Article
Chemistry, Analytical
Hao Chen, Yuefei Zhang, Haichao Zhou, Weiran Chen, Jiayi Peng, Yang Feng, Linyuan Fan, Jun Li, Jin Zi, Yan Ren, Qidan Li, Siqi Liu
Summary: Spatial proteomics plays an important role in the era of single-cell biology. In this study, a new routine workflow was developed for proteomic analysis of micro-FFPE tissues, allowing the construction of a spatial proteomic atlas of mouse brain, which exhibited typical characteristics of spatial-dependent protein abundance and functional enrichment.
ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Ekenedirichukwu N. Obi, Daniel A. Tellock, Gabriel J. Thomas, Timothy D. Veenstra
Summary: The recent developments in mass spectrometry (MS) have provided new opportunities in biomarker discovery and diagnostics, particularly in analyzing clinical samples at a deeper level. While most developments have focused on blood, there is potential in utilizing archived formalin-fixed paraffin-embedded (FFPE) tissues, which were previously considered difficult to analyze using proteomics techniques. Researchers have developed methods to extract proteins from FFPE tissues, allowing for their analysis using state-of-the-art technologies like MS and protein arrays. This review discusses the history of these developments and their current applications in identifying biomarkers and diagnosing diseases such as cancer.
Article
Chemistry, Analytical
Kenneth Weke, Sachin Kote, Jakub Faktor, Sofian Al Shboul, Naomi Uwugiaren, Paul M. Brennan, David R. Goodlett, Ted R. Hupp, Irena Dapic
Summary: Developments in quantitative proteomics and DIA methodology have enabled protein quantification in biological samples, including formalin-fixed paraffin-embedded (FFPE) tissues. In this study, a simple and precise DIA-MS workflow was established to detect and quantify immune- and glioblastoma (GBM)-relevant proteins in FFPE patient materials. The results showed successful detection and quantification of more than 1700 proteins, including GBM-relevant proteins and immune-related proteins. This strategy has great potential for routine protein quantification in FFPE tissue samples.
ANALYTICA CHIMICA ACTA
(2022)
Article
Medicine, Research & Experimental
Bradley L. Ackermann, Ryan D. Morrison, Salisha Hill, Matthew D. Westfall, Brent D. Butts, Michael D. Soper, Jeff A. Fill, Andrew E. Schade, Daniel C. Liebler, Aaron M. Gruver
Summary: MS analysis allows accurate protein quantification from stained paraffin-embedded tissue sections, providing valuable data for the assessment of clinical tissue specimens.
LABORATORY INVESTIGATION
(2023)
Article
Biochemistry & Molecular Biology
Hua Zhang, Vamsi Krishna Polavarapu, Pengwei Xing, Miao Zhao, Lucy Mathot, Linxuan Zhao, Gabriela Rosen, Fredrik J. Swartling, Tobias Sjoblom, Xingqi Chen
Summary: Archived FFPE samples are widely used for cancer research, and we developed a highly sensitive method (FFPE-ATAC) to decode chromatin accessibility in FFPE tissues. This method generates high-quality chromatin accessibility profiles and allows analysis of chromatin profiles in regions of interest from a single FFPE tissue section.
Review
Oncology
Amin Talebi, Jean Paul Thiery, Mohammad Amin Kerachian
Summary: Chimeric transcripts are important for diagnosis and prognosis, but their identification from FFPE tissues is limited due to the reduced quality and quantity of RNA. Strategies need to be developed to overcome these limitations and maximize the potential of FFPE tissues as a source for fusion transcript identification.
CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY
(2021)
Article
Biochemical Research Methods
Hanan Schoffman, Yishai Levin, Ayelet Itzhaki-Alfia, Lea Tselekovits, Lior Gonen, Gilad Wolf Vainer, Goni Hout-Siloni, Iris Barshack, Zvi R. Cohen, Nevo Margalit, Tal Shahar
Summary: This study compared the effects of formaldehyde-fixed paraffin-embedded (FFPE) tissue blocks and fresh frozen tissue (FFT) on the quantifiable proteome. The results showed that both methods yield a similar number of proteins, but there are significant differences in the proteome composition, with FFPE specimens enriched with smaller proteins.
