Article
Chemistry, Multidisciplinary
Vusala Ibrahimova, Hang Zhao, Emmanuel Ibarboure, Elisabeth Garanger, Sebastien Lecommandoux
Summary: A new class of hybrid lipoprotein mimics was designed using chemical post-modification reactions, allowing the formation of biomimetic vesicles with controlled permeability, correlated to the temperature-responsiveness of ELPs.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Genetics & Heredity
Igor Fijalkowski, Marlies K. R. Peeters, Petra Van Damme
Summary: With the rapid growth in sequenced genomes, genome annotation efforts rely heavily on automated pipelines. Despite their usefulness, these methods often underestimate the true complexity of genomes, particularly in the annotation of small open reading frames and their protein products. Advanced translatomics has improved reannotation efforts, but proteomics validation of these discoveries remains challenging due to the short length and variable properties of these small proteins.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Sonia Podvin, Zhenze Jiang, Ben Boyarko, Leigh-Ana Rossitto, Anthony O'Donoghue, Robert A. Rissman, Vivian Hook
Summary: This study evaluated neuropeptide signatures and tau peptide signatures in Alzheimer's disease (AD) brains compared to age-matched controls. The results showed distinct profiles of neuropeptides and unique tau peptides in AD, indicating differences in proteolytic processing. These findings suggest that the dysregulation of neuropeptides and tau peptides may contribute to the cognitive deficits observed in AD.
ACS CHEMICAL NEUROSCIENCE
(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
Chemistry, Applied
Tessa B. Moyer, Wyatt J. Schug, Leslie M. Hicks
Summary: This study utilizes in silico predictions, proteomics, and simulated gastrointestinal digestions to identify digestion resistant cysteine-rich peptides (CRPs) within Amaranthus hypochondriacus seeds. Thirteen in silico predicted CRPs were detected in a seed extract, providing evidence for the translation of five CRP families. Mature forms of six CRPs were characterized via top-down proteomics, revealing multiple post translational modifications. All six peptides demonstrated resistance to simulated gastrointestinal digestion, suggesting that A. hypochondriacus CRPs may exhibit bioactivity after consumption and should be prioritized for further characterization.
Article
Biochemical Research Methods
Pieter M. Dekker, Sjef Boeren, Johannes B. van Goudoever, Jacques J. M. Vervoort, Kasper A. Hettinga
Summary: The study found significant interindividual variation in proteins and peptides in human milk, and identified distinct characteristics in different protein and peptide clusters through weighted correlation network analysis. Several associations between different data sets and specific sample characteristics were also discovered.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Analytical
Gijs J. C. Vreeke, Wouter Lubbers, Jean-Paul Vincken, Peter A. Wierenga
Summary: Automated approaches from proteomics are used to characterize peptides for food applications and in protein digests. This study provides a structured approach to determine criteria that yield highly reproducible annotations. The researchers found that setting appropriate filters can ensure reliable annotations while maintaining maximum amount of information when analyzing protein hydrolysates.
ANALYTICA CHIMICA ACTA
(2022)
Article
Biochemical Research Methods
Milton Y. Nishiyama-Jr, Alexandre K. Tashima, Erika S. Nishiduka, Thiago F. Abreu, Fernanda Midori Abukawa, Ursula C. Oliveira, Caio E. O. Tardivo, Soraia M. Nascimento, Gabriel O. Meissner, Olga M. Chaim, Maria A. Juliano, Eduardo S. Kitano, Andre Zelanis, Solange M. T. Serrano, Pedro I. da Silva Jr, Inacio L. Junqueira-de-Azevedo
Summary: This study provides a comprehensive analysis of the venom composition of Acanthoscurria juruenicola spider using multiomics approaches. The venom was found to contain various proteins and peptides. Quantitative analysis and biochemical assays confirmed the presence of active components in the venom, which were responsible for the paralytic effects observed in crickets. These findings are important for understanding the venom composition of A. juruenicola and its potential biotechnological and pharmacological applications.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Biochemical Research Methods
Liam Cassidy, Philipp T. Kaulich, Sandra Maass, Juergen Bartel, Doerte Becher, Andreas Tholey
Summary: This study highlights the developed bottom-up and top-down proteomics approaches for the analysis of SEPs, including sample preparation, mass spectrometry, data interpretation, quantification, and analysis of post-translational modifications. These methods not only cover the analytics of SEPs but also include the low molecular weight proteome, and can be used for the proteome-wide analysis of proteolytic processing events.
