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Zhai Y, Fu X, Xu W. Miniature mass spectrometers and their potential for clinical point-of-care analysis. MASS SPECTROMETRY REVIEWS 2024; 43:1172-1191. [PMID: 37610153 DOI: 10.1002/mas.21867] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023]
Abstract
Mass spectrometry (MS) has become a powerful technique for clinical applications with high sensitivity and specificity. Different from conventional MS diagnosis in laboratory, point-of-care (POC) analyses in clinics require mass spectrometers and analytical procedures to be friendly for novice users and applicable for on-site clinical diagnosis. The recent decades have seen the progress in the development of miniature mass spectrometers, providing a promising solution for clinical POC applications. In this review, we report recent advances of miniature mass spectrometers and their exploration in clinical applications, mainly including the rapid analysis of illegal drugs, on-site monitoring of therapeutic drugs, and detection of biomarkers. With improved analytical performance, miniature mass spectrometers are also expected to apply to more and more clinical applications. Some promising POC analyses that can be performed by miniature mass spectrometers in the future are discussed. Lastly, we also provide our perspectives on the challenges in technical development of miniature mass spectrometers for clinical POC analysis.
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Affiliation(s)
- Yanbing Zhai
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
| | - Xinyan Fu
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
| | - Wei Xu
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
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2
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Ogrinc N, Barka EA, Clément C, Salzet M, Sanchez L, Fournier I. In Vivo and Real-Time Metabolic Profiling of Plant-Microbe Interactions in Leaves, Stems, and Roots of Bacterially Inoculated Chardonnay Plantlets using SpiderMass. Anal Chem 2024. [PMID: 39155838 DOI: 10.1021/acs.analchem.4c01470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
There is growing interest in limiting the use of fungicides and implementing innovative, environmentally friendly strategies, such as the use of beneficial bacteria-triggered immunity, to protect grapevines from natural pathogens. Therefore, we need rapid and innovative ways to translate the knowledge of the molecular mechanisms underlying the activation of grapevine defenses against pathogens to induced resistance. Here, we have implemented an in vivo minimally invasive approach to study the interaction between plants and beneficial bacteria based on metabolic signatures. Paraburkholderia phytofirmans strain PsJN and PsJN-grapevine were used as bacterial and plant-bacterium interaction models, respectively. Using an innovative tool, SpiderMass, based on water-assisted laser desorption ionization with an IR microsampling probe, we simultaneously detect metabolic and lipidomic species. A metabolomic spectrum was thus generated, which was used to build a library and identify the most variable and discriminative peaks between the two conditions. We then showed that caftaric acid (m/z 311.04), caftaric acid dimer (m/z 623.09), derived caftaric acid (m/z 653.15), and quercetin-O-glucuronide tended to accumulate in grapevine leaves after root bacterization with PsJN. In addition, together with these phenolic messengers, we identified lipid biomarkers such as palmitic acid, linoleic acid, and α-linoleic acid as important messengers of enhanced defense mechanisms in Chardonnay plantlets. Taken together, SpiderMass is the next-generation methodology for studying plant-microorganism metabolic interactions with the prospect of in vivo real-time analysis in viticulture.
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Affiliation(s)
- Nina Ogrinc
- Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Essaïd Ait Barka
- Unité de Recherche RIBP (Résistance Induite et Bioprotec-tion des Plantes), USC INRAE 1488, Université de Reims Champagne-Ardenne Moulin de la Housse BP 1039, 51687 Reim Cedex 2, France
| | - Christophe Clément
- Unité de Recherche RIBP (Résistance Induite et Bioprotec-tion des Plantes), USC INRAE 1488, Université de Reims Champagne-Ardenne Moulin de la Housse BP 1039, 51687 Reim Cedex 2, France
| | - Michel Salzet
- Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
| | - Lisa Sanchez
- Unité de Recherche RIBP (Résistance Induite et Bioprotec-tion des Plantes), USC INRAE 1488, Université de Reims Champagne-Ardenne Moulin de la Housse BP 1039, 51687 Reim Cedex 2, France
- Institut Universitaire de France (IUF), Paris, France, https://www.iufrance.fr/
| | - Isabelle Fournier
- Inserm, CHU Lille, U1192-Protéomique Réponse Inflammatoire Spectrométrie de Masse (PRISM), Université de Lille, F-59000 Lille, France
- Institut Universitaire de France (IUF), Paris, France, https://www.iufrance.fr/
