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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2021-2022. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38925550 DOI: 10.1002/mas.21873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/12/2024] [Indexed: 06/28/2024]
Abstract
The use of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry for the analysis of carbohydrates and glycoconjugates is a well-established technique and this review is the 12th update of the original article published in 1999 and brings coverage of the literature to the end of 2022. As with previous review, this review also includes a few papers that describe methods appropriate to analysis by MALDI, such as sample preparation, even though the ionization method is not MALDI. The review follows the same format as previous reviews. It is divided into three sections: (1) general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, quantification and the use of computer software for structural identification. (2) Applications to various structural types such as oligo- and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals, and (3) other general areas such as medicine, industrial processes, natural products and glycan synthesis where MALDI is extensively used. Much of the material relating to applications is presented in tabular form. MALDI is still an ideal technique for carbohydrate analysis, particularly in its ability to produce single ions from each analyte and advancements in the technique and range of applications show little sign of diminishing.
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Kobeissy F, Goli M, Yadikar H, Shakkour Z, Kurup M, Haidar MA, Alroumi S, Mondello S, Wang KK, Mechref Y. Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects. Front Neurol 2023; 14:1288740. [PMID: 38073638 PMCID: PMC10703396 DOI: 10.3389/fneur.2023.1288740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/01/2023] [Indexed: 02/12/2024] Open
Abstract
Neuroproteomics, an emerging field at the intersection of neuroscience and proteomics, has garnered significant attention in the context of neurotrauma research. Neuroproteomics involves the quantitative and qualitative analysis of nervous system components, essential for understanding the dynamic events involved in the vast areas of neuroscience, including, but not limited to, neuropsychiatric disorders, neurodegenerative disorders, mental illness, traumatic brain injury, chronic traumatic encephalopathy, and other neurodegenerative diseases. With advancements in mass spectrometry coupled with bioinformatics and systems biology, neuroproteomics has led to the development of innovative techniques such as microproteomics, single-cell proteomics, and imaging mass spectrometry, which have significantly impacted neuronal biomarker research. By analyzing the complex protein interactions and alterations that occur in the injured brain, neuroproteomics provides valuable insights into the pathophysiological mechanisms underlying neurotrauma. This review explores how such insights can be harnessed to advance personalized medicine (PM) approaches, tailoring treatments based on individual patient profiles. Additionally, we highlight the potential future prospects of neuroproteomics, such as identifying novel biomarkers and developing targeted therapies by employing artificial intelligence (AI) and machine learning (ML). By shedding light on neurotrauma's current state and future directions, this review aims to stimulate further research and collaboration in this promising and transformative field.
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Affiliation(s)
- Firas Kobeissy
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Hamad Yadikar
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zaynab Shakkour
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO, United States
| | - Milin Kurup
- Alabama College of Osteopathic Medicine, Dothan, AL, United States
| | | | - Shahad Alroumi
- Department of Biological Sciences Faculty of Science, Kuwait University, Safat, Kuwait
| | - Stefania Mondello
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy
| | - Kevin K. Wang
- Department of Neurobiology, School of Medicine, Neuroscience Institute, Atlanta, GA, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
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Sarkar S, Squire A, Diab H, Rahman MK, Perdomo A, Awosile B, Calle A, Thompson J. Effect of Tryptic Digestion on Sensitivity and Specificity in MALDI-TOF-Based Molecular Diagnostics through Machine Learning. SENSORS (BASEL, SWITZERLAND) 2023; 23:8042. [PMID: 37836873 PMCID: PMC10575185 DOI: 10.3390/s23198042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/15/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
The digestion of protein into peptide fragments reduces the size and complexity of protein molecules. Peptide fragments can be analyzed with higher sensitivity (often > 102 fold) and resolution using MALDI-TOF mass spectrometers, leading to improved pattern recognition by common machine learning algorithms. In turn, enhanced sensitivity and specificity for bacterial sorting and/or disease diagnosis may be obtained. To test this hypothesis, four exemplar case studies have been pursued in which samples are sorted into dichotomous groups by machine learning (ML) software based on MALDI-TOF spectra. Samples were analyzed in 'intact' mode in which the proteins present in the sample were not digested with protease prior to MALDI-TOF analysis and separately after the standard overnight tryptic digestion of the same samples. For each case, sensitivity (sens), specificity (spc), and the Youdin index (J) were used to assess the ML model performance. The proteolytic digestion of samples prior to MALDI-TOF analysis substantially enhanced the sensitivity and specificity of dichotomous sorting. Two exceptions were when substantial differences in chemical composition between the samples were present and, in such cases, both 'intact' and 'digested' protocols performed similarly. The results suggest proteolytic digestion prior to analysis can improve sorting in MALDI/ML-based workflows and may enable improved biomarker discovery. However, when samples are easily distinguishable protein digestion is not necessary to obtain useful diagnostic results.
