Article
Biochemical Research Methods
Yoonsung Joh, Kangbae Lee, Hyunwoo Kim, Heejin Park
Summary: A novel approach, called progressive search, efficiently obtains analysis results for updated databases in tandem mass spectrometry. Compared to performing a normal search from scratch, progressive search achieves the same results much faster.
BMC BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Chen Zhou, Shuaijian Dai, Yuanqiao Lin, Sheng Lian, Xiaodan Fan, Ning Li, Weichuan Yu
Summary: In this paper, a comprehensive cross-linking search method called ECL-PF is proposed for cleavable XL-MS data analysis, which can improve the sensitivity of protein-protein interaction detection and protein structure probing.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Soroosh Gholamizoj, Bin Ma
Summary: SPEQ is a spectrum quality assessment tool that classifies spectra into high-quality and low-quality using a deep neural network, which has demonstrated improved prediction accuracy compared to other models.
Article
Biochemical Research Methods
Chen Zhou, Shuaijian Dai, Shengzhi Lai, Yuanqiao Lin, Xuechen Zhang, Ning Li, Weichuan Yu
Summary: Cross-linking mass spectrometry (XL-MS) is a powerful technique for detecting protein-protein interactions (PPIs) and modeling protein structures. However, the imbalance in fragmentation efficiency of cross-linkers hinders the identification of spectra. To address this challenge, researchers have developed novel cross-linking reagents, optimized sample preparation protocols, and developed data analysis algorithms. Applying a protein feedback mechanism has shown promise in improving the sensitivity of analysis methods.
BMC BIOINFORMATICS
(2023)
Article
Chemistry, Analytical
Daoyang Chen, Zhichang Yang, Xiaojing Shen, Liangliang Sun
Summary: Top-down proteomics (TDP) is an ideal approach for deciphering the histone code and requires new analytical tools with high-capacity separation and highly sensitive detection of proteoforms. In this study, capillary zone electrophoresis (CZE) -MS/MS was used to identify a large number of histone proteoforms with higher sensitivity compared to traditional methods.
ANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Michelle T. Berger, Daniel Hemmler, Philippe Diederich, Michael Rychlik, James W. Marshall, Philippe Schmitt-Kopplin
Summary: Identification of chemically modified peptides in mass spectrometry-based glycation studies is a challenging task. This study presents an open search approach using classic and modified peptide fragment ions to match tandem mass spectrometry data, allowing for known and unknown peptide glycation modifications. The authors demonstrate that using a multi-step matching algorithm, including a triple-ion strategy, significantly increases the interpretability of glycation product MS/MS spectra. They also apply their approach to characterize Amadori products and identify diagnostic ions, as well as discover two previously undescribed peptide glycation modifications. Integration with isotopically labeled glycation products enhances the validity of non-targeted structure identification.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Yunong Li, Hao Li, Taibo Luo, Guohui Lin, Liang Li
Summary: Liquid chromatography mass spectrometry (LC-MS) is widely used for metabolome analysis, and the critical step of metabolite identification in LC-MS workflow is related to peak mass measurement. In this study, a simple and convenient method called intensity-dependent mass search (IDMS) was developed to improve metabolite matching by determining the relation between peak intensity and mass error. The method involves running sodium formate mass calibrants and curve-fitting the measured mass errors and peak intensities. The results showed that mass accuracy is generally reduced as peak intensity decreases in quadrupole time-of-flight (QTOF) mass analyzers. The IDMS method was successfully implemented in the MCID database, which provides a comprehensive resource for metabolite identification.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
Frank Lawrence Nii Adoquaye Acquaye, Attila Kertesz-Farkas, William Stafford Noble
Summary: The analysis of protein tandem mass spectrometry data starts with searching observed spectra against a protein database, where the search engine digests proteins into peptides based on user-controlled digestion rules. The choice of digestion parameters and post-translational modifications (PTMs) can greatly affect the search space and statistical power. A new implementation of the Tide search engine separates peptide indexing from database searching, resulting in significant resource savings and the ability to generate large peptide databases. This improved implementation provides insights into the relationship between database size and digestion/PTM parameters, as well as database size and statistical power, helping practitioners choose appropriate parameters.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Chemistry, Analytical
Fenglong Jiao, Fangyuan Gao, Yuanyuan Liu, Zhiya Fan, Xiaochao Xiang, Chaoshuang Xia, Yayao Lv, Yuping Xie, Haihong Bai, Wanjun Zhang, Weijie Qin, Xiaohong Qian
Summary: Small extracellular vesicles (SEVs) are cell-derived nanometer-sized vesicles that play vital roles in diseases and biomarker research. Current techniques for SEVs isolation face challenges, but Ti4+-modified magnetic graphene-oxide composites may offer a new approach for phosphoproteome studies of SEVs.