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Keating MF, Wolfe CA, Liebenberg K, Montgomery A, Porcari AM, Fleming ND, Makarov A, Eberlin LS. Data Acquisition and Intraoperative Tissue Analysis on a Mobile, Battery-Operated, Orbitrap Mass Spectrometer. Anal Chem 2024; 96:8234-8242. [PMID: 38739527 DOI: 10.1021/acs.analchem.4c00722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Mass spectrometry has been increasingly explored in intraoperative studies as a potential technology to help guide surgical decision making. Yet, intraoperative experiments using high-performance mass spectrometry instrumentation present a unique set of operational challenges. For example, standard operating rooms are often not equipped with the electrical requirements to power a commercial mass spectrometer and are not designed to accommodate their permanent installation. These obstacles can impact progress and patient enrollment in intraoperative clinical studies because implementation of MS instrumentation becomes limited to specific operating rooms that have the required electrical connections and space. To expand our intraoperative clinical studies using the MasSpec Pen technology, we explored the feasibility of transporting and acquiring data on Orbitrap mass spectrometers operating on battery power in hospital buildings. We evaluated the effect of instrument movement including acceleration and rotational speeds on signal stability and mass accuracy by acquiring data using direct infusion electrospray ionization. Data were acquired while rolling the systems in/out of operating rooms and while descending/ascending a freight elevator. Despite these movements and operating the instrument on battery power, the relative standard deviation of the total ion current was <5% and the magnitude of the mass error relative to the internal calibrant never exceeded 5.06 ppm. We further evaluated the feasibility of performing intraoperative MasSpec Pen analysis while operating the Orbitrap mass spectrometer on battery power during an ovarian cancer surgery. We observed that the rich and tissue-specific molecular profile commonly detected from ovarian tissues was conserved when running on battery power. Together, these results demonstrate that Orbitrap mass spectrometers can be operated and acquire data on battery power while in motion and in rotation without losses in signal stability or mass accuracy. Furthermore, Orbitrap mass spectrometers can be used in conjunction to the MasSpec Pen while on battery power for intraoperative tissue analysis.
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Affiliation(s)
- Michael F Keating
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Charles A Wolfe
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Keziah Liebenberg
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Ashley Montgomery
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Andreia M Porcari
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
- MS4Life Laboratory of Mass Spectrometry, Health Sciences Postgraduate Program, Universidade São Francisco, Bragança Paulista, SP 12916-900, Brazil
| | - Nicole D Fleming
- Department of Surgery, MD Anderson Cancer Center, Houston, Texas 77030, United States
| | | | - Livia S Eberlin
- Department of Surgery, Baylor College of Medicine, Houston, Texas 77030, United States
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4
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Zirem Y, Ledoux L, Roussel L, Maurage CA, Tirilly P, Le Rhun É, Meresse B, Yagnik G, Lim MJ, Rothschild KJ, Duhamel M, Salzet M, Fournier I. Real-time glioblastoma tumor microenvironment assessment by SpiderMass for improved patient management. Cell Rep Med 2024; 5:101482. [PMID: 38552622 PMCID: PMC11031375 DOI: 10.1016/j.xcrm.2024.101482] [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: 09/14/2023] [Revised: 01/15/2024] [Accepted: 03/01/2024] [Indexed: 04/19/2024]
Abstract
Glioblastoma is a highly heterogeneous and infiltrative form of brain cancer associated with a poor outcome and limited therapeutic effectiveness. The extent of the surgery is related to survival. Reaching an accurate diagnosis and prognosis assessment by the time of the initial surgery is therefore paramount in the management of glioblastoma. To this end, we are studying the performance of SpiderMass, an ambient ionization mass spectrometry technology that can be used in vivo without invasiveness, coupled to our recently established artificial intelligence pipeline. We demonstrate that we can both stratify isocitrate dehydrogenase (IDH)-wild-type glioblastoma patients into molecular sub-groups and achieve an accurate diagnosis with over 90% accuracy after cross-validation. Interestingly, the developed method offers the same accuracy for prognosis. In addition, we are testing the potential of an immunoscoring strategy based on SpiderMass fingerprints, showing the association between prognosis and immune cell infiltration, to predict patient outcome.
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Affiliation(s)
- Yanis Zirem
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Léa Ledoux
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Lucas Roussel
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | | | - Pierre Tirilly
- Université de Lille, CNRS, Centrale Lille, UMR 9189 CRIStAL, 59000 Lille, France
| | - Émilie Le Rhun
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France; Departments of Neurosurgery and Neurology, Clinical Neuroscience Center, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Bertrand Meresse
- Université de Lille, Inserm, CHU Lille, U1286 - INFINITE - Institute for Translational Research in Inflammation, 59000 Lille, France
| | | | | | - Kenneth J Rothschild
- AmberGen, Inc., Billerica, MA, USA; Department of Physics and Photonics Center, Boston University, Boston, MA, USA
| | - Marie Duhamel
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France
| | - Michel Salzet
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France; Institut Universitaire de France (IUF), Paris, France.
| | - Isabelle Fournier
- Université de Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, 59000 Lille, France; Institut Universitaire de France (IUF), Paris, France.