Article
Medicine, Research & Experimental
Lisa Kreutzer, Peter Weber, Theresa Heider, Mathias Heikenwaelder, Tobias Riedl, Philipp Baumeister, Frederick Klauschen, Claus Belka, Axel Walch, Horst Zitzelsberger, Julia Hess, Kristian Unger
Summary: This study presents a method for simultaneous measurement of the whole exome and the transcriptome from formalin-fixed paraffin-embedded tissue sections. The data demonstrate the feasibility and reproducibility of this approach, expanding the possibilities of multi-omics integration in cancer research.
LABORATORY INVESTIGATION
(2022)
Article
Biology
Masachika Ikegami, Shinji Kohsaka, Takeshi Hirose, Toshihide Ueno, Satoshi Inoue, Naoki Kanomata, Hideko Yamauchi, Taisuke Mori, Shigeki Sekine, Yoshihiro Inamoto, Yasushi Yatabe, Hiroshi Kobayashi, Sakae Tanaka, Hiroyuki Mano
Summary: The researchers developed MicroSEC, a filtering pipeline to remove sequencing artifacts from archival formalin-fixed and paraffin-embedded samples. The sensitivity and specificity of MicroSEC were confirmed to be 97% and 96% respectively using amplicon-based sequencing with 97 mutations. This tool may improve the reliability of clinical sequencing and advance cancer research using formalin-fixed, paraffin-embedded samples, which are of great interest for genomic analysis.
COMMUNICATIONS BIOLOGY
(2021)
Article
Chemistry, Analytical
Rory T. Steven, Marcel Niehaus, Adam J. Taylor, Ammar Nasif, Efstathios Elia, Richard J. A. Goodwin, Zoltan Takats, Josephine Bunch
Summary: Mass spectrometry imaging (MSI) is a powerful technique for providing spatially resolved atomic and molecular information from almost any sample type. Optimizing MSI methods for analysis of FFPE tissue is necessary due to the prevalence and importance of FFPE tissue storage.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Yunxia Guo, Junjie Ma, Zhengyue Li, Kaitong Dang, Qinyu Ge, Yan Huang, Guang-zhong Wang, Xiangwei Zhao
Summary: This study investigates the effects of fixation and storage time on the nuclear transcriptome signatures of the brain. The fixation time has a greater impact on the transcriptomic profiles than the retention time of FFPE samples. The findings will guide the preparation of FFPE samples for single-nucleus RNA-seq, especially in transcriptomic studies of brain diseases.
ANALYTICA CHIMICA ACTA
(2023)
Article
Medical Laboratory Technology
Feng-Ming Hsu, Yih-Leong Chang, Chung-Yung Chen, Shu-Rung Lin, Jason Chia-Hsien Cheng
Summary: HPR is an alternative RNA profiling approach with high sensitivity, reproducibility, robustness, and capability for molecular diagnostics in FFPE tumor biopsy specimens of lung and esophageal cancer.
CLINICAL CHEMISTRY
(2023)
Article
Endocrinology & Metabolism
Norifusa Iwahashi, Hironobu Umakoshi, Masatoshi Ogata, Tazuru Fukumoto, Hiroki Kaneko, Eriko Terada, Shunsuke Katsuhara, Naohiro Uchida, Katsuhiko Sasaki, Maki Yokomoto-Umakoshi, Yayoi Matsuda, Ryuichi Sakamoto, Yoshihiro Ogawa
Summary: This study evaluated the utility of transcriptome data from formalin-fixed paraffin-embedded (FFPE) samples in adrenocortical tumor research. The results demonstrated that FFPE samples can serve as a reliable alternative to fresh frozen samples for whole transcriptome profiling of adrenocortical tumors, enabling distinction of tumor types and detection of marker genes.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Dymph Klay, Karin M. Kazemier, Joanne J. van der Vis, Hidde M. Smits, Jan C. Grutters, Coline H. M. van Moorsel
Summary: This study found differences between sporadic idiopathic pulmonary fibrosis, telomere mutation-induced pulmonary fibrosis, and surfactant related gene mutation-induced pulmonary fibrosis, as well as a significant association between high expression of a high number of endoplasmic reticulum stress genes and shorter survival time.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Kristina G. Hulten, Robert M. Genta, Ira N. Kalfus, Yi Zhou, Hongjun Zhang, David Y. Graham
Summary: This study compared the antimicrobial susceptibility testing of H. pylori using targeted next-generation sequencing (NGS) and culture-based methods. The results showed that NGS was reliable in predicting resistance to clarithromycin, levofloxacin, rifabutin, and tetracycline, while having fair consistency for metronidazole and amoxicillin. Culture-based testing can effectively predict treatment outcomes with clarithromycin and levofloxacin, and further studies are needed to compare the predictive ability of both methods for other antibiotics.
