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Li J, Zhan X. Mass spectrometry analysis of phosphotyrosine-containing proteins. MASS SPECTROMETRY REVIEWS 2024; 43:857-887. [PMID: 36789499 DOI: 10.1002/mas.21836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 12/19/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Tyrosine phosphorylation is a crucial posttranslational modification that is involved in various aspects of cell biology and often has functions in cancers. It is necessary not only to identify the specific phosphorylation sites but also to quantify their phosphorylation levels under specific pathophysiological conditions. Because of its high sensitivity and accuracy, mass spectrometry (MS) has been widely used to identify endogenous and synthetic phosphotyrosine proteins/peptides across a range of biological systems. However, phosphotyrosine-containing proteins occur in extremely low abundance and they degrade easily, severely challenging the application of MS. This review highlights the advances in both quantitative analysis procedures and enrichment approaches to tyrosine phosphorylation before MS analysis and reviews the differences among phosphorylation, sulfation, and nitration of tyrosine residues in proteins. In-depth insights into tyrosine phosphorylation in a wide variety of biological systems will offer a deep understanding of how signal transduction regulates cellular physiology and the development of tyrosine phosphorylation-related drugs as cancer therapeutics.
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Affiliation(s)
- Jiajia Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Central South University, Changsha, Hunan, People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, Shandong, Jinan, People's Republic of China
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2
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Schlachter S, Tadus K, Weiss R, Reiter E, Strnad I, Cichna-Markl M, D'Amico S. Simultaneous Determination of Animal Products from Ruminant, Pig, Poultry, and Fish in Feedingstuff by Targeted High-Resolution LC-MS/MS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38941278 DOI: 10.1021/acs.jafc.4c00516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
The prohibition of processed animal proteins (PAPs) has been relaxed gradually since 2007. The official control method for PAPs in feedingstuff, a combination of light microscopy (LM) followed by PCR, is no longer sufficient. Thus, a targeted LC-MS/MS method was developed, which enables a tissue-specific distinction between egg and dairy products, gelatine, and PAPs derived from blood or muscle tissue of the species ruminants, pigs, poultry, and fish. Tissue-specific proteins were analyzed after tryptic digestion to peptides with high-resolution ESI-QTOF-MS. A targeted method was developed based on untargeted proteomics approaches and the selection of specific peptides (45 unique peptides in total). Proficiency testing of blank and spiked samples revealed excellent results for trueness and selectivity. Furthermore, sensitivity was achieved at a level of 0.1% (w/w) for assessed peptides. Summing up, the developed method seems to be suitable for routine analysis after verification by ring trials.
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Affiliation(s)
- Sara Schlachter
- Austrian Agency for Health and Food Safety, Institute for Animal Nutrition and Feed, Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Klaudia Tadus
- Austrian Agency for Health and Food Safety, Institute for Animal Nutrition and Feed, Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Roland Weiss
- Austrian Agency for Health and Food Safety, Institute for Animal Nutrition and Feed, Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Elisabeth Reiter
- Austrian Agency for Health and Food Safety, Institute for Animal Nutrition and Feed, Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Irmengard Strnad
- Austrian Agency for Health and Food Safety, Institute for Animal Nutrition and Feed, Spargelfeldstraße 191, 1220 Vienna, Austria
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria
| | - Stefano D'Amico
- Austrian Agency for Health and Food Safety, Institute for Animal Nutrition and Feed, Spargelfeldstraße 191, 1220 Vienna, Austria
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3
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Prims S, Van Ginneken C, Van Ostade X, Casteleyn C. Welfare Assessment in Pigs Using the Salivary Proteome. Animals (Basel) 2024; 14:1703. [PMID: 38891749 PMCID: PMC11171187 DOI: 10.3390/ani14111703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Identifying the potential presence of stress at the pig farm is fundamental since it affects pig welfare. As a result, a reliable and straightforward tool to monitor stress could record the welfare status of the animals. Although numerous methods to assess the welfare of pigs have been developed in the past, no gold standard has been established yet. Recently, the value of saliva as a tool to identify chronic stress in piglets was explored, as it can be collected fast and non-invasively. Since the protein composition, i.e., the proteome of porcine saliva, responds to stress, the affected proteins could be used as salivary stress biomarkers. The present review first defines stress and its relationship with welfare. Next, the porcine gland-specific salivary proteome is characterized. Finally, six potential salivary biomarkers for stress are proposed, i.e., odorant-binding protein, vomeromodulin-like protein, chitinase, lipocalin-1, long palate lung and nasal epithelium protein, and alpha-2-HS-glycoprotein.