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5
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Fan J, Ma W, Yu Y, Li Y, Nie Z. Recent advances in entirely hand-held ionization sources for mass spectrometry. Anal Bioanal Chem 2024; 416:2057-2063. [PMID: 37930374 DOI: 10.1007/s00216-023-05022-w] [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: 08/25/2023] [Revised: 10/07/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023]
Abstract
Ambient ionization mass spectrometry (AIMS) has been developing explosively since its first debut. The ionization process was hence able to be achieved under atmospheric pressure, facilitating on-site field analysis in a variety of areas, such as clinical diagnosis, metabolic phenotyping, and surface analysis. As part of the ambitious goal of making MS a general device that can be used in everyday life, lots of efforts have been paid to miniaturize the ionization source. This review discusses avant-garde sources that could be entirely hand-held without any accessories. The structure and applications of the devices are described in detail as well. They could be expediently used in real-time and on-site analysis, presenting a great future potential for the routinizing of MS.
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Affiliation(s)
- Jinghan Fan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenbo Ma
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan, 750021, China
| | - Yile Yu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuze Li
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan, 750021, China.
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, College of Chemistry and Chemical Engineering, Ningxia University, Yinchuan, 750021, China.
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6
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Manoli E, Higginson J, Tolley N, Darzi A, Kinross J, Temelkuran B, Takats Z. Human robotic surgery with intraoperative tissue identification using rapid evaporation ionisation mass spectrometry. Sci Rep 2024; 14:1027. [PMID: 38200062 PMCID: PMC10781715 DOI: 10.1038/s41598-023-50942-3] [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: 11/15/2022] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Instantaneous, continuous, and reliable information on the molecular biology of surgical target tissue could significantly contribute to the precision, safety, and speed of the intervention. In this work, we introduced a methodology for chemical tissue identification in robotic surgery using rapid evaporative ionisation mass spectrometry. We developed a surgical aerosol evacuation system that is compatible with a robotic platform enabling consistent intraoperative sample collection and assessed the feasibility of this platform during head and neck surgical cases, using two different surgical energy devices. Our data showed specific, characteristic lipid profiles associated with the tissue type including various ceramides, glycerophospholipids, and glycerolipids, as well as different ion formation mechanisms based on the energy device used. This platform allows continuous and accurate intraoperative mass spectrometry-based identification of ablated/resected tissue and in combination with robotic registration of images, time, and anatomical positions can improve the current robot-assisted surgical platforms and guide surgical strategy.
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Affiliation(s)
- Eftychios Manoli
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - James Higginson
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Neil Tolley
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Ara Darzi
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - James Kinross
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Burak Temelkuran
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- The Hamlyn Centre for Robotic Surgery, Imperial College London, London, UK
| | - Zoltan Takats
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Univ. Lille, INSERM U1192, Lille, France.
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Villacob RA, Feizi N, Beno SC, Solouki T. Collision-Induced Unfolding, Tandem MS, Bottom-up Proteomics, and Interactomics for Identification of Protein Complexes in Native Surface Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:13-30. [PMID: 38095581 DOI: 10.1021/jasms.3c00261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
Endogenously occurring salts and nonvolatile matrix components in untreated biological surfaces can suppress protein ionization and promote adduct formation, challenging protein identification. Characterization of labile proteins within biological specimens is particularly demanding because additional purification or sample treatment steps can be time-intensive and can disrupt noncovalent interactions. It is demonstrated that the combined use of collision-induced unfolding, tandem mass spectrometry, and bottom-up proteomics improves protein characterization in native surface mass spectrometry (NSMS). This multiprong analysis is achieved by acquiring NSMS, MS/MS, ion mobility (IM), and bottom-up proteomics data from a single surface extracted sample. The validity of this multiprong approach was confirmed by the successful characterization of nine surface-deposited proteins, with molecular weights ranging from 8 to 147 kDa, in two separate mixtures. Bottom-up proteomics provided a list of proteins to match against observed proteins in NSMS and their detected subunits in tandem MS. The method was applied to characterize endogenous proteins from untreated chicken liver samples. The subcapsular liver sampling for NSMS analysis allowed for the detection of endogenous proteins with molecular weights of up to ∼220 kDa. Moreover, using IM-MS, collision cross sections and collision-induced unfolding pathways of enzymatic proteins and protein complexes of up to 145 kDa were obtained.
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Affiliation(s)
- Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Neda Feizi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Sarah C Beno
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76798, United States
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Vlocskó M, Piffkó J, Janovszky Á. Intraoperative Assessment of Resection Margin in Oral Cancer: The Potential Role of Spectroscopy. Cancers (Basel) 2023; 16:121. [PMID: 38201548 PMCID: PMC10777979 DOI: 10.3390/cancers16010121] [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: 10/25/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
In parallel with the increasing number of oncological cases, the need for faster and more efficient diagnostic tools has also appeared. Different diagnostic approaches are available, such as radiological imaging or histological staining methods, but these do not provide adequate information regarding the resection margin, intraoperatively, or are time consuming. The purpose of this review is to summarize the current knowledge on spectrometric diagnostic modalities suitable for intraoperative use, with an emphasis on their relevance in the management of oral cancer. The literature agrees on the sensitivity, specificity, and accuracy of spectrometric diagnostic modalities, but further long-term prospective, multicentric clinical studies are needed, which may standardize the intraoperative assessment of the resection margin and the use of real-time spectroscopic approaches.