Review
Spectroscopy
Carla Harkin, Karl W. Smith, Faye L. Cruickshank, C. Logan Mackay, Bryn Flinders, Ron M. A. Heeren, Tara Moore, Simon Brockbank, Diego F. Cobice
Summary: Mass spectrometry imaging (MSI) combines molecular and spatial information, making it a valuable tool in various applications. Chemical derivatization (CD) has proven to be an effective solution for ionization issues. On-tissue chemical derivatization (OTCD) is a powerful tool for studying the spatial distribution of poorly ionizable molecules within tissues.
MASS SPECTROMETRY REVIEWS
(2022)
Article
Biochemical Research Methods
Anna M. Kip, Juan Manuel Valverde, Maarten Altelaar, Ron M. A. Heeren, Inca H. R. Hundscheid, Cornelis H. C. Dejong, Steven W. M. Olde Damink, Benjamin Balluff, Kaatje Lenaerts
Summary: This study investigated the proteome and phosphoproteome changes in the human intestine during ischemia-reperfusion using LC-MS/MS and MSI techniques. The findings revealed alterations in proteins related to intestinal absorption, innate immunity, and extracellular matrix organization, as well as the activity of MAPK and CDK families during IR. The study highlights the importance of complementary use of different MS methodologies in understanding molecular changes during IR.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Analytical
Aljoscha Korber, Joel D. Keelor, Britt S. R. Claes, Ron M. A. Heeren, Ian G. M. Anthony
Summary: In this study, a new method called fast mass microscopy is proposed, which combines a Timepix3 detector with continuously sampling secondary ion mass spectrometry mass microscope to achieve high throughput imaging at lower mass resolution compared to conventional MSI. This method enables the acquisition of submicron, gigapixel images of fingerprints and rat tissue at significantly faster speeds than traditional microprobe-mode MSI.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Britt S. R. Claes, Kasper K. Krestensen, Gargey Yagnik, Andrej Grgic, Christel Kuik, Mark J. Lim, Kenneth J. Rothschild, Michiel Vandenbosch, Ron M. A. Heeren
Summary: A novel technology called MALDIIHC was published, which combined MALDI-MSI and IHC to achieve targeted imaging of biomolecules in tissue. The utility of targeted MALDIIHC and its complementarity with untargeted on-tissue proteomics was explored using breast cancer tissue. MALDI-2 was also investigated and demonstrated to improve MALDI-IHC. The combination of multiplexed MALDI-IHC with image-guided proteomics showed great potential in studying diseases.
ANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Anjusha Mathew, Joel D. Keelor, Gert B. Eijkel, Ian G. M. Anthony, Jingming Long, Jord Prangsma, Ron M. A. Heeren, Shane R. Ellis
Summary: This study presents the coupling of the TPX3 chip with a TOF MS system, resulting in improved time resolution and extended m/z detection range for ions. The additional information provided by TPX3 enhances the quality of mass spectrum in terms of signal-to-noise ratio. Furthermore, the imaging capabilities of TPX3 allow for spatial and temporal separation of neutral fragments.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Kasper Krijnen, Joel D. Keelor, Sebastian Boehm, Shane R. Ellis, Claus Koester, Jens Hoehndorf, Ron M. A. Heeren, Ian G. M. Anthony
Summary: Mass spectrometry imaging (MSI) is a surface analysis technique used for biological research, and multimodal imaging combining multiple imaging modes can provide a more comprehensive view of samples. In this study, a prototype Bruker timsTOF fleX instrument was modified to include secondary ion mass spectrometry (SIMS) and secondary electron (SE) imaging capabilities while preserving matrix-assisted laser desorption/ionization (MALDI) capability. The modified instrument showed improved efficiency in multimodal imaging, allowing for easy registration of images and eliminating the need for sample transfer.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Multidisciplinary Sciences
Andrej Grgic, Kasper K. Krestensen, Ron M. A. Heeren
Summary: Glycans play diverse roles in biology, and variations in N-glycosylation state within tissues have clinical diagnostic value. A protocol for MALDI MSI of N-glycans from fresh frozen tissue was developed, matching the current standard of FFPE analysis. This protocol significantly improves signal intensity and spatial resolution, enhancing the clinical application of MALDI MSI for N-glycan analysis.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Britt S. R. Claes, Andrew P. Bowman, Berwyck L. J. Poad, Ron M. A. Heeren, Stephen J. Blanksby, Shane R. Ellis
Summary: The biological functions of lipids highly depend on their molecular structures, specifically even small changes in structure such as different positions of unsaturation serve as critical indicators for changes in metabolism. However, conventional mass spectrometry imaging faces challenges in differentiating lipid isomers with mixture and structural complexity. Recent advances in ozone-induced dissociation coupled with matrix-assisted laser desorption/ionization have shown potential in mapping individual double-bond isomers and visualizing lipid desaturation in adjacent tissue types. This study employs a high-speed gas-phase reaction between ionized lipids and ozone to interrogate anionic glycerophospholipids isomers in biological tissues, providing valuable information on unsaturation and acyl chain composition from a single mass spectrum.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Article
Polymer Science
Lidia Molina-Millan, Aljoscha Koerber, Bryn Flinders, Berta Cillero-Pastor, Eva Cuypers, Ron M. A. Heeren
Summary: Synthetic polymers, when improperly disposed of, accumulate in the environment and pose potential health risks by degrading into micro- and nanoparticles (MNPs). Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) can be used to study biological or toxicological changes in organisms exposed to MNPs. MALDI-2 has been found to enhance the sensitivity of polymer analysis, making it a promising tool for studying the distribution of polymers in biological systems.
