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Sun M, Otsuka Y, Okada M, Shimma S, Toyoda M. Probe oscillation control in tapping-mode scanning probe electrospray ionization for stabilization of mass spectrometry imaging. Analyst 2024; 149:4011-4019. [PMID: 38953117 DOI: 10.1039/d4an00712c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Mass spectrometry imaging (MSI) is used for visualizing the distribution of components in solid samples, such as biological tissues, and requires a technique to ionize the components from local areas of the sample. Tapping-mode scanning probe electrospray ionization (t-SPESI) uses an oscillating capillary probe to extract components from a local area of a sample with a small volume of solvent and to perform electrospray ionization of those components at high speed. MSI can be conducted by scanning the sample surface with a capillary probe. To ensure stable extraction and ionization for MSI, the probe oscillation during measurements must be understood. In this study, we examined the changes in oscillation amplitude and phase due to the interaction between the oscillating probe and the brain tissue section when the probe tip was dynamically brought close to the sample surface. The changes in the probe oscillation depended on the oscillation frequency and polarity of the bias voltage applied to the solvent because an electrostatic force shifted the frequency of the probe oscillation. These findings suggest that controlling the probe oscillation frequency is important for stabilizing MSI by t-SPESI.
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Affiliation(s)
- Mengze Sun
- Department of Physics, Graduate School of Science, Osaka University, Japan.
| | - Yoichi Otsuka
- Department of Physics, Graduate School of Science, Osaka University, Japan.
- Forefront Research Center, Graduate School of Science, Osaka University, Japan
| | - Maki Okada
- Department of Physics, Graduate School of Science, Osaka University, Japan.
| | - Shuichi Shimma
- Department of Bioengineering, Graduate School of Engineering, Osaka University, Japan
| | - Michisato Toyoda
- Department of Physics, Graduate School of Science, Osaka University, Japan.
- Forefront Research Center, Graduate School of Science, Osaka University, Japan
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2
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Alicehajic A, Duivenvoorden AAM, Lenaerts K. Unveiling the molecular complexity of intestinal ischemia-reperfusion injury through omics technologies. Proteomics 2024; 24:e2300160. [PMID: 38477684 DOI: 10.1002/pmic.202300160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024]
Abstract
Intestinal ischemia-reperfusion injury (IR) is implicated in various clinical conditions and causes damage to the intestinal epithelium resulting in intestinal barrier loss. This presents a substantial clinical challenge, emphasizing the importance of gaining a comprehensive understanding of molecular events to aid in the identification of novel therapeutic targets. This review systematically explores the extent to which omics technologies-transcriptomics, proteomics, metabolomics, and metagenomics-have already contributed to deciphering the molecular mechanisms contributing to intestinal IR injury, in in vivo and in vitro animal and human models, and in clinical samples. Recent breakthroughs involve applying omics methodologies on exosomes, organoids, and single cells, shedding light on promising avenues and valuable targets to reduce intestinal IR injury. Future directions aimed at expediting clinical translation are discussed as well and include multi-omics data integration to facilitate the identification of key regulatory nodes driving intestinal IR injury and advancing human organoid models based on the novel insights by single-cell omics technologies, offering hope for clinical application of therapeutic strategies in the years to come.