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Affiliation(s)
| | | | - Ágnes Janovszky
- Department of Oral and Maxillofacial Surgery, Albert Szent-Györgyi Medical School, University of Szeged, Kálvária 57, H-6725 Szeged, Hungary; (M.V.); (J.P.)
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Chung HH, Huang P, Chen CL, Lee C, Hsu CC. Next-generation pathology practices with mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2023; 42:2446-2465. [PMID: 35815718 DOI: 10.1002/mas.21795] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/13/2022] [Accepted: 04/22/2022] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) is a powerful technique that reveals the spatial distribution of various molecules in biological samples, and it is widely used in pathology-related research. In this review, we summarize common MSI techniques, including matrix-assisted laser desorption/ionization and desorption electrospray ionization MSI, and their applications in pathological research, including disease diagnosis, microbiology, and drug discovery. We also describe the improvements of MSI, focusing on the accumulation of imaging data sets, expansion of chemical coverage, and identification of biological significant molecules, that have prompted the evolution of MSI to meet the requirements of pathology practices. Overall, this review details the applications and improvements of MSI techniques, demonstrating the potential of integrating MSI techniques into next-generation pathology practices.
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Affiliation(s)
- Hsin-Hsiang Chung
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Penghsuan Huang
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Chih-Lin Chen
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
| | - Chuping Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Cheng-Chih Hsu
- Department of Chemistry, National Taiwan University, Taipei City, Taiwan
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Ledoux L, Zirem Y, Renaud F, Duponchel L, Salzet M, Ogrinc N, Fournier I. Comparing MS imaging of lipids by WALDI and MALDI: two technologies for evaluating a common ground truth in MS imaging. Analyst 2023; 148:4982-4986. [PMID: 37740342 DOI: 10.1039/d3an01096a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
In this study, we conducted a direct comparison of water-assisted laser desorption ionization (WALDI) and matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging, with MALDI serving as the benchmark for label-free molecular tissue analysis in biomedical research. Specifically, we investigated the lipidomic profiles of several biological samples and calculated the similarity of detected peaks and Pearson's correlation of spectral profile intensities between the two techniques. We show that, overall, MALDI MS and WALDI MS present very close lipidomic analyses and that the highest similarity is obtained for the norharmane MALDI matrix. Indeed, for norharmane in negative ion mode, the lipidomic spectra revealed 100% similarity of detected peaks and over 0.90 intensity correlation between both technologies for five samples. The MALDI-MSI positive ion lipid spectra displayed more than 83% similarity of detected peaks compared to those of WALDI-MSI. However, we observed a lower percentage (77%) of detected peaks when comparing WALDI-MSI with MALDI-MSI due to the rich WALDI-MSI lipid spectra. Despite this difference, the global lipidomic spectra showed high consistency between the two technologies, indicating that they are governed by similar processes. Thanks to this similarity, we can increase datasets by including data from both modalities to either co-train classification models or obtain cross-interrogation.
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Affiliation(s)
- Léa Ledoux
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Yanis Zirem
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Florence Renaud
- Unité mixte SIRIC CURAMUS et 938, Inserm. Université Paris Sorbonne, France
| | | | - Michel Salzet
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
- Institut Universitaire de France (IUF), Paris, France
| | - Nina Ogrinc
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
| | - Isabelle Fournier
- Univ. Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.
- Institut Universitaire de France (IUF), Paris, France
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11
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DeHoog RJ, King ME, Keating MF, Zhang J, Sans M, Feider CL, Garza KY, Bensussan A, Krieger A, Lin JQ, Badal S, Alore E, Pirko C, Brahmbhatt K, Yu W, Grogan R, Eberlin LS, Suliburk J. Intraoperative Identification of Thyroid and Parathyroid Tissues During Human Endocrine Surgery Using the MasSpec Pen. JAMA Surg 2023; 158:1050-1059. [PMID: 37531134 PMCID: PMC10398548 DOI: 10.1001/jamasurg.2023.3229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/08/2023] [Indexed: 08/03/2023]
Abstract