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Affiliation(s)
- Sara Prims
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.P.); (C.V.G.)
| | - Chris Van Ginneken
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.P.); (C.V.G.)
| | - Xaveer Van Ostade
- Laboratory of Protein Science, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium;
| | - Christophe Casteleyn
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium; (S.P.); (C.V.G.)
- Department of Morphology, Medical Imaging, Orthopedics, Physiotherapy and Nutrition, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
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4
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Zhong Z, Deng W, Wu J, Shang H, Tong Y, He Y, Huang Q, Ba X, Chen Z, Tang K. Cell membrane coated nanoparticles as a biomimetic drug delivery platform for enhancing cancer immunotherapy. NANOSCALE 2024; 16:8708-8738. [PMID: 38634521 DOI: 10.1039/d4nr00284a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
Cancer immunotherapy, a burgeoning modality for cancer treatment, operates by activating the autoimmune system to impede the growth of malignant cells. Although numerous immunotherapy strategies have been employed in clinical cancer therapy, the resistance of cancer cells to immunotherapeutic medications and other apprehensions impede the attainment of sustained advantages for most patients. Recent advancements in nanotechnology for drug delivery hold promise in augmenting the efficacy of immunotherapy. However, the efficacy is currently constrained by the inadequate specificity of delivery, low rate of response, and the intricate immunosuppressive tumor microenvironment. In this context, the investigation of cell membrane coated nanoparticles (CMNPs) has revealed their ability to perform targeted delivery, immune evasion, controlled release, and immunomodulation. By combining the advantageous features of natural cell membranes and nanoparticles, CMNPs have demonstrated their unique potential in the realm of cancer immunotherapy. This review aims to emphasize recent research progress and elucidate the underlying mechanisms of CMNPs as an innovative drug delivery platform for enhancing cancer immunotherapy. Additionally, it provides a comprehensive overview of the current immunotherapeutic strategies involving different cell membrane types of CMNPs, with the intention of further exploration and optimization.
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Affiliation(s)
- Zichen Zhong
- Department of Urology, Tongji Hospital, Tongji medical college, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
| | - Wen Deng
- Department of Urology, Tongji Hospital, Tongji medical college, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
| | - Jian Wu
- Department of Urology, Tongji Hospital, Tongji medical college, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
| | - Haojie Shang
- Department of Urology, Tongji Hospital, Tongji medical college, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
| | - Yonghua Tong
- Department of Urology, Tongji Hospital, Tongji medical college, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
| | - Yu He
- Department of Urology, Tongji Hospital, Tongji medical college, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
| | - Qiu Huang
- Department of Urology, Tongji Hospital, Tongji medical college, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
| | - Xiaozhuo Ba
- Department of Urology, Tongji Hospital, Tongji medical college, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
| | - Zhiqiang Chen
- Department of Urology, Tongji Hospital, Tongji medical college, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
| | - Kun Tang
- Department of Urology, Tongji Hospital, Tongji medical college, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China.
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5
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Wang Y, Li H, Wang D, Li Y, Shen Y, Fu Y, Li Y, Gao M, Zhang D. Changes of PK/PD of Meropenem in patients with abdominal septic shock and exploration of clinical rational administration plan: a prospective exploratory study. Sci Rep 2024; 14:10173. [PMID: 38702351 PMCID: PMC11068909 DOI: 10.1038/s41598-024-60909-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
This study aimed to explore the changes of pharmacokinetic parameters after meropenem in patients with abdominal septic shock after gastrointestinal perforation, and to simulate the probability of different dosing regimens achieving different pharmacodynamic goals. The study included 12 patients, and utilized high performance liquid chromatography-tandem mass spectrometry to monitor the plasma concentration of meropenem. The probability of target attainment (PTA) for different minimum inhibitory concentration (MIC) values and %fT > 4MIC was compared among simulated dosing regimens. The results showed that in 96 blood samples from 12 patients, the clearance (CL) of meropenem in the normal and abnormal creatinine clearance subgroups were 7.7 ± 1.8 and 4.4 ± 1.1 L/h, respectively, and the apparent volume of distribution (Vd) was 22.6 ± 5.1 and 17.2 ± 5.8 L, respectively. 2. Regardless of the subgroup, 0.5 g/q6h infusion over 6 h regimen achieved a PTA > 90% when MIC ≤ 0.5 mg/L. 1.0 g/q6h infusion regimen compared with other regimen, in most cases, the probability of making PTA > 90% is higher. For patients at low MIC, 0.5 g/q6h infusion over 6 h may be preferable. For patients at high MIC, a dose regimen of 1.0 g/q6 h infusion over 6 h may be preferable. Further research is needed to confirm this exploratory result.