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Affiliation(s)
- Anja Alicehajic
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Annet Adriana Maria Duivenvoorden
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Kaatje Lenaerts
- Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
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3
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Choi HP, Yang JH, Azadzoi KM. Differential Post-Translational Modifications of Proteins in Bladder Ischemia. Biomedicines 2023; 12:81. [PMID: 38255188 PMCID: PMC10813800 DOI: 10.3390/biomedicines12010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Clinical and basic research suggests that bladder ischemia may be an independent variable in the development of lower urinary tract symptoms (LUTS). We have reported that ischemic changes in the bladder involve differential expression and post-translational modifications (PTMs) of the protein's functional domains. In the present study, we performed in-depth analysis of a previously reported proteomic dataset to further characterize proteins PTMs in bladder ischemia. Our proteomic analysis of proteins in bladder ischemia detected differential formation of non-coded amino acids (ncAAs) that might have resulted from PTMs. In-depth analysis revealed that three groups of proteins in the bladder proteome, including contractile proteins and their associated proteins, stress response proteins, and cell signaling-related proteins, are conspicuously impacted by ischemia. Differential PTMs of proteins by ischemia seemed to affect important signaling pathways in the bladder and provoke critical changes in the post-translational structural integrity of the stress response, contractile, and cell signaling-related proteins. Our data suggest that differential PTMs of proteins may play a role in the development of cellular stress, sensitization of smooth muscle cells to contractile stimuli, and deferential cell signaling in bladder ischemia. These observations may provide the foundation for future research to validate and define clinical translation of the modified biomarkers for precise diagnosis of bladder dysfunction and the development of new therapeutic targets against LUTS.
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Affiliation(s)
- Han-Pil Choi
- Proteomics Laboratory, VA Boston Healthcare System, Boston, MA 02130, USA;
| | - Jing-Hua Yang
- Proteomics Laboratory, Department of Surgery, VA Boston Healthcare System, Boston University School of Medicine, Boston, MA 02130, USA;
| | - Kazem M. Azadzoi
- Departments of Urology and Pathology, VA Boston Healthcare System, Boston University School of Medicine, Boston, MA 02130, USA
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4
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Guo RR, Lageveen-Kammeijer GSM, Wang W, Dalebout H, Zhang W, Wuhrer M, Liu L, Heijs B, Voglmeir J. Analysis of Immunogenic Galactose-α-1,3-galactose-Containing N-Glycans in Beef, Mutton, and Pork Tenderloin by Combining Matrix-Assisted Laser Desorption/Ionization-Mass Spectroscopy and Capillary Electrophoresis Hyphenated with Mass Spectrometry via Electrospray Ionization. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:4184-4192. [PMID: 36809004 DOI: 10.1021/acs.jafc.2c08067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Severe allergic reactions to certain types of meat following tick bites have been reported in geographic regions which are endemic with ticks. This immune response is directed to a carbohydrate antigen (galactose-α-1,3-galactose or α-Gal), which is present in glycoproteins of mammalian meats. At the moment, asparagine-linked complex carbohydrates (N-glycans) with α-Gal motifs in meat glycoproteins and in which cell types or tissue morphologies these α-Gal moieties are present in mammalian meats are still unclear. In this study, we analyzed α-Gal-containing N-glycans in beef, mutton, and pork tenderloin and provided for the first time the spatial distribution of these types of N-glycans in various meat samples. Terminal α-Gal-modified N-glycans were found to be highly abundant in all analyzed samples (55, 45, and 36% of N-glycome in beef, mutton, and pork, respectively). Visualizations of the N-glycans with α-Gal modification revealed that this motif was mainly present in the fibroconnective tissue. To conclude, this study contributes to a better understanding of the glycosylation biology of meat samples and provides guidance for processed meat products, in which only meat fibers are required as an ingredient (i.e., sausages or canned meat).