Article
Microbiology
Alison J. Scott, Alexis A. Smith, Ron M. A. Heeren, Utpal Pal, Robert K. Ernst
Summary: Spatially aware de novo discovery methods play a crucial role in identifying therapeutic targets in complex interphylum interactions. This study evaluated the potential of matrix-assisted desorption/ionization mass spectrometry imaging (MALDI-MSI) as a spatial omics method to simultaneously profile an arthropod vector and a mammalian skin in a bite model. The results demonstrated the feasibility of using MSI to analyze lipids and observe lipid reorganization at the bite site in both the tick and mammalian skin.
Article
Chemistry, Analytical
Britt S. R. Claes, Kasper K. Krestensen, Gargey Yagnik, Andrej Grgic, Christel Kuik, Mark J. Lim, Kenneth J. Rothschild, Michiel Vandenbosch, Ron M. A. Heeren
Summary: A novel technique called MALDIIHC was published recently, which combines MALDI-MSI and IHC to achieve targeted imaging of biomolecules in tissue. This study explored the utility of targeted MALDIIHC and its complementarity with untargeted spatial proteomics using breast cancer tissue. The combination of multiplexed MALDI-IHC with image-guided proteomics showed great potential for disease investigation. Additionally, the effect of MALDI-2 in improving MALDI-IHC was investigated.
ANALYTICAL CHEMISTRY
(2023)
Article
Food Science & Technology
Mudita Vats, Berta Cillero-Pastor, Bryn Flinders, Eva Cuypers, Ron M. A. Heeren
Summary: This study utilized MALDI-MSI to determine the spatial distribution of flavor compounds in edible button mushrooms and optimized the sample preparation protocol and investigated the effect of heat on the distribution.
JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE
(2023)
Review
Chemistry, Analytical
Kasper K. Krestensen, Ron M. A. Heeren, Benjamin Balluff
Summary: Mass spectrometry imaging (MSI) has evolved from a niche technique to a widely used spatial biology tool. This review provides an overview of state-of-the-art MSI applications in both established and emerging biomedical fields, serving as a reference framework for new researchers in the field.
Article
Medical Laboratory Technology
Laura Van Hese, Steven De Vleeschouwer, Tom Theys, Emma Lariviere, Lien Solie, Raf Sciot, Tiffany Porta Siegel, Steffen Rex, Ron M. A. Heeren, Eva Cuypers
Summary: This study developed and validated a mass spectrometry-based technique for molecular characterization of high- and low-grade glioma tissue during surgery. The rapid evaporative ionization mass spectrometry (REIMS) technique could differentiate between different glioma subtypes with high accuracy, providing real-time information for intra-operative decision-making.
JOURNAL OF MASS SPECTROMETRY AND ADVANCES IN THE CLINICAL LAB
(2022)
Article
Medical Laboratory Technology
Benjamin Balluff, Ron M. A. Heeren, Alan M. Race
Summary: Mass spectrometry imaging (MSI) is widely used in clinical research, requiring accurate image registration to align data from different imaging modalities. As technology advances, the accuracy and precision of image registration need to be increased accordingly.
JOURNAL OF MASS SPECTROMETRY AND ADVANCES IN THE CLINICAL LAB
(2022)