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Affiliation(s)
| | | | | | | | | | | | | | - Jonathan Thompson
- School of Veterinary Medicine, Texas Tech University, 7671 Evans Dr., Amarillo, TX 79106, USA; (S.S.); (A.S.); (M.K.R.)
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Stabile AM, Pistilli A, Mariangela R, Rende M, Bartolini D, Di Sante G. New Challenges for Anatomists in the Era of Omics. Diagnostics (Basel) 2023; 13:2963. [PMID: 37761332 PMCID: PMC10529314 DOI: 10.3390/diagnostics13182963] [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: 07/31/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Anatomic studies have traditionally relied on macroscopic, microscopic, and histological techniques to investigate the structure of tissues and organs. Anatomic studies are essential in many fields, including medicine, biology, and veterinary science. Advances in technology, such as imaging techniques and molecular biology, continue to provide new insights into the anatomy of living organisms. Therefore, anatomy remains an active and important area in the scientific field. The consolidation in recent years of some omics technologies such as genomics, transcriptomics, proteomics, and metabolomics allows for a more complete and detailed understanding of the structure and function of cells, tissues, and organs. These have been joined more recently by "omics" such as radiomics, pathomics, and connectomics, supported by computer-assisted technologies such as neural networks, 3D bioprinting, and artificial intelligence. All these new tools, although some are still in the early stages of development, have the potential to strongly contribute to the macroscopic and microscopic characterization in medicine. For anatomists, it is time to hitch a ride and get on board omics technologies to sail to new frontiers and to explore novel scenarios in anatomy.
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Affiliation(s)
- Anna Maria Stabile
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Alessandra Pistilli
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Ruggirello Mariangela
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Mario Rende
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
| | - Desirée Bartolini
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
- Department of Pharmaceutical Sciences, University of Perugia, 06126 Perugia, Italy
| | - Gabriele Di Sante
- Department of Medicine and Surgery, Section of Human, Clinical and Forensic Anatomy, University of Perugia, 60132 Perugia, Italy; (A.M.S.); (A.P.); (R.M.); (M.R.)
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King ME, Lin M, Spradlin M, Eberlin LS. Advances and Emerging Medical Applications of Direct Mass Spectrometry Technologies for Tissue Analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:1-25. [PMID: 36944233 DOI: 10.1146/annurev-anchem-061020-015544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Offering superb speed, chemical specificity, and analytical sensitivity, direct mass spectrometry (MS) technologies are highly amenable for the molecular analysis of complex tissues to aid in disease characterization and help identify new diagnostic, prognostic, and predictive markers. By enabling detection of clinically actionable molecular profiles from tissues and cells, direct MS technologies have the potential to guide treatment decisions and transform sample analysis within clinical workflows. In this review, we highlight recent health-related developments and applications of direct MS technologies that exhibit tangible potential to accelerate clinical research and disease diagnosis, including oncological and neurodegenerative diseases and microbial infections. We focus primarily on applications that employ direct MS technologies for tissue analysis, including MS imaging technologies to map spatial distributions of molecules in situ as well as handheld devices for rapid in vivo and ex vivo tissue analysis.