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Affiliation(s)
- Rui-Rui Guo
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | | | - Wenjun Wang
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Wangang Zhang
- National Center of Meat Quality and Safety Control, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bram Heijs
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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5
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Claes BR, Krestensen KK, Yagnik G, Grgic A, Kuik C, Lim MJ, Rothschild KJ, Vandenbosch M, Heeren RMA. MALDI-IHC-Guided In-Depth Spatial Proteomics: Targeted and Untargeted MSI Combined. Anal Chem 2023; 95:2329-2338. [PMID: 36638208 PMCID: PMC9893213 DOI: 10.1021/acs.analchem.2c04220] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Recently, a novel technology was published, utilizing the strengths of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) and immunohistochemistry (IHC), achieving highly multiplexed, targeted imaging of biomolecules in tissue. This new technique, called MALDI-IHC, opened up workflows to target molecules of interest using MALDI-MSI that are usually targeted by standard IHC. In this paper, the utility of targeted MALDI-IHC and its complementarity with untargeted on-tissue bottom-up spatial proteomics is explored using breast cancer tissue. Furthermore, the MALDI-2 effect was investigated and demonstrated to improve MALDI-IHC. Formalin-fixed paraffin-embedded (FFPE) human breast cancer tissue sections were stained for multiplex MALDI-IHC with six photocleavable mass-tagged (PC-MT) antibodies constituting a breast cancer antibody panel (CD20, actin-αSM, HER2, CD68, vimentin, and panCK). K-means spatial clusters were created based on the MALDI-IHC images and cut out using laser-capture microdissection (LMD) for further untargeted LC-MS-based bottom-up proteomics analyses. Numerous peptides could be tentatively assigned to multiple proteins, of which three proteins were also part of the antibody panel (vimentin, keratins, and actin). Post-ionization with MALDI-2 showed an increased intensity of the PC-MTs and suggests options for the development of new mass-tags. Although the on-tissue digestion covered a wider range of proteins, the MALDI-IHC allowed for easy and straightforward identification of proteins that were not detected in untargeted approaches. The combination of the multiplexed MALDI-IHC with image-guided proteomics showed great potential to further investigate diseases by providing complementary information from the same tissue section and without the need for customized instrumentation.
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Affiliation(s)
- Britt
S. R. Claes
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Kasper K. Krestensen
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Gargey Yagnik
- AmberGen,
Inc., 44 Manning Road, Billerica, Massachusetts 01821, United States
| | - Andrej Grgic
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Christel Kuik
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Mark J. Lim
- AmberGen,
Inc., 44 Manning Road, Billerica, Massachusetts 01821, United States
| | - Kenneth J. Rothschild
- AmberGen,
Inc., 44 Manning Road, Billerica, Massachusetts 01821, United States,Molecular
Biophysics Laboratory, Department of Physics and Photonics Center, Boston University, Boston, Massachusetts 02215, United States
| | - Michiel Vandenbosch
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands
| | - Ron M. A. Heeren
- The
Maastricht MultiModal Molecular Imaging (M4I) institute, Division
of Imaging Mass Spectrometry (IMS), Maastricht
University, 6229 ER Maastricht, The Netherlands,
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6
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Hu H, Laskin J. Emerging Computational Methods in Mass Spectrometry Imaging. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2203339. [PMID: 36253139 PMCID: PMC9731724 DOI: 10.1002/advs.202203339] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 09/17/2022] [Indexed: 05/10/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful analytical technique that generates maps of hundreds of molecules in biological samples with high sensitivity and molecular specificity. Advanced MSI platforms with capability of high-spatial resolution and high-throughput acquisition generate vast amount of data, which necessitates the development of computational tools for MSI data analysis. In addition, computation-driven MSI experiments have recently emerged as enabling technologies for further improving the MSI capabilities with little or no hardware modification. This review provides a critical summary of computational methods and resources developed for MSI data analysis and interpretation along with computational approaches for improving throughput and molecular coverage in MSI experiments. This review is focused on the recently developed artificial intelligence methods and provides an outlook for a future paradigm shift in MSI with transformative computational methods.