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Affiliation(s)
- Youquan Wang
- Department of Critical Care Medicine, The First Hospital of Jilin University, Chaoyang District, Changchun City, 130021, Jilin Province, China
| | - Hongxiang Li
- Department of Critical Care Medicine, The First Hospital of Jilin University, Chaoyang District, Changchun City, 130021, Jilin Province, China
| | - Dongxia Wang
- Department of Critical Care Medicine, The First Hospital of Jilin University, Chaoyang District, Changchun City, 130021, Jilin Province, China
| | - Yuting Li
- Department of Critical Care Medicine, The First Hospital of Jilin University, Chaoyang District, Changchun City, 130021, Jilin Province, China
| | | | - Yao Fu
- Department of Critical Care Medicine, The First Hospital of Jilin University, Chaoyang District, Changchun City, 130021, Jilin Province, China
| | - Yanhua Li
- Department of Critical Care Medicine, The First Hospital of Jilin University, Chaoyang District, Changchun City, 130021, Jilin Province, China
| | - Meng Gao
- Department of Critical Care Medicine, The First Hospital of Jilin University, Chaoyang District, Changchun City, 130021, Jilin Province, China
| | - Dong Zhang
- Department of Critical Care Medicine, The First Hospital of Jilin University, Chaoyang District, Changchun City, 130021, Jilin Province, China.
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6
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Chen YT, Liao WR, Wang HT, Chen HW, Chen SF. Targeted protein quantitation in human body fluids by mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:2379-2403. [PMID: 35702881 DOI: 10.1002/mas.21788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Human body fluids (biofluids) contain various proteins, some of which reflect individuals' physiological conditions or predict diseases. Therefore, the analysis of biofluids can provide substantial information on novel biomarkers for clinical diagnosis and prognosis. In the past decades, mass spectrometry (MS)-based technologies have been developed as proteomic strategies not only for the identification of protein biomarkers but also for biomarker verification/validation in body fluids for clinical applications. The main advantage of targeted MS-based methodologies is the accurate and specific simultaneous quantitation of multiple biomarkers with high sensitivity. Here, we review MS-based methodologies that are currently used for the targeted quantitation of protein components in human body fluids, especially in plasma, urine, cerebrospinal fluid, and saliva. In addition, the currently used MS-based methodologies are summarized with a specific focus on applicable clinical sample types, MS configurations, and acquisition modes.
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Affiliation(s)
- Yi-Ting Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Kidney Research Center, Linkou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Rou Liao
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Hsueh-Ting Wang
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
| | - Hsiao-Wei Chen
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
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7
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Dowling P, Swandulla D, Ohlendieck K. Mass Spectrometry-Based Proteomic Technology and Its Application to Study Skeletal Muscle Cell Biology. Cells 2023; 12:2560. [PMID: 37947638 PMCID: PMC10649384 DOI: 10.3390/cells12212560] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/27/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Voluntary striated muscles are characterized by a highly complex and dynamic proteome that efficiently adapts to changed physiological demands or alters considerably during pathophysiological dysfunction. The skeletal muscle proteome has been extensively studied in relation to myogenesis, fiber type specification, muscle transitions, the effects of physical exercise, disuse atrophy, neuromuscular disorders, muscle co-morbidities and sarcopenia of old age. Since muscle tissue accounts for approximately 40% of body mass in humans, alterations in the skeletal muscle proteome have considerable influence on whole-body physiology. This review outlines the main bioanalytical avenues taken in the proteomic characterization of skeletal muscle tissues, including top-down proteomics focusing on the characterization of intact proteoforms and their post-translational modifications, bottom-up proteomics, which is a peptide-centric method concerned with the large-scale detection of proteins in complex mixtures, and subproteomics that examines the protein composition of distinct subcellular fractions. Mass spectrometric studies over the last two decades have decisively improved our general cell biological understanding of protein diversity and the heterogeneous composition of individual myofibers in skeletal muscles. This detailed proteomic knowledge can now be integrated with findings from other omics-type methodologies to establish a systems biological view of skeletal muscle function.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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8
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Teunissen CE, Kimble L, Bayoumy S, Bolsewig K, Burtscher F, Coppens S, Das S, Gogishvili D, Fernandes Gomes B, Gómez de San José N, Mavrina E, Meda FJ, Mohaupt P, Mravinacová S, Waury K, Wojdała AL, Abeln S, Chiasserini D, Hirtz C, Gaetani L, Vermunt L, Bellomo G, Halbgebauer S, Lehmann S, Månberg A, Nilsson P, Otto M, Vanmechelen E, Verberk IMW, Willemse E, Zetterberg H. Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias. Mol Cell Proteomics 2023; 22:100629. [PMID: 37557955 PMCID: PMC10594029 DOI: 10.1016/j.mcpro.2023.100629] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