Importance Intraoperative identification of tissues through gross inspection during thyroid and parathyroid surgery is challenging yet essential for preserving healthy tissue and improving outcomes for patients. Objective To evaluate the performance and clinical applicability of the MasSpec Pen (MSPen) technology for discriminating thyroid, parathyroid, and lymph node tissues intraoperatively. Design, Setting, and Participants In this diagnostic/prognostic study, the MSPen was used to analyze 184 fresh-frozen thyroid, parathyroid, and lymph node tissues in the laboratory and translated to the operating room to enable in vivo and ex vivo tissue analysis by endocrine surgeons in 102 patients undergoing thyroidectomy and parathyroidectomy procedures. This diagnostic study was conducted between August 2017 and March 2020. Fresh-frozen tissues were analyzed in a laboratory. Clinical analyses occurred in an operating room at an academic medical center. Of the analyses performed on 184 fresh-frozen tissues, 131 were included based on sufficient signal and postanalysis pathologic diagnosis. From clinical tests, 102 patients undergoing surgery were included. A total of 1015 intraoperative analyses were performed, with 269 analyses subject to statistical classification. Statistical classifiers for discriminating thyroid, parathyroid, and lymph node tissues were generated using training sets comprising both laboratory and intraoperative data and evaluated on an independent test set of intraoperative data. Data were analyzed from July to December 2022. Main Outcomes and Measures Accuracy for each tissue type was measured for classification models discriminating thyroid, parathyroid, and lymph node tissues using MSPen data compared to gross analysis and final pathology results. Results Of the 102 patients in the intraoperative study, 80 were female (78%) and the median (IQR) age was 52 (42-66) years. For discriminating thyroid and parathyroid tissues, an overall accuracy, defined as agreement with pathology, of 92.4% (95% CI, 87.7-95.4) was achieved using MSPen data, with 82.6% (95% CI, 76.5-87.4) accuracy achieved for the independent test set. For distinguishing thyroid from lymph node and parathyroid from lymph node, overall training set accuracies of 97.5% (95% CI, 92.8-99.1) and 96.1% (95% CI, 91.2-98.3), respectively, were achieved. Conclusions and Relevance In this study, the MSPen showed high performance for discriminating thyroid, parathyroid, and lymph node tissues intraoperatively, suggesting this technology may be useful for providing near real-time feedback on tissue type to aid in surgical decision-making.
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Affiliation(s)
- Rachel J. DeHoog
- Department of Surgery, Baylor College of Medicine, Houston, Texas
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Mary E. King
- Department of Surgery, Baylor College of Medicine, Houston, Texas
- Department of Chemistry, The University of Texas at Austin, Austin
| | | | - Jialing Zhang
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Marta Sans
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Clara L. Feider
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Kyana Y. Garza
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Alena Bensussan
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Anna Krieger
- Department of Chemistry, The University of Texas at Austin, Austin
| | - John Q. Lin
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Sunil Badal
- Department of Chemistry, The University of Texas at Austin, Austin
| | - Elizabeth Alore
- Department of Surgery, Baylor College of Medicine, Houston, Texas
| | | | | | - Wendong Yu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Raymon Grogan
- Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - Livia S. Eberlin
- Department of Surgery, Baylor College of Medicine, Houston, Texas
| | - James Suliburk
- Department of Surgery, Baylor College of Medicine, Houston, Texas
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12
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Stadlhofer R, Moritz M, Fuh MM, Heeren J, Zech H, Clauditz TS, Schlüter H, Betz CS, Eggert D, Böttcher A, Hahn J. Lipidome Analysis of Oropharyngeal Tumor Tissues Using Nanosecond Infrared Laser (NIRL) Tissue Sampling and Subsequent Mass Spectrometry. Int J Mol Sci 2023; 24:ijms24097820. [PMID: 37175533 PMCID: PMC10178251 DOI: 10.3390/ijms24097820] [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: 03/23/2023] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Ultrashort pulse infrared lasers can simultaneously sample and homogenize biological tissue using desorption by impulsive vibrational excitation (DIVE). With growing attention on alterations in lipid metabolism in malignant disease, mass spectrometry (MS)-based lipidomic analysis has become an emerging topic in cancer research. In this pilot study, we investigated the feasibility of tissue sampling with a nanosecond infrared laser (NIRL) for the subsequent lipidomic analysis of oropharyngeal tissues, and its potential to discriminate oropharyngeal squamous cell carcinoma (OPSCC) from non-tumorous oropharyngeal tissue. Eleven fresh frozen oropharyngeal tissue samples were ablated. The produced aerosols were collected by a glass fiber filter, and the lipidomes were analyzed with mass spectrometry. Data was evaluated by principal component analysis and Welch's t-tests. Lipid profiles comprised 13 lipid classes and up to 755 lipid species. We found significant inter- and intrapatient alterations in lipid profiles for tumor and non-tumor samples (p-value < 0.05, two-fold difference). Thus, NIRL tissue sampling with consecutive MS lipidomic analysis is a feasible and promising approach for the differentiation of OPSCC and non-tumorous oropharyngeal tissue and may provide new insights into lipid composition alterations in OPSCC.