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Affiliation(s)
- Hang Hu
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN47907USA
| | - Julia Laskin
- Department of ChemistryPurdue University560 Oval DriveWest LafayetteIN47907USA
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7
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Wang C, Liu G, Liu Y, Yang Z, Xin W, Wang M, Li Y, Yang L, Mu H, Zhou C. Novel serum proteomic biomarkers for early diagnosis and aggressive grade identification of prostate cancer. Front Oncol 2022; 12:1004015. [PMID: 36276156 PMCID: PMC9582260 DOI: 10.3389/fonc.2022.1004015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/20/2022] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Prostate cancer (PCa) is one of the most common tumors and the second leading cause of cancer-related death in men. The discovery of novel biomarkers for PCa diagnosis in the early stage, as well as discriminating aggressive PCa from non-aggressive PCa continue to pose a challenge. The aim of this study was to identify serum proteins that were sensitive and specific enough to detect early-stage and aggressive PCa. METHODS The serum proteomic profiling of patients with PCa and benign prostatic hyperplasia (BPH) was comprehensively analyzed using data-independent acquisition mass spectrometry (DIA-MS), and the bioinformatics analysis was performed. The differentially expressed proteins (DEPs) of interest were further verified by enzyme-linked immunosorbent assay (ELISA) and immunoturbidimetry assay. RESULTS Statistically significant difference in abundance showed 56 DEPs between early-stage PCa and BPH and 47 DEPs between aggressive and non-aggressive PCa patients. In addition, the verification results showed that serum L-selectin concentration was significantly higher (p<0.05) in Gleason 6 PCa when compared with BPH, and the concentration of osteopontin (SPP1) and ceruloplasmin (CP) increased with higher Gleason score. CONCLUSIONS DIA-MS has great potential in cancer-related biomarker screening. Our data demonstrated that adding SPP1 and CP to PSA improved the separation of Gleason 7 (4 + 3) or above from Gleason 7 (3 + 4) or below compared with PSA diagnosis alone. Serum SPP1 and CP could be effective biomarkers to differentiate aggressive PCa (especially Gleason 7 (4 + 3) or above) from non-aggressive disease.
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Affiliation(s)
- Ce Wang
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Guangming Liu
- Department of Urology Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Yehua Liu
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Zhanpo Yang
- Department of Urology Surgery, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Weiwei Xin
- Department of Pathology, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Meng Wang
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Yang Li
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Lan Yang
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Hong Mu
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
| | - Chunlei Zhou
- Department of Clinical Laboratory, Tianjin First Central Hospital, School of Medicine, Nankai University, Tianjin, China
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8
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Wan Y, Dong P, Zhu X, Lei Y, Shen J, Liu W, Liu K, Zhang X. Bibliometric and visual analysis of intestinal ischemia reperfusion from 2004 to 2022. Front Med (Lausanne) 2022; 9:963104. [PMID: 36052333 PMCID: PMC9426633 DOI: 10.3389/fmed.2022.963104] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/27/2022] [Indexed: 11/23/2022] Open
Abstract
Background Intestinal ischemia/reperfusion (I/R) injury is a common tissue-organ damage occurring in surgical practice. This study aims to comprehensively review the collaboration and impact of countries, institutions, authors, subject areas, journals, keywords, and critical literature on intestinal I/R injury from a bibliometric perspective, and to assess the evolution of clustering of knowledge structures and identify hot trends and emerging topics. Methods Articles and reviews related to intestinal I/R were retrieved through subject search from Web of Science Core Collection. Bibliometric analyses were conducted on Excel 365, CiteSpace, VOSviewer, and Bibliometrix (R-Tool of R-Studio). Results A total of 1069 articles and reviews were included from 2004 to 2022. The number of articles on intestinal I/R injury gradually plateaued, but the number of citations increased. These publications were mainly from 985 institutions in 46 countries, led by China and the United States. Liu Kx published the most papers, while Chiu Cj had the largest number of co-citations. Analysis of the journals with the most outputs showed that most journals focused on surgical sciences, cell biology, and immunology. Macroscopic sketch and microscopic characterization of the entire knowledge domain were achieved through co-citation analysis. The roles of cell death, exosomes, intestinal flora, and anesthetics in intestinal I/R injury are the current and developing research focuses. The keywords "dexmedetomidine", "proliferation", and "ferroptosis" may also become new trends and focus of future research. Conclusion This study comprehensively reviews the research on intestinal I/R injury using bibliometric and visualization methods, and will help scholars better understand the dynamic evolution of intestinal I/R injury and provide directions for future research.