Neurodegenerative dementias are progressive diseases that cause neuronal network breakdown in different brain regions often because of accumulation of misfolded proteins in the brain extracellular matrix, such as amyloids or inside neurons or other cell types of the brain. Several diagnostic protein biomarkers in body fluids are being used and implemented, such as for Alzheimer's disease. However, there is still a lack of biomarkers for co-pathologies and other causes of dementia. Such biofluid-based biomarkers enable precision medicine approaches for diagnosis and treatment, allow to learn more about underlying disease processes, and facilitate the development of patient inclusion and evaluation tools in clinical trials. When designing studies to discover novel biofluid-based biomarkers, choice of technology is an important starting point. But there are so many technologies to choose among. To address this, we here review the technologies that are currently available in research settings and, in some cases, in clinical laboratory practice. This presents a form of lexicon on each technology addressing its use in research and clinics, its strengths and limitations, and a future perspective.
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Affiliation(s)
- Charlotte E Teunissen
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands.
| | - Leighann Kimble
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; KIN Center for Digital Innovation, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Sherif Bayoumy
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Katharina Bolsewig
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Felicia Burtscher
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Salomé Coppens
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; National Measurement Laboratory at LGC, Teddington, United Kingdom
| | - Shreyasee Das
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; ADx NeuroSciences, Gent, Belgium
| | - Dea Gogishvili
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Bárbara Fernandes Gomes
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Nerea Gómez de San José
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Neurology, University of Ulm, Ulm, Germany
| | - Ekaterina Mavrina
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; KIN Center for Digital Innovation, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Francisco J Meda
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Pablo Mohaupt
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; LBPC-PPC, IRMB CHU Montpellier, INM INSERM, Université de Montpellier, Montpellier, France
| | - Sára Mravinacová
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Katharina Waury
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Anna Lidia Wojdała
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Neurology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Sanne Abeln
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Davide Chiasserini
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Physiology and Biochemistry, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Christophe Hirtz
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; LBPC-PPC, IRMB CHU Montpellier, INM INSERM, Université de Montpellier, Montpellier, France
| | - Lorenzo Gaetani
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Neurology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Lisa Vermunt
- Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Giovanni Bellomo
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Section of Neurology, Department of Medicine and Surgery, University of Perugia, Perugia, Italy
| | - Steffen Halbgebauer
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Neurology, University of Ulm, Ulm, Germany; German Center for Neurodegenerative Diseases (DZNE e.V.), Ulm, Germany
| | - Sylvain Lehmann
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; LBPC-PPC, IRMB CHU Montpellier, INM INSERM, Université de Montpellier, Montpellier, France
| | - Anna Månberg
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Peter Nilsson
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Markus Otto
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Neurology, University of Ulm, Ulm, Germany; Department of Neurology, Martin-Luther-University Halle-Wittenberg, Halle, Germany
| | - Eugeen Vanmechelen
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; ADx NeuroSciences, Gent, Belgium
| | - Inge M W Verberk
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Eline Willemse
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Neurochemistry Lab, Department of Laboratory Medicine, Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, Netherlands
| | - Henrik Zetterberg
- MIRIADE Consortium, Multiomics Interdisciplinary Research Integration to Address DEmentia diagnosis, Amsterdam, The Netherlands; Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden; Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden; Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; UK Dementia Research Institute at UCL, London, UK; Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China; Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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9
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Fresnais M, Jung I, Klein UB, Theile D, Liang S, Haefeli WE, Burhenne J, Longuespée R. Quantification of Biologically Active DNA Alkylation in Temozolomide-Exposed Glioblastoma Cell Lines by Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry: Method Development and Recommendations for Validation. ACS OMEGA 2023; 8:23695-23705. [PMID: 37426236 PMCID: PMC10324051 DOI: 10.1021/acsomega.3c01818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/02/2023] [Indexed: 07/11/2023]
Abstract
Quantitative monitoring of biologically active methylations of guanines in samples exposed to temozolomide (TMZ) would be useful in glioblastoma research for preclinical TMZ experiments, for clinical pharmacology questions regarding appropriate exposure, and ultimately for precision oncology. The known biologically active alkylation of DNA induced by TMZ takes place on O6 position of guanines. However, when developing mass spectrometric (MS) assays, the possible signal overlap of O6-methyl-2'-deoxyguanosine (O6-m2dGO) with other methylated 2'-deoxyguanosine species in DNA and methylated guanosines in RNA must be considered. Liquid chromatography-tandem MS (LC-MS/MS) offers the analytical requirements for such assays in terms of specificity and sensitivity, especially when multiple reaction monitoring (MRM) is available. In preclinical research, cancer cell lines are still the gold standard model for in vitro drug screening. Here, we present the development of ultra-performance LC-MRM-MS assays for the quantification of O6-m2dGO in a TMZ-treated glioblastoma cell line. Furthermore, we propose adapted parameters for method validation relevant to the quantification of drug-induced DNA modifications.