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Affiliation(s)
- Rupert Stadlhofer
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Manuela Moritz
- Section/Core Facility Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marceline M Fuh
- Department of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Jörg Heeren
- Department of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Henrike Zech
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Till S Clauditz
- Department of Pathology, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Christian S Betz
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Dennis Eggert
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Arne Böttcher
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Jan Hahn
- Section/Core Facility Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
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13
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Bogusiewicz J, Bojko B. Insight into new opportunities in intra-surgical diagnostics of brain tumors. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.117043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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14
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Bormotov DS, Eliferov VA, Peregudova OV, Zavorotnyuk DS, Bocharov KV, Pekov SI, Sorokin AA, Nikolaev EN, Popov IA. Incorporation of a Disposable ESI Emitter into Inline Cartridge Extraction Mass Spectrometry Improves Throughput and Spectra Stability. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:119-122. [PMID: 36535019 DOI: 10.1021/jasms.2c00207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Rapid and reliable methods for detecting tumor margins are crucial for neuro-oncology. Several mass spectrometry-based methods have been recently proposed to address this problem. Inline Cartridge Extraction (ICE) demonstrates the potential for clinical application, based on ex-vivo analysis of dissected tissues, but requires time-consuming steps to avoid cross-contamination. In this work, a method of incorporating a disposable electrospray emitter into the ICE cartridge by PEEK sleeves melting is developed. It reduces total analysis time and improves throughput. The proposed setup also improves the robustness of the ICE molecular profiling as demonstrated with human glial tumor samples in that stability and reproducibility of the spectra were increased.
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Affiliation(s)
- Denis S Bormotov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
| | - Vasily A Eliferov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
| | - Olga V Peregudova
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
| | - Denis S Zavorotnyuk
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
| | - Konstantin V Bocharov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
| | - Stanislav I Pekov
- Skolkovo Institute of Science and Technology, Moscow 121205, Russian Federation
- Siberian State Medical University, Tomsk 634050, Russian Federation
| | - Anatoly A Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
| | - Eugene N Nikolaev
- Skolkovo Institute of Science and Technology, Moscow 121205, Russian Federation
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russian Federation
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15
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Ogrinc N, Chaillou P, Kruszewski A, Duriez C, Salzet M, Fournier I. Ambient Mass Spectrometry Imaging by Water-Assisted Laser Desorption/Ionization for Ex Vivo and in Vivo Applications. Methods Mol Biol 2023; 2688:83-94. [PMID: 37410286 DOI: 10.1007/978-1-0716-3319-9_8] [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] [Indexed: 07/07/2023]
Abstract
Water-assisted laser desorption/ionization mass spectrometry (WALDI-MS), also known as SpiderMass, is an emerging ambient ionization technique for in vivo and real-time analysis. It employs a remote infrared (IR) laser tuned to excite the most intense vibrational band (O-H) of water. The water molecules act as an endogenous matrix leading to the desorption/ionization of a variety of biomolecules from tissues, particularly metabolites and lipids. WALDI-MS was recently advanced into an imaging modality for ex vivo 2D sections and 3D in vivo real-time imaging. Here, we describe the methodological aspects for performing 2D and 3D imaging experiments with WALDI-MSI and the parameters for optimizing the image acquisition.
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Affiliation(s)
- Nina Ogrinc
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Paul Chaillou
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Alexandre Kruszewski
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Cristian Duriez
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Michel Salzet
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France
| | - Isabelle Fournier
- Université de Lille, Inserm, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, Lille, France.
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16
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Aggregation of Multimodal ICE-MS Data into Joint Classifier Increases Quality of Brain Cancer Tissue Classification. DATA 2022. [DOI: 10.3390/data8010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mass spectrometry fingerprinting combined with multidimensional data analysis has been proposed in surgery to determine if a biopsy sample is a tumor. In the specific case of brain tumors, it is complicated to obtain control samples, leading to model overfitting due to unbalanced sample cohorts. Usually, classifiers are trained using a single measurement regime, most notably single ion polarity, but mass range and spectral resolution could also be varied. It is known that lipid groups differ significantly in their ability to produce positive or negative ions; hence, using only one polarity significantly restricts the chemical space available for sample discrimination purposes. In this work, we have developed an approach employing mass spectrometry data obtained by eight different regimes of measurement simultaneously. Regime-specific classifiers are trained, then a mixture of experts techniques based on voting or mean probability is used to aggregate predictions of all trained classifiers and assign a class to the whole sample. The aggregated classifiers have shown a much better performance than any of the single-regime classifiers and help significantly reduce the effect of an unbalanced dataset without any augmentation.
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17
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Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival. Nat Commun 2022; 13:6665. [PMID: 36333286 PMCID: PMC9636229 DOI: 10.1038/s41467-022-34208-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Molecular heterogeneity is a key feature of glioblastoma that impedes patient stratification and leads to large discrepancies in mean patient survival. Here, we analyze a cohort of 96 glioblastoma patients with survival ranging from a few months to over 4 years. 46 tumors are analyzed by mass spectrometry-based spatially-resolved proteomics guided by mass spectrometry imaging. Integration of protein expression and clinical information highlights three molecular groups associated with immune, neurogenesis, and tumorigenesis signatures with high intra-tumoral heterogeneity. Furthermore, a set of proteins originating from reference and alternative ORFs is found to be statistically significant based on patient survival times. Among these proteins, a 5-protein signature is associated with survival. The expression of these 5 proteins is validated by immunofluorescence on an additional cohort of 50 patients. Overall, our work characterizes distinct molecular regions within glioblastoma tissues based on protein expression, which may help guide glioblastoma prognosis and improve current glioblastoma classification.