Article
Biochemical Research Methods
Siti Hajar Amir, Mohd Hafis Yuswan, Wan Mohd Aizat, Muhammad Kamaruzaman Mansor, Mohd Nasir Mohd Desa, Yus Aniza Yusof, Lai Kok Song, Shuhaimi Mustafa
Summary: This study evaluated the performance of different search engines in halal analysis and found that combining different search engines can provide a comprehensive protein list, which is helpful for future precise halal analysis.
JOURNAL OF PROTEOMICS
(2021)
Article
Biochemical Research Methods
Agnes Revesz, Marton Gyula Milley, Kinga Nagy, Daniel Szabo, Gergo Kallo, Eva Csosz, Karoly Vekey, Laszlo Drahos
Summary: Bottom-up proteomics relies on identifying peptides from tandem mass spectra using sequence databases. Changes in collision energy affect identification scores for different search engines, impacting protein identification and coverage. Adjusting experimental parameters based on the choice of engine can optimize results.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Microbiology
Charlotte Mappa, Beatrice Alpha-Bazin, Olivier Pible, Jean Armengaud
Summary: Shotgun proteomics is a promising alternative technique for identifying pathogens and characterizing their antimicrobial resistance genes. Proteotyping microorganisms through tandem mass spectrometry is expected to be essential in modern healthcare, and it also plays a crucial role in developing new biotechnological applications through culturomics. Phylopeptidomics is a new strategy that improves the quantification of microbial contributions by estimating phylogenetic distances and calculating the ratio of shared peptides. The study established the limit of detection for tandem mass spectrometry proteotyping and demonstrated the independence of bacterial identification by phylopeptidomics from their growth stage and the robustness of the method in the presence of additional bacteria.
Article
Biochemistry & Molecular Biology
Krzysztof Jan Abram, Douglas McCloskey
Summary: The study aims to learn interpretable and instrument-agnostic digital representations of metabolites directly from MS/MS spectra using generative modeling and representation learning. They find that variational autoencoders can disentangle the factors of generation in tandem mass spectra data and propose a two-step approach to select disentangled models.
Article
Chemistry, Analytical
Azadeh Mohammadi, Aline Tschanz, Alexander Leitner
Summary: Carboxyl-group specific chemical cross-linking, using a combination of dihydrazide linkers and DMTMM as coupling reagent, can be adjusted to favor one reaction product over the other by varying the ratios of the two reagents. This strategy significantly increases the number of identified cross-linked peptides in model proteins and demonstrates complementarity and increased cross-link coverage in larger protein complexes like the bovine 20S proteasome and the Escherichia coli 70S ribosome.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Andrea Laguillo-Gomez, Enrique Calvo, Noa Martin-Cofreces, Marta Lozano-Prieto, Francisco Sanchez-Madrid, Jesus Vazquez
Summary: Open-search methods with prior knowledge improve identification performance of protein post-translational modifications by minimizing experimental errors and precursor mass assignation. The introduction of a novel approach enables the study of a wider variety of PTMs, including unknown or unexpected modifications.
JOURNAL OF PROTEOMICS
(2023)
Article
Engineering, Biomedical
Long Zhang, Miranda L. Gardner, Lakmal Jayasinghe, Michael Jordan, Julian Aldana, Nicolas Burns, Michael A. Freitas, Peixuan Guo
Summary: The study presents a label-free method for detecting single amino acid modifications in peptides using reengineered phi29 DNA packaging motor channels, enabling the differentiation of single or multiple modifications in the MinION (TM) system. This advancement represents a significant step towards developing a high-throughput detection platform for clinical diagnosis based on PTM utilizing nanopores.
Article
Biology
Pang-Hung Hsu, Wei-Hsuan Chen, Chen Juan-Lu, Shu-Chen Hsieh, Shih-Chao Lin, Ru-Tsun Mai, Shiow-Yi Chen
Summary: Combining hesperidin and chlorogenic acid in breast cancer patients undergoing chemotherapy can have a synergistic effect in inhibiting cancer cell growth by regulating mitochondria and ATP production, without generating reactive oxygen species.