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10
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Prims S, Van Ostade X, Ayuso M, Dom M, Van Raemdonck G, Van Cruchten S, Casteleyn C, Van Ginneken C. Chronic exposure to multiple stressors alters the salivary proteome of piglets. PLoS One 2023; 18:e0286455. [PMID: 37235602 DOI: 10.1371/journal.pone.0286455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Monitoring chronic stress in pigs is not only essential in view of animal welfare but is also important for the farmer, given that stress influences the zootechnical performance of the pigs and increases their susceptibility to infectious diseases. To investigate the use of saliva as a non-invasive, objective chronic stress monitoring tool, twenty-four 4-day-old piglets were transferred to artificial brooders. At the age of 7 days, they were assigned to either the control or the stressed group and reared for three weeks. Piglets in the stressed group were exposed to overcrowding, absence of cage enrichment, and frequent mixing of animals between pens. Shotgun analysis using an isobaric labelling method (iTRAQ) for tandem mass spectrometry performed on saliva samples taken after three weeks of chronic stress identified 392 proteins, of which 20 proteins displayed significantly altered concentrations. From these 20 proteins, eight were selected for further validation using parallel reaction monitoring (PRM). For this validation, saliva samples that were taken one week after the start of the experiment and samples that were taken at the end of the experiment were analysed to verify the profile over time. We wanted to investigate whether the candidate biomarkers responded fast or rather slowly to the onset of chronic exposure to multiple stressors. Furthermore, this validation could indicate whether age influenced the baseline concentrations of these salivary proteins, both in healthy and stressed animals. This targeted PRM analysis confirmed that alpha-2-HS-glycoprotein was upregulated in the stressed group after one and three weeks, while odorant-binding protein, chitinase, long palate lung and nasal epithelium protein 5, lipocalin-1, and vomeromodulin-like protein were present in lower concentrations in the saliva of the stressed pigs, albeit only after three weeks. These results indicate that the porcine salivary proteome is altered by chronic exposure to multiple stressors. The affected proteins could be used as salivary biomarkers to identify welfare problems at the farm and facilitate research to optimise rearing conditions.
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Affiliation(s)
- Sara Prims
- Laboratory of Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Xaveer Van Ostade
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
- Center for Proteomics (CfP), University of Antwerp, Antwerp, Belgium
| | - Miriam Ayuso
- Laboratory of Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Martin Dom
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Geert Van Raemdonck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
- Center for Proteomics (CfP), University of Antwerp, Antwerp, Belgium
| | - Steven Van Cruchten
- Laboratory of Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Christophe Casteleyn
- Laboratory of Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Chris Van Ginneken
- Laboratory of Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
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11
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Prokai L, Zaman K, Prokai-Tatrai K. Mass spectrometry-based retina proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1032-1062. [PMID: 35670041 PMCID: PMC9730434 DOI: 10.1002/mas.21786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
A subfield of neuroproteomics, retina proteomics has experienced a transformative growth since its inception due to methodological advances in enabling chemical, biochemical, and molecular biology techniques. This review focuses on mass spectrometry's contributions to facilitate mammalian and avian retina proteomics to catalog and quantify retinal protein expressions, determine their posttranslational modifications, as well as its applications to study the proteome of the retina in the context of biology, health and diseases, and therapy developments.