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18
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Ogrinc N, Schneider S, Bourmaud A, Gengler N, Salzet M, Fournier I. Direct In Vivo Analysis of CBD- and THC-Acid Cannabinoids and Classification of Cannabis Cultivars Using SpiderMass. Metabolites 2022; 12:metabo12060480. [PMID: 35736414 PMCID: PMC9227750 DOI: 10.3390/metabo12060480] [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: 12/27/2021] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
In recent years, cannabis and hemp-based products have become increasingly popular for recreational use, edibles, beverages, health care products, and medicines. The rapid detection and differentiation of phytocannabinoids is, therefore, essential to assess the potency and the therapeutic and nutritional values of cannabis cultivars. Here, we implemented SpiderMass technology for in vivo detection of cannabidiolic acid (CBDA) and ∆9-tetrahydrocannabinolicacid (∆9-THCA), and other endogenous organic plant compounds, to access distribution gradients within the plants and differentiate between cultivars. The SpiderMass system is composed of an IR-laser handheld microsampling probe connected to a mass spectrometer through a transfer tube. The analysis was performed on different plant organs from freshly cultivated cannabis plants in only a few seconds. SpiderMass analysis easily discriminated the two acid phytocannabinoid isomers via MS/MS, and the built statistical models differentiated between four cannabis cultivars. Different abundancies of the two acid phytocannabinoids were found along the plant as well as between different cultivars. Overall, these results introduce direct analysis by SpiderMass as a compelling analytical alternative for rapid hemp analysis.
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Affiliation(s)
- Nina Ogrinc
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (N.O.); (M.S.)
| | - Serge Schneider
- Service de Toxicologie Analytique–Chimie Pharmaceutique, Laboratoire National de Santé (LNS), Dudelange, L-3555 Luxembourg, Luxembourg; (S.S.); (A.B.); (N.G.)
| | - Adèle Bourmaud
- Service de Toxicologie Analytique–Chimie Pharmaceutique, Laboratoire National de Santé (LNS), Dudelange, L-3555 Luxembourg, Luxembourg; (S.S.); (A.B.); (N.G.)
| | - Nicolas Gengler
- Service de Toxicologie Analytique–Chimie Pharmaceutique, Laboratoire National de Santé (LNS), Dudelange, L-3555 Luxembourg, Luxembourg; (S.S.); (A.B.); (N.G.)
| | - Michel Salzet
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (N.O.); (M.S.)
- Institut Universitaire de France (IUF), F-75000 Paris, France
| | - Isabelle Fournier
- Laboratoire Protéomique, Réponse Inflammatoire et Spectrométrie de Masse (PRISM), Inserm U1192, Université de Lille, F-59000 Lille, France; (N.O.); (M.S.)
- Institut Universitaire de France (IUF), F-75000 Paris, France
- Correspondence:
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19
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Ouni E, Nedbal V, Da Pian M, Cao H, Haas KT, Peaucelle A, Van Kerk O, Herinckx G, Marbaix E, Dolmans MM, Tuuri T, Otala M, Amorim CA, Vertommen D. Proteome-wide and matrisome-specific atlas of the human ovary computes fertility biomarker candidates and open the way for precision oncofertility. Matrix Biol 2022; 109:91-120. [PMID: 35341935 DOI: 10.1016/j.matbio.2022.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/04/2022] [Accepted: 03/20/2022] [Indexed: 10/18/2022]
Abstract
Our modern era is witnessing an increasing infertility rate worldwide. Although some of the causes can be attributed to our modern lifestyle (e.g., persistent organic pollutants, late pregnancy), our knowledge of the human ovarian tissue has remained limited and insufficient to reverse the infertility statistics. Indeed, all efforts have been focused on the endocrine and cellular function in support of the cell theory that dates back to the 18th century, while the human ovarian matrisome is still under-described. Hereby, we unveil the extracellular side of the story during different periods of the ovary life, demonstrating that follicle survival and development, and ultimately fertility, would not be possible without its involvement. We examined the human ovarian matrisome and described its remodeling from prepuberty until menopause, creating the first ovarian proteomic codex. Here, we confidently identified and quantified 98 matrisome proteins present in the three ovary groups. Among them, 26 were expressed differently among age groups, delineating a peculiar matrisomal fingerprint at each stage. Such proteins could be potential biomarkers phenotyping ovarian ECM at each age phase of female reproductive life. Beyond proteomics, our study presents a unique approach to understanding the data and depicting the spatiotemporal ECM-intracellular signaling networks and remodeling with age through imaging, advanced text-mining based on natural language processing technology, machine learning, and data sonification. Our findings provide essential context for healthy ovarian physiology, identifying and characterizing disease states, and recapitulating physiological tissues or development in vitro. This comprehensive proteomics analysis represents the ovarian proteomic codex and contributes to an improved understanding of the critical roles that ECM plays throughout the ovarian life span.