Article
Virology
Yung-Kuo Lee, Wen-Chiu Chang, Ekambaranellore Prakash, Yu-Ju Peng, Zhi-Jay Tu, Chun-Hung Lin, Pang-Hung Hsu, Chuan-Fa Chang
Summary: The study found that the SARS-CoV-2 spike protein S1 subunit specifically binds to blood group A and B antigens, while the S2 subunit has a preference for Le(a) antigens. Additionally, ACE2 was identified as a glycoprotein containing a blood group A antigen, and 6-sulfo N-acetyllactosamine was found to inhibit the binding of the spike protein S1 subunit with blood group A RBCs and reduce the interaction with ACE2.
Article
Genetics & Heredity
Aleksandra Adamovich, Mariame Diabate, Tapahsama Banerjee, Gregory Nagy, Nahum Smith, Kathryn Duncan, Erika Mendoza Mendoza, Gisselle Prida, Michael A. Freitas, Lea M. Starita, Jeffrey D. Parvin
Summary: Pathogenic variants in BRCA1 are associated with an increased risk of hereditary breast and ovarian cancer. This study used functional assays to evaluate a large number of BRCA1 variants, finding consistent results in terms of repair function and drug resistance. These results are valuable for characterizing variants that are individually detected too infrequently in the population.
AMERICAN JOURNAL OF HUMAN GENETICS
(2022)
Article
Multidisciplinary Sciences
Matthew S. Conrad, Miranda L. Gardner, Christine Miguel, Michael A. Freitas, Kara M. Rood, Marwan Ma'ayeh
Summary: Fetal growth restriction and pre-eclampsia alter the structure and composition of the umbilical cord, with significant differences in proteins related to extracellular matrix, cellular process, inflammation, and angiogenesis pathways. Further research on these protein differences may help identify therapeutic targets for FGR and FGR with PreE.
Article
Infectious Diseases
Wen-Jung Lu, Yan-Jyun Huang, Hsuan-Ju Lin, Chun-Ju Chang, Pang-Hung Hsu, Gui-Xia Ooi, Mei-Ying Huang, Hong-Ting Victor Lin
Summary: The plant phenolic compound ethyl 3,4-dihydroxybenzoate (EDHB) was found to have limited antibacterial activity but can enhance the activity of antibiotics against drug-resistant Escherichia coli by interfering with bacterial efflux pumps.
Article
Biochemical Research Methods
Gordon T. Luu, Michael A. Freitas, Itzel Lizama-Chamu, Catherine S. McCaughey, Laura M. Sanchez, Mingxun Wang
Summary: In this paper, we present TIMSCONVERT, a high-throughput data conversion workflow that converts timsTOF Pro/fleX mass spectrometer raw data files to mzML and imzML formats while incorporating ion mobility data and maintaining compatibility with popular data analysis tools.
Article
Genetics & Heredity
August E. Woerner, Benjamin Crysup, F. Curtis Hewitt, Myles W. Gardner, Michael A. Freitas, Bruce Budowle
Summary: Forensic genetic investigations often rely on DNA analysis, but when the DNA is limited, protein can be used as an alternative target. However, interpreting protein polymorphisms in a forensic context requires addressing certain complexities. This study presents a novel approach that converts genomic information into proteomic information to overcome these complexities. The results show that this method performs well in simulated samples.
FORENSIC SCIENCE INTERNATIONAL-GENETICS
(2022)
Article
Genetics & Heredity
Kuo-Sheng Hung, Shiow-Yi Chen, Pang-Hung Hsu, Bo-An Lin, Chin-Hua Hu, Cing-Han Yang, Tun-Wen Pai, Wen-Shyong Tzou, Hsin-Yu Chung
Summary: This study investigated the differential gene expression changes during hypoxia in five organs of common carp. The analysis revealed that each organ had specific gene expression properties and pathways involved in adaptation to hypoxia. Furthermore, the study found some hypoxia-regulated genes related to human diseases, indicating the potential for advancing disease research using integrative bioinformatics.