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Affiliation(s)
- Mary E King
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA;
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA;
| | - Monica Lin
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA;
| | - Meredith Spradlin
- Department of Chemistry, The University of Texas at Austin, Austin, Texas, USA;
| | - Livia S Eberlin
- Department of Surgery, Baylor College of Medicine, Houston, Texas, USA;
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Rittel MF, Schmidt S, Weis CA, Birgin E, van Marwick B, Rädle M, Diehl SJ, Rahbari NN, Marx A, Hopf C. Spatial Omics Imaging of Fresh-Frozen Tissue and Routine FFPE Histopathology of a Single Cancer Needle Core Biopsy: A Freezing Device and Multimodal Workflow. Cancers (Basel) 2023; 15:2676. [PMID: 37345020 DOI: 10.3390/cancers15102676] [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: 01/14/2023] [Revised: 04/16/2023] [Accepted: 05/06/2023] [Indexed: 06/23/2023] Open
Abstract
The complex molecular alterations that underlie cancer pathophysiology are studied in depth with omics methods using bulk tissue extracts. For spatially resolved tissue diagnostics using needle biopsy cores, however, histopathological analysis using stained FFPE tissue and the immunohistochemistry (IHC) of a few marker proteins is currently the main clinical focus. Today, spatial omics imaging using MSI or IRI is an emerging diagnostic technology for the identification and classification of various cancer types. However, to conserve tissue-specific metabolomic states, fast, reliable, and precise methods for the preparation of fresh-frozen (FF) tissue sections are crucial. Such methods are often incompatible with clinical practice, since spatial metabolomics and the routine histopathology of needle biopsies currently require two biopsies for FF and FFPE sampling, respectively. Therefore, we developed a device and corresponding laboratory and computational workflows for the multimodal spatial omics analysis of fresh-frozen, longitudinally sectioned needle biopsies to accompany standard FFPE histopathology of the same biopsy core. As a proof-of-concept, we analyzed surgical human liver cancer specimens using IRI and MSI with precise co-registration and, following FFPE processing, by sequential clinical pathology analysis of the same biopsy core. This workflow allowed for a spatial comparison between different spectral profiles and alterations in tissue histology, as well as a direct comparison for histological diagnosis without the need for an extra biopsy.
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Affiliation(s)
- Miriam F Rittel
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Stefan Schmidt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
| | - Cleo-Aron Weis
- Institute of Pathology, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Emrullah Birgin
- Department of Surgery, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Björn van Marwick
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
| | - Matthias Rädle
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Steffen J Diehl
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Clinic of Clinical Radiology and Nuclear Medicine, University Medical Center Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Nuh N Rahbari
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Department of Surgery, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Alexander Marx
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Institute of Pathology, University Medical Centre Mannheim, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Institute of Medical Technology, Heidelberg University and Mannheim University of Applied Sciences, Paul-Wittsack-Str. 10, 68163 Mannheim, Germany
- Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
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Spratt SJ, Mizuguchi T, Akaboshi H, Kosakamoto H, Okada R, Obata F, Ozeki Y. Imaging the uptake of deuterated methionine in Drosophila with stimulated Raman scattering. Front Chem 2023; 11:1141920. [PMID: 37065821 PMCID: PMC10090404 DOI: 10.3389/fchem.2023.1141920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
Introduction: Visualizing small individual biomolecules at subcellular resolution in live cells and tissues can provide valuable insights into metabolic activity in heterogeneous cells, but is challenging.Methods: Here, we used stimulated Raman scattering (SRS) microscopy to image deuterated methionine (d-Met) incorporated into Drosophila tissues in vivo.Results: Our results demonstrate that SRS can detect a range of previously uncharacterized cell-to-cell differences in d-Met distribution within a tissue at the subcellular level.Discussion: These results demonstrate the potential of SRS microscopy for metabolic imaging of less abundant but important amino acids such as methionine in tissue.