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Affiliation(s)
- Laszlo Prokai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Khadiza Zaman
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Katalin Prokai-Tatrai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
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12
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A Proof of Principle Proteomic Study Detects Dystrophin in Human Plasma: Implications in DMD Diagnosis and Clinical Monitoring. Int J Mol Sci 2023; 24:ijms24065215. [PMID: 36982290 PMCID: PMC10049465 DOI: 10.3390/ijms24065215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a rare neuromuscular disease caused by pathogenic variations in the DMD gene. There is a need for robust DMD biomarkers for diagnostic screening and to aid therapy monitoring. Creatine kinase, to date, is the only routinely used blood biomarker for DMD, although it lacks specificity and does not correlate with disease severity. To fill this critical gap, we present here novel data about dystrophin protein fragments detected in human plasma by a suspension bead immunoassay using two validated anti-dystrophin-specific antibodies. Using both antibodies, a reduction of the dystrophin signal is detected in a small cohort of plasma samples from DMD patients when compared to healthy controls, female carriers, and other neuromuscular diseases. We also demonstrate the detection of dystrophin protein by an antibody-independent method using targeted liquid chromatography mass spectrometry. This last assay detects three different dystrophin peptides in all healthy individuals analysed and supports our finding that dystrophin protein is detectable in plasma. The results of our proof-of-concept study encourage further studies in larger sample cohorts to investigate the value of dystrophin protein as a low invasive blood biomarker for diagnostic screening and clinical monitoring of DMD.
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13
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Kim H, Cheon DH, Yang WS, Baek JH. Simultaneous Quantification of Apolipoprotein C-III O-Glycoforms by Protein-MRM. J Proteome Res 2023; 22:91-100. [PMID: 36412001 DOI: 10.1021/acs.jproteome.2c00490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Apolipoprotein C-III (APOC-III) regulates triglyceride levels, associated with a risk of cardiovascular disease. One gene generates several proteoforms, each with a different molecular mass and a unique function. Unlike peptide multiple reaction monitoring (MRM), protein-MRM without digestion is required to analyze clinically relevant individual proteoforms. We developed a protein-MRM method without digestion to individually quantify APOC-III proteoforms in human serum. We optimized the protein-MRM method following 60% acetonitrile extraction with C18 filtration. Bovine serum and myoglobin served as supporting cushions and the internal standard during sample preparation, respectively. Furthermore, we evaluated the LOD, lower limit of quantification, linearity, accuracy, and precision. Good correlation compared with turbidimetric immunoassay (TIA) and peptide-MRM was observed using 30 clinical sera. Individual APOC-III O-glycoforms were identified by top-down proteomics and simultaneously quantified using the protein-MRM method. The sum abundance of APOC-III proteoforms was significantly correlated with TIA and peptide-MRM. Our protein-MRM method provides an affordable and rapid quantification of potential disease-specific proteoforms. Precise quantification of each proteoform allows investigators to identify novel biological roles potentially related to cardiovascular disease or novel biomarkers. We expect our protein-oriented method to be more clinically useful than antibody-based immunoassays and peptide-oriented MRM analysis, especially for quantification of a biomarker proteoform with certain post-translational modifications.
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Affiliation(s)
- Hyojin Kim
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
| | - Dong Huey Cheon
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
| | - Won Suk Yang
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
| | - Je-Hyun Baek
- R&D Center for Clinical Mass Spectrometry, Seegene Medical Foundation, Seongdong-gu, Seoul 04805, Korea
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14
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Obi EN, Tellock DA, Thomas GJ, Veenstra TD. Biomarker Analysis of Formalin-Fixed Paraffin-Embedded Clinical Tissues Using Proteomics. Biomolecules 2023; 13:biom13010096. [PMID: 36671481 PMCID: PMC9855471 DOI: 10.3390/biom13010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
The relatively recent developments in mass spectrometry (MS) have provided novel opportunities for this technology to impact modern medicine. One of those opportunities is in biomarker discovery and diagnostics. Key developments in sample preparation have enabled a greater range of clinical samples to be characterized at a deeper level using MS. While most of these developments have focused on blood, tissues have also been an important resource. Fresh tissues, however, are difficult to obtain for research purposes and require significant resources for long-term storage. There are millions of archived formalin-fixed paraffin-embedded (FFPE) tissues within pathology departments worldwide representing every possible tissue type including tumors that are rare or very small. Owing to the chemical technique used to preserve FFPE tissues, they were considered intractable to many newer proteomics techniques and primarily only useful for immunohistochemistry. In the past couple of decades, however, researchers have been able to develop methods to extract proteins from FFPE tissues in a form making them analyzable using state-of-the-art technologies such as MS and protein arrays. This review will discuss the history of these developments and provide examples of how they are currently being used to identify biomarkers and diagnose diseases such as cancer.
