-Choudhury, Charles A. Hefer, Nicola M. Schreurs, Carolina E. Realini
Summary: This study compared the protein composition of lamb longissimus thoracis from six commercial forage production systems in New Zealand. The results showed that different production groups could be distinguished based on the abundances of 16 proteins. Furthermore, lamb loins from ewes were found to have higher abundances of some myofibrillar and sarcoplasmic proteins, while a diet of chicory and older age at slaughter were associated with lower abundances of some myofibrillar proteins.
Article
Chemistry, Applied
Alastair B. Ross, Evelyne Maes, Erin J. Lee, Ines Homewood, Jennifer M. Marsh, Stephanie L. Davis, Robert J. Willicut
Summary: This study used lipidomics to investigate the impact of UV light on hair lipids. The results showed that UV exposure decreased several lipid classes and increased others.
INTERNATIONAL JOURNAL OF COSMETIC SCIENCE
(2022)
Editorial Material
Dentistry, Oral Surgery & Medicine
Dirk Valkenborg, Axel-Jan Rousseau, Melvin Geubbelmans, Tomasz Burzykowski
AMERICAN JOURNAL OF ORTHODONTICS AND DENTOFACIAL ORTHOPEDICS
(2023)
Article
Dentistry, Oral Surgery & Medicine
Dirk Valkenborg, Melvin Geubbelmans, Axel-Jan Rousseau, Tomasz Burzykowski
AMERICAN JOURNAL OF ORTHODONTICS AND DENTOFACIAL ORTHOPEDICS
(2023)
Editorial Material
Dentistry, Oral Surgery & Medicine
Dirk Valkenborg, Axel-Jan Rousseau, Melvin Geubbelmans, Tomasz Burzykowski
AMERICAN JOURNAL OF ORTHODONTICS AND DENTOFACIAL ORTHOPEDICS
(2023)
Article
Biology
Kerlijne Moorkens, Jo L. M. R. Leroy, Jusal Quanico, Geert Baggerman, Waleed F. A. Marei
Summary: This study investigated the changes in lipid metabolism in the oviduct of mice fed an obesogenic diet. The results showed that the obesogenic diet led to an increase in the overall lipid levels and differential regulation of specific lipids in the oviductal epithelium. These lipidomic changes may impact reproductive events in the oviduct, such as fertilization and early embryo development.