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Affiliation(s)
- Spencer J. Spratt
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Takaha Mizuguchi
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Hikaru Akaboshi
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Hina Kosakamoto
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Rina Okada
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Fumiaki Obata
- Laboratory for Nutritional Biology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Laboratory of Molecular Cell Biology and Development, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
- *Correspondence: Yasuyuki Ozeki,
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8
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Piol D, Robberechts T, Da Cruz S. Lost in local translation: TDP-43 and FUS in axonal/neuromuscular junction maintenance and dysregulation in amyotrophic lateral sclerosis. Neuron 2023; 111:1355-1380. [PMID: 36963381 DOI: 10.1016/j.neuron.2023.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/21/2022] [Accepted: 02/16/2023] [Indexed: 03/26/2023]
Abstract
Key early features of amyotrophic lateral sclerosis (ALS) are denervation of neuromuscular junctions and axonal degeneration. Motor neuron homeostasis relies on local translation through controlled regulation of axonal mRNA localization, transport, and stability. Yet the composition of the local transcriptome, translatome (mRNAs locally translated), and proteome during health and disease remains largely unexplored. This review covers recent discoveries on axonal translation as a critical mechanism for neuronal maintenance/survival. We focus on two RNA binding proteins, transactive response DNA binding protein-43 (TDP-43) and fused in sarcoma (FUS), whose mutations cause ALS and frontotemporal dementia (FTD). Emerging evidence points to their essential role in the maintenance of axons and synapses, including mRNA localization, transport, and local translation, and whose dysfunction may contribute to ALS. Finally, we describe recent advances in omics-based approaches mapping compartment-specific local RNA and protein compositions, which will be invaluable to elucidate fundamental local processes and identify key targets for therapy development.
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Affiliation(s)
- Diana Piol
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Tessa Robberechts
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium
| | - Sandrine Da Cruz
- VIB-KU Leuven Center for Brain and Disease Research, Department of Neurosciences, KU Leuven, Leuven Brain Institute, Leuven, Belgium.
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Casadonte R, Kriegsmann J, Kriegsmann M, Kriegsmann K, Torcasio R, Gallo Cantafio ME, Viglietto G, Amodio N. A Comparison of Different Sample Processing Protocols for MALDI Imaging Mass Spectrometry Analysis of Formalin-Fixed Multiple Myeloma Cells. Cancers (Basel) 2023; 15:cancers15030974. [PMID: 36765932 PMCID: PMC9913598 DOI: 10.3390/cancers15030974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Sample processing of formalin-fixed specimens constitutes a major challenge in molecular profiling efforts. Pre-analytical factors such as fixative temperature, dehydration, and embedding media affect downstream analysis, generating data dependent on technical processing rather than disease state. In this study, we investigated two different sample processing methods, including the use of the cytospin sample preparation and automated sample processing apparatuses for proteomic analysis of multiple myeloma (MM) cell lines using imaging mass spectrometry (IMS). In addition, two sample-embedding instruments using different reagents and processing times were considered. Three MM cell lines fixed in 4% paraformaldehyde were either directly centrifuged onto glass slides using cytospin preparation techniques or processed to create paraffin-embedded specimens with an automatic tissue processor, and further cut onto glass slides for IMS analysis. The number of peaks obtained from paraffin-embedded samples was comparable between the two different sample processing instruments. Interestingly, spectra profiles showed enhanced ion yield in cytospin compared to paraffin-embedded samples along with high reproducibility compared to the sample replicate.
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Affiliation(s)
- Rita Casadonte
- Proteopath GmbH, 54296 Trier, Germany
- Correspondence: (R.C.); (N.A.)
| | - Jörg Kriegsmann
- Proteopath GmbH, 54296 Trier, Germany
- Department of Medicine, Faculty of Medicine and Dentistry, Danube Private University, 3500 Krems, Austria
| | - Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, Heidelberg University, 69120 Heidelberg, Germany
| | - Roberta Torcasio
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Laboratory of Cellular and Molecular Cardiovascular Pathophysiology, Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, Arcavacata di Rende, 87036 Cosenza, Italy
| | | | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Nicola Amodio
- Department of Experimental and Clinical Medicine, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Correspondence: (R.C.); (N.A.)