Article
Medicine, Research & Experimental
Pang-Hung Hsu, Yi-Hsuan Chen, Pin-I. Huang, Pai-An Hwang
Summary: Fucoidans extracted from brown seaweed have been found to inhibit radiotherapy-induced cell damage and fibrosis. In this study, mass spectrometry-based proteomics analysis was used to examine the protein profiles in rat hind limbs irradiated and treated with low molecular weight fucoidan (LMF). The analysis identified 233 significantly up-regulated proteins after irradiation and down-regulated after LMF treatment. Pathway and protein-protein interaction network analyses revealed that four proteins were clustered in tight junction and regulation of actin cytoskeleton pathways, suggesting their potential as biomarkers for skin fibrosis detection and recovery following LMF treatment.
BIOMEDICINE & PHARMACOTHERAPY
(2022)
Article
Biotechnology & Applied Microbiology
Pang-Hung Hsu, Lee-Kuo Kang, Wui-Ting Lim, Pai-An Hwang
Summary: This study investigates the influence of nitrogen sources on the growth of Caulerpa lentillifera and explores the biological relevance behind its nonlinear growth phenomenon under different nitrate concentrations. The results showed that neither the number of branches nor the percentage weight gain of C. lentillifera increased linearly with nitrate concentration. Growth retardation was observed at 220 μmol/L nitrate concentration, but the concentrations of chlorophyll a, b, and beta-carotene showed no difference under all nitrate conditions. Proteomics analysis confirmed that 17 proteins were significantly upregulated under the 4x condition, suggesting that eIF4A may serve as a potential marker for the growth retardation phenomenon of C. lentillifera.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2023)
Article
Microbiology
Tsung-Yu Chao, Yi-Ying Cheng, Zi-Yun Wang, Tien-Fang Fang, Yu-Ruei Chang, Chi-Shane Fuh, Mei-Tzu Su, Yuan-Wei Su, Pang-Hung Hsu, Yu-Chen Su, Yu-Ching Chang, Ting-Yau Lee, Wei-Han Chou, Jaap M. Middeldorp, Jaakko Saraste, Mei-Ru Chen
Summary: Upon EBV lytic reactivation, the virus-encoded DNA replication machinery functions in the nucleus, while the newly synthesized DNA is encapsidated and transported to the cytoplasm for final virus assembly. The single-stranded DNA binding protein BALF2 executing functions within the nucleus was also identified in the tegument layer of mature virions. We are interested in how BALF2 is packaged into the tegument of virions.
MICROBIOLOGY SPECTRUM
(2023)
Article
Chemistry, Multidisciplinary
Wen-Jung Lu, Ya-Chin Tsui, Chun-Ju Chang, Pang-Hung Hsu, Mei-Ying Huang, Margaret Lai, Yu-Wei Lian, Chia-Lin Chen, Hong-Ting Victor Lin
Summary: This study evaluated the potential of ethanolic extracts of the red seaweed Gracilaria sp. as β-lactamase inhibitors and found that it can enhance the activity of β-lactam antibiotics against Vibrio strains.
Article
Medicine, Research & Experimental
Chih-Chin Hsu, Jong-Shyan Wang, Yu-Chiau Shyu, Tieh-Cheng Fu, Yu-Hsiang Juan, Shin-Sheng Yuan, Chao-Hung Wang, Chi-Hsiao Yeh, Po-Cheng Liao, Hsin-Yi Wu, Pang-Hung Hsu
Summary: This translational research examined the implications of DNA methylation associated with high-intensity interval training (HIIT) on cardiac fibrosis in patients with heart failure (HF). The study found that HIIT can reduce cardiac fibrosis and improve cardiorespiratory fitness. This was confirmed through a variety of tests on HF patients, including cardiovascular magnetic resonance imaging and cardiopulmonary exercise tests, as well as cell experiments and proteomics analysis.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Multidisciplinary Sciences
Li-Tzu Cheng, Grace Y. T. Tan, Fang-Pei Chang, Cheng-Kai Wang, Yu-Chi Chou, Pang-Hung Hsu, Wendy W. Hwang-Verslues
Summary: The expression of LGR5 in intestinal crypt cells is regulated by the circadian core clock gene BMAL1 and the BMAL1-regulated RNA-binding protein MEX3A. This intrinsic regulatory pathway contributes to the maintenance of LGR5 expression and intestinal stem cell homeostasis.
SCIENTIFIC REPORTS
(2023)