Review
Chemistry, Analytical
Rachel M. Miller, Lloyd M. Smith
Summary: Proteins are crucial actors in cells, and understanding the complexity of the proteome is important for scientific research and clinical applications. Mass spectrometry-based proteomics is a key method for protein analysis, but further advancements are needed for a more comprehensive view of the proteome.
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
Chemistry, Multidisciplinary
Ayako Takemori, Yusuke Kawashima, Nobuaki Takemori
Summary: This method introduced is simple and suitable for low-microgram level samples containing sodium dodecyl sulfate and Coomassie dye, and can be completed within a few hours.
CHEMICAL COMMUNICATIONS
(2022)
Article
Chemistry, Analytical
Simona Sedlackova, Martin Hubalek, Vladimir Vrkoslav, Miroslava Blechova, Josef Cvacka
Summary: This study systematically investigates the ionization efficiencies of peptides in ESI, APCI, and APPI and their applicability in proteomics. The results show that gas-phase ionization techniques, particularly APPI, are interesting alternatives for detecting peptides and providing complementary data in proteomics.
Review
Chemistry, Multidisciplinary
Rui Vitorino, Sofia Guedes, Joao Pinto da Costa, Vaclav Kasicka
Summary: Microfluidics is an advanced microtechnology for manipulating fluids in small channels, offering tools for controlling chemical, biological, and physical processes. It plays a crucial role in various fields and is often combined with mass spectrometry for analysis. Recent developments include applications in proteomics, peptidomics, cell analysis, and detection methods for clinical questions.
Article
Toxicology
Douglas O. Mariano, Juliana M. Sciani, Marta M. Antoniazzi, Carlos Jared, Katia Conceicao, Daniel C. Pimenta
Summary: Amphibians have skin rich in bioactive molecules, including antimicrobial peptides. Peptidomic and proteomic analyses of Pithecopus nordestinus revealed slight differences in the composition of skin secretion between juveniles and adults, but with similar quantities.
JOURNAL OF VENOMOUS ANIMALS AND TOXINS INCLUDING TROPICAL DISEASES
(2021)
Article
Cell Biology
Tanxi Cai, Qing Zhang, Bowen Wu, Jifeng Wang, Na Li, Tingting Zhang, Zhipeng Wang, Jianjun Luo, Xiaojing Guo, Xiang Ding, Zhensheng Xie, Lili Niu, Weihai Ning, Zhen Fan, Xiaowei Chen, Xiangqian Guo, Runsheng Chen, Hongwei Zhang, Fuquan Yang
Summary: Advancements in omics-based technologies have revealed the abundant presence of microproteins in extracellular vesicles (EVs) derived from glioma cancer cells, suggesting a novel mechanism for intercellular communication. Circulating microproteins are primarily enriched in EVs in human plasma, with preliminary data indicating potential diagnostic applications in identifying glioma patients based on divergent expression profiles of EV microproteins compared to healthy donors.
JOURNAL OF EXTRACELLULAR VESICLES
(2021)
Article
Chemistry, Analytical
Mingwei Sun, Qing Zhang, Baofeng Zhao, Qiuling Huang, Wenfeng Wu, Peiyang Fan, Lihua Zhang, Xiaofei Zhang
Summary: Ubiquitination is a reversible post-translational modification that plays a crucial role in various biological processes. This study proposes an Antibody-Free approach for Ubiquitination Profiling (AFUP), which selectively clicks the ubiquitinated lysine to enrich and profile endogenous ubiquitinated peptides using mass spectrometry. The results demonstrate that AFUP is a robust alternative strategy for ubiquitomics research, with the ability to identify numerous ubiquitination sites and their regulation in different cellular contexts.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Qing Zhang, Erzhong Wu, Yiheng Tang, Tanxi Cai, Lili Zhang, Jifeng Wang, Yajing Hao, Bao Zhang, Yue Zhou, Xiaojing Guo, Jianjun Luo, Runsheng Chen, Fuquan Yang
Summary: Many small ORFs embedded in long noncoding RNA (lncRNA) transcripts have been shown to encode biologically functional polypeptides (SEPs), but their identification is challenging. A new database was built using the NONCODE repository to collect and validate a large number of SEPs, offering valuable resources for further functional studies.
MOLECULAR & CELLULAR PROTEOMICS
(2021)