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Brum FL, Martins GR, Mohana-Borges R, Sant'Ana da Silva A. The acquisition of thin sections of açaí (Euterpe oleracea Mart.) seed with elevated potassium content for molecular mapping by mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023:e9474. [PMID: 36694976 DOI: 10.1002/rcm.9474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
RATIONALE Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) of tissues became popular in the last decade. Consequently, adapting sample preparation methods for different materials turned out to be a pivotal step for successful analysis due to the requirement of sample slices of 12-20 μm thickness. However, acquiring thin sections compatible with MALDI-IMS for unusual samples is challenging, as existing histological protocols may not be suitable, thus requiring new methods. Açaí (Euterpe oleracea Mart.) seed is an example of a challenging material due to its toughness and resistance to crack, therefore our goal was to develop a methodology to obtain thin (12-20 μm) and entire sections of açaí seeds for MALDI-IMS analysis. METHODS Different strategies were evaluated for obtaining thin sections of seeds, and the combination of the following steps was found to be the most suitable option: (i) softening of seeds by water immersion for 24 h; (ii) transversal cut of seeds to obtain half-seeds using a razor blade and a hammer; (iii) half-seeds imbibition in gelatin; (iv) samples sectioning using a cryostat at -20°C to obtain samples with 12-20 μm thickness; (v) collection of samples in an indium tin oxide-coated glass slide covered by double-sided copper tape to avoid sample wrapping and ensure adhesion after unfreezing; and (vi) storage of samples in a -80°C freezer, if necessary. RESULTS This adapted sample preparation method enabled the analysis of açaí seeds by MALDI-IMS, providing spatial distribution of carbohydrates in the endosperm. CONCLUSIONS The adaptations developed for sample preparation will help investigate the metabolic and physiological properties of açaí seeds in future studies.
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Affiliation(s)
- Felipe Lopes Brum
- Instituto de Biofísica Carlos Chagas Filho, Centro de Espectrometria de Massas de Biomoléculas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Instituto Nacional de Tecnologia, Laboratório de Biocatálise, Rio de Janeiro, RJ, Brazil
| | - Gabriel R Martins
- Instituto Nacional de Tecnologia, Laboratório de Biocatálise, Rio de Janeiro, RJ, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Ronaldo Mohana-Borges
- Instituto de Biofísica Carlos Chagas Filho, Centro de Espectrometria de Massas de Biomoléculas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ayla Sant'Ana da Silva
- Instituto Nacional de Tecnologia, Laboratório de Biocatálise, Rio de Janeiro, RJ, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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11
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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12
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Feucherolles M, Frache G. MALDI Mass Spectrometry Imaging: A Potential Game-Changer in a Modern Microbiology. Cells 2022; 11:cells11233900. [PMID: 36497158 PMCID: PMC9738593 DOI: 10.3390/cells11233900] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/24/2022] [Accepted: 11/28/2022] [Indexed: 12/11/2022] Open
Abstract
Nowadays, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) is routinely implemented as the reference method for the swift and straightforward identification of microorganisms. However, this method is not flawless and there is a need to upgrade the current methodology in order to free the routine lab from incubation time and shift from a culture-dependent to an even faster independent culture system. Over the last two decades, mass spectrometry imaging (MSI) gained tremendous popularity in life sciences, including microbiology, due to its ability to simultaneously detect biomolecules, as well as their spatial distribution, in complex samples. Through this literature review, we summarize the latest applications of MALDI-MSI in microbiology. In addition, we discuss the challenges and avenues of exploration for applying MSI to solve current MALDI-TOF MS limits in routine and research laboratories.
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