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15
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Park DB, Kim L, Hwang JH, Kim KT, Park JE, Choi JS, An HJ. Temporal quantitative profiling of sialyllactoses and sialic acids after oral administration of sialyllactose to mini-pigs with osteoarthritis. RSC Adv 2023; 13:1115-1124. [PMID: 36686942 PMCID: PMC9811936 DOI: 10.1039/d2ra05912f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
Sialyllactose (SL) is the most abundant acidic oligosaccharide in human breast milk and plays a primary role in various biological processes. Recently, SL has attracted attention as an excellent dietary supplement for arthritis because it is effective in cartilage protection and treatment. Despite the superior function of SL, there are few pharmacological studies of SL according to blood concentrations in arthritis models. In this study, we investigated quantitative changes in SL and sialic acids in the plasma obtained from mini-pigs with osteoarthritis throughout exogenous administration of SL using liquid chromatography-multiple reaction monitoring mass spectrometry. Plasma concentrations of SL and sialic acids in the SL-fed group showed a significant difference compared to the control group. Mini pigs were fed only Neu5Ac bound to SL, but the concentration patterns of the two types of sialic acid, Neu5Ac and Neu5Gc, were similar. In addition, the relative mRNA expression level of matrix metalloproteinases (MMPs), which is known as a critical factor in cartilage matrix degradation, was remarkably decreased in the synovial membrane of the SL-fed group. Consequently, the temporal quantitative profiling suggests that dietary SL can be metabolized and utilized in the body and may protect against cartilage degradation by suppressing MMP expression during osteoarthritis progression.
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Affiliation(s)
- Dan Bi Park
- GeneChem Inc.Yuseong-guDaejeon 34025Republic of Korea,Graduate School of Analytical Science and Technology, Chungnam National UniversityDaejeon 34134Republic of Korea
| | - Lila Kim
- GeneChem Inc.Yuseong-guDaejeon 34025Republic of Korea
| | - Jeong Ho Hwang
- Animal Model Research Group, Jeonbuk Branch Institute, Korea Institute of ToxicologyJeollabukdo56212Republic of Korea
| | - Kyung-Tai Kim
- Animal Model Research Group, Jeonbuk Branch Institute, Korea Institute of ToxicologyJeollabukdo56212Republic of Korea
| | - Ji Eun Park
- Graduate School of Analytical Science and Technology, Chungnam National UniversityDaejeon 34134Republic of Korea,Asia Glycomics Reference SiteDaejeon 34134Republic of Korea
| | - Jong-Soon Choi
- Graduate School of Analytical Science and Technology, Chungnam National UniversityDaejeon 34134Republic of Korea,Research Center for Materials Analysis, Korea Basic Science InstituteDaejeon34133Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National UniversityDaejeon 34134Republic of Korea,Asia Glycomics Reference SiteDaejeon 34134Republic of Korea
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16
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Machida K, Kotani A, Hayashi Y, Hakamata H. Effects of digital processing on repeatability assessment of a multiple reaction monitoring liquid chromatography-tandem mass spectrometry system by ISO 11843-7. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4877. [PMID: 35941806 DOI: 10.1002/jms.4877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/24/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
ISO 11843 part 7 (ISO 11843-7) can provide a standard deviation (SD) of area measurements of a target peak through the stochastic behaviors of instrumental noises. The purpose of this study is to demonstrate that ISO 11843-7 can be applied to assess repeatability in an isocratic liquid chromatography-tandem mass spectrometry (LC-MS/MS) system without repetitive measurements. The relative standard deviation (RSD) of the peak area of ergosterol picolinyl ester, which was used as an example, on a multiple reaction monitoring (MRM) chromatogram was determined by ISO 11843-7. The RSD by ISO 11843-7 (N = 1) was within a 95% confidence band of the RSD by repetitive measurements (N = 6). Moreover, the effects of digital smoothing, such as moving average, were also examined on the repeatability assessment in LC-MS/MS by ISO 11843-7. From the results of the comparisons of the RSDs obtained by ISO 11843-7 and the repetitive measurements, it was shown that suitable RSDs of the peak area were obtained from the smoothed MRM chromatograms by the moving average for narrow data point windows (e.g., one-sixth of the peak width). In conclusion, the utility of repeatability assessment based on ISO 11843-7 has been expanded for the validation of an LC-MS/MS system.