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Affiliation(s)
- Yantong Wan
- College of Anesthesiology, Southern Medical University, Guangzhou, China
| | - Peng Dong
- College of Anesthesiology, Southern Medical University, Guangzhou, China
| | - Xiaobing Zhu
- Department of Anesthesiology, Hospital of Traditional Chinese Medicine of Zhongshan City, Zhongshan, China
| | - Yuqiong Lei
- Department of Anesthesiology, Nan Fang Hospital, Southern Medical University, Guangzhou, China
| | - Junyi Shen
- The Second Clinical Medical College, Southern Medical University, Guangzhou, China
| | - Weifeng Liu
- Department of Anesthesiology, Nan Fang Hospital, Southern Medical University, Guangzhou, China
| | - Kexuan Liu
- Department of Anesthesiology, Nan Fang Hospital, Southern Medical University, Guangzhou, China
| | - Xiyang Zhang
- Department of Anesthesiology, Nan Fang Hospital, Southern Medical University, Guangzhou, China
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9
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Nie LX, Huang LY, Wang XP, Lv LF, Yang XX, Jia XF, Kang S, Yao LW, Dai Z, Ma SC. Desorption Electrospray Ionization Mass Spectrometry Imaging Illustrates the Quality Characters of Isatidis Radix. FRONTIERS IN PLANT SCIENCE 2022; 13:897528. [PMID: 35783961 PMCID: PMC9240750 DOI: 10.3389/fpls.2022.897528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
For a long history, herbal medicines have made significant contributions to human health all around the world. However, the exploration of an effective approach to illustrate their inner quality remains a challenge. So, it is imperative to develop new methods and technologies to characterize and identify quality markers of herbal medicines. Taking Isatidis Radix, the dried root of Isatis indigotica as an example, desorption electrospray ionization (DESI), in combination with quadrupole-time-of-flight mass spectrometry (Q-TOF/MS), was applied in this work for the first time to reveal the comprehensive spatial distribution of metabolites and, further, to illustrate quality characters of this herbal medicine. After simple pretreatment, 102 metabolites including alkaloids, sulfur-containing compounds, phenylpropanoids, nucleosides, amino acids, organic acids, flavonoids, phenols, terpenes, saccharides, peptides, and sphingolipids were characterized, some of which were successfully localized and visualized in the transverse section of the root. Based on the ion images, samples with different quality characters were distinguished unambiguously by the pattern recognition method of orthogonal partial least squares discrimination analysis (OPLS-DA). Simultaneously, 11 major influencing components exerting higher ion intensities in superior samples were identified as the potential quality markers of Isatidis Radix. Desorption electrospray ionization (DESI) mass spectrometry imaging (MSI), together with chemometric analysis could not only improve the understanding of the plant biology of herbal medicines but also be beneficial in the identification of quality markers, so as to carry out better quality control of herbal medicines.
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Affiliation(s)
- Li-Xing Nie
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
- WHO Collaborating Center for Herbal Medicine (CHN-139), Beijing, China
| | - Lie-Yan Huang
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Xin-Ping Wang
- Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Lin-Feng Lv
- Shaoxing Institutes for Food and Drug Control, Shaoxing, China
| | | | | | - Shuai Kang
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Ling-Wen Yao
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Zhong Dai
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
| | - Shuang-Cheng Ma
- National Institutes for Food and Drug Control, National Medical Products Administration, Beijing, China
- WHO Collaborating Center for Herbal Medicine (CHN-139), Beijing, China
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10
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Data-Independent Acquisition-Based Mass Spectrometry (DIA-MS) for Quantitative Analysis of Human Intestinal Ischemia/Reperfusion. Appl Biochem Biotechnol 2022; 194:4156-4168. [PMID: 35666382 DOI: 10.1007/s12010-022-04005-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2022] [Indexed: 11/02/2022]
Abstract
Intestinal ischemia-reperfusion (II/R) injury is a complex pathologic process, which is of great significance to unravel the underlying mechanisms and pathophysiology. Our study represented a comprehensive proteomic analysis in the human intestine with ischemia-reperfusion injury. The proteomics analysis measured a total of 5,230 proteins, and 417 differently expressed proteins (DEPs) were identified between II/R and control samples. GO and KEGG analysis demonstrated that the 290 upregulated DEPs in II/R were significantly involved in immune-related biological process and tight junction, focal adhesion, and cAMP signaling pathway, whereas the 127 downregulated DEPs in II/R were enriched in lipid metabolic process and metabolic pathway. Furthermore, we screened out 20 hub proteins from the protein-protein interaction (PPI) network according to the degree of connectivity, and six clusters were identified. Combined with the result of KEGG analysis, 6 from the 20 hub proteins, ACTB, CAV1, FLNA, MYLK, ACTN1, and MYL9, were identified as the key proteins in the progress of II/R injury. According to the previous studies, FLNA and MYL9 were selected as the novel disease-related proteins for the first time. In conclusion, this study extended our understanding of the alteration in the human intestine during ischemia and reperfusion and highlighted the potential role of FLNA and MYL9 in the progress of II/R injury, which need to be further studied.
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11
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Høiem TS, Andersen MK, Martin-Lorenzo M, Longuespée R, Claes BSR, Nordborg A, Dewez F, Balluff B, Giampà M, Sharma A, Hagen L, Heeren RMA, Bathen TF, Giskeødegård GF, Krossa S, Tessem MB. An optimized MALDI MSI protocol for spatial detection of tryptic peptides in fresh frozen prostate tissue. Proteomics 2022; 22:e2100223. [PMID: 35170848 PMCID: PMC9285595 DOI: 10.1002/pmic.202100223] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/19/2022] [Accepted: 02/07/2022] [Indexed: 11/29/2022]
Abstract
MALDI MS imaging (MSI) is a powerful analytical tool for spatial peptide detection in heterogeneous tissues. Proper sample preparation is crucial to achieve high quality, reproducible measurements. Here we developed an optimized protocol for spatially resolved proteolytic peptide detection with MALDI time‐of‐flight MSI of fresh frozen prostate tissue sections. The parameters tested included four different tissue washes, four methods of protein denaturation, four methods of trypsin digestion (different trypsin densities, sprayers, and incubation times), and five matrix deposition methods (different sprayers, settings, and matrix concentrations). Evaluation criteria were the number of detected and excluded peaks, percentage of high mass peaks, signal‐to‐noise ratio, spatial localization, and average intensities of identified peptides, all of which were integrated into a weighted quality evaluation scoring system. Based on these scores, the optimized protocol included an ice‐cold EtOH+H2O wash, a 5 min heating step at 95°C, tryptic digestion incubated for 17h at 37°C and CHCA matrix deposited at a final amount of 1.8 μg/mm2. Including a heat‐induced protein denaturation step after tissue wash is a new methodological approach that could be useful also for other tissue types. This optimized protocol for spatial peptide detection using MALDI MSI facilitates future biomarker discovery in prostate cancer and may be useful in studies of other tissue types.
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Affiliation(s)
- Therese S Høiem
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Maria K Andersen
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Marta Martin-Lorenzo
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, Netherlands
| | - Rémi Longuespée
- Department of Clinical Pharmacology and Pharmacoepidemiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Britt S R Claes
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, Netherlands
| | - Anna Nordborg
- Department of Biotechnology and Nanomedicine, SINTEF Industry, Trondheim, Norway
| | - Frédéric Dewez
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, Netherlands
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, Netherlands
| | - Marco Giampà
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, NTNU - Norwegian University of Science and Technology and the Central Norway Regional Health Authority Norway, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics, NTNU - Norwegian University of Science and Technology and the Central Norway Regional Health Authority Norway, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging Institute (M4I), Maastricht University, Maastricht, Netherlands
| | - Tone F Bathen
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Department of radiology and nuclear medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Guro F Giskeødegård
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Sebastian Krossa
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - May-Britt Tessem
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway.,Department of Surgery, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
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