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Affiliation(s)
- Koichi Machida
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Akira Kotani
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | | | - Hideki Hakamata
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
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17
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Kulyyassov A, Ramankulov Y, Ogryzko V. Generation of Peptides for Highly Efficient Proximity Utilizing Site-Specific Biotinylation in Cells. Life (Basel) 2022; 12:life12020300. [PMID: 35207587 PMCID: PMC8875956 DOI: 10.3390/life12020300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 11/16/2022] Open
Abstract
Protein tags are peptide sequences genetically embedded into a recombinant protein for various purposes, such as affinity purification, Western blotting, and immunofluorescence. Another recent application of peptide tags is in vivo labeling and analysis of protein–protein interactions (PPI) by proteomics methods. One of the common workflows involves site-specific in vivo biotinylation of an AviTag-fused protein in the presence of the biotin ligase BirA. However, due to the rapid kinetics of labeling, this tag is not ideal for analysis of PPI. Here we describe the rationale, design, and protocol for the new biotin acceptor peptides BAP1070 and BAP1108 using modular assembling of biotin acceptor fragments, DNA sequencing, transient expression of proteins in cells, and Western blotting methods. These tags were used in the Proximity Utilizing Biotinylation (PUB) method, which is based on coexpression of BAP-X and BirA-Y in mammalian cells, where X or Y are candidate interacting proteins of interest. By changing the sequence of these peptides, a low level of background biotinylation is achieved, which occurs due to random collisions of proteins in cells. Over 100 plasmid constructs, containing genes of transcription factors, histones, gene repressors, and other nuclear proteins were obtained during implementation of projects related to this method.
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Affiliation(s)
- Arman Kulyyassov
- Republican State Enterprise “National Center for Biotechnology” under the Science Committee of Ministry of Education and Science of the Republic of Kazakhstan, 13/5 Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan;
- Correspondence: ; Tel.: +7-7172-707534
| | - Yerlan Ramankulov
- Republican State Enterprise “National Center for Biotechnology” under the Science Committee of Ministry of Education and Science of the Republic of Kazakhstan, 13/5 Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan;
| | - Vasily Ogryzko
- UMR8126, Institut de Cancerologie Gustave Roussy, Universite Paris-Sud 11, CNRS, 94805 Villejuif, France;
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18
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Kulyyassov A. Application of Skyline for Analysis of Protein-Protein Interactions In Vivo. Molecules 2021; 26:molecules26237170. [PMID: 34885753 PMCID: PMC8658920 DOI: 10.3390/molecules26237170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/19/2022] Open
Abstract
Quantitative and qualitative analyses of cell protein composition using liquid chromatography/tandem mass spectrometry are now standard techniques in biological and clinical research. However, the quantitative analysis of protein–protein interactions (PPIs) in cells is also important since these interactions are the bases of many processes, such as the cell cycle and signaling pathways. This paper describes the application of Skyline software for the identification and quantification of the biotinylated form of the biotin acceptor peptide (BAP) tag, which is a marker of in vivo PPIs. The tag was used in the Proximity Utilizing Biotinylation (PUB) method, which is based on the co-expression of BAP-X and BirA-Y in mammalian cells, where X or Y are interacting proteins of interest. A high level of biotinylation was detected in the model experiments where X and Y were pluripotency transcription factors Sox2 and Oct4, or heterochromatin protein HP1γ. MRM data processed by Skyline were normalized and recalculated. Ratios of biotinylation levels in experiment versus controls were 86 ± 6 (3 h biotinylation time) and 71 ± 5 (9 h biotinylation time) for BAP-Sox2 + BirA-Oct4 and 32 ± 3 (4 h biotinylation time) for BAP-HP1γ + BirA-HP1γ experiments. Skyline can also be applied for the analysis and identification of PPIs from shotgun proteomics data downloaded from publicly available datasets and repositories.
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Affiliation(s)
- Arman Kulyyassov
- Republican State Enterprise "National Center for Biotechnology" under the Science Committee of Ministry of Education and Science of the Republic of Kazakhstan, 13/5, Kurgalzhynskoye Road, Nur-Sultan 010000, Kazakhstan
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