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Affiliation(s)
- Emna Ouni
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Valerie Nedbal
- Global Technical Enablement, SAS Institute GmbH, 69118 Heidelberg, Germany
| | | | | | - Kalina T Haas
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Alexis Peaucelle
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France
| | - Olivier Van Kerk
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Gaetan Herinckx
- PHOS Unit & MASSPROT platform de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Etienne Marbaix
- Cell Biology Unit, de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium; Gynecology and Andrology Department, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Marie-Madeleine Dolmans
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200 Brussels, Belgium; Gynecology and Andrology Department, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Timo Tuuri
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, 00029 Helsinki, Finland
| | - Marjut Otala
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, 00029 Helsinki, Finland
| | - Christiani A Amorim
- Pôle de Recherche en Gynécologie, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, 1200 Brussels, Belgium.
| | - Didier Vertommen
- PHOS Unit & MASSPROT platform de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
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20
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Maiju L, Anna A, Artturi V, Teemu T, Anton K, Markus K, Antti V, Antti R, Niku O. Laser desorption tissue imaging with Differential Mobility Spectrometry. Exp Mol Pathol 2022; 125:104759. [PMID: 35337806 DOI: 10.1016/j.yexmp.2022.104759] [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: 09/08/2021] [Revised: 02/27/2022] [Accepted: 03/19/2022] [Indexed: 11/04/2022]
Abstract
Pathological gross examination of breast carcinoma samples is sometimes laborious. A tissue pre-mapping method could indicate neoplastic areas to the pathologist and enable focused sampling. Differential Mobility Spectrometry (DMS) is a rapid and affordable technology for complex gas mixture analysis. We present an automated tissue laser analysis system for imaging approaches (iATLAS), which utilizes a computer-controlled laser evaporator unit coupled with a DMS gas analyzer. The system is demonstrated in the classification of porcine tissue samples and three human breast carcinomas. Tissue samples from eighteen landrace pigs were classified with the system based on a pre-designed matrix (spatial resolution 1-3 mm). The smoke samples were analyzed with DMS, and tissue classification was performed with several machine learning approaches. Porcine skeletal muscle (n = 1030), adipose tissue (n = 1329), normal breast tissue (n = 258), bone (n = 680), and liver (n = 264) were identified with 86% cross-validation (CV) accuracy with a convolutional neural network (CNN) model. Further, a panel tissue that comprised all five tissue types was applied as an independent validation dataset. In this test, 82% classification accuracy with CNN was achieved. An analogous procedure was applied to demonstrate the feasibility of iATLAS in breast cancer imaging according to 1) macroscopically and 2) microscopically annotated data with 10-fold CV and SVM (radial kernel). We reached a classification accuracy of 94%, specificity of 94%, and sensitivity of 93% with the macroscopically annotated data from three breast cancer specimens. The microscopic annotation was applicable to two specimens. For the first specimen, the classification accuracy was 84% (specificity 88% and sensitivity 77%). For the second, the classification accuracy was 72% (specificity 88% and sensitivity 24%). This study presents a promising method for automated tissue imaging in an animal model and lays foundation for breast cancer imaging.
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Affiliation(s)
- Lepomäki Maiju
- Surgery, Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Building, Arvo Ylpön katu 34, 33520 Tampere, Finland; Department of Pathology, Fimlab Laboratories, Arvo Ylpön katu 4, FI-33520 Tampere, Finland.
| | - Anttalainen Anna
- Olfactomics Ltd, Kampusareena, Korkeakoulunkatu 7, FI-33720 Tampere, Finland; Sensor Technology and Biomeasurements, Faculty of Medicine and Health Technology, Tampere University, Hervanta Campus, Sähkötalo Building, Korkeakoulunkatu 3, FI-33720 Tampere, Finland
| | - Vuorinen Artturi
- Sensor Technology and Biomeasurements, Faculty of Medicine and Health Technology, Tampere University, Hervanta Campus, Sähkötalo Building, Korkeakoulunkatu 3, FI-33720 Tampere, Finland
| | - Tolonen Teemu
- Department of Pathology, Fimlab Laboratories, Arvo Ylpön katu 4, FI-33520 Tampere, Finland
| | - Kontunen Anton
- Olfactomics Ltd, Kampusareena, Korkeakoulunkatu 7, FI-33720 Tampere, Finland; Sensor Technology and Biomeasurements, Faculty of Medicine and Health Technology, Tampere University, Hervanta Campus, Sähkötalo Building, Korkeakoulunkatu 3, FI-33720 Tampere, Finland
| | - Karjalainen Markus
- Olfactomics Ltd, Kampusareena, Korkeakoulunkatu 7, FI-33720 Tampere, Finland; Sensor Technology and Biomeasurements, Faculty of Medicine and Health Technology, Tampere University, Hervanta Campus, Sähkötalo Building, Korkeakoulunkatu 3, FI-33720 Tampere, Finland
| | - Vehkaoja Antti
- Sensor Technology and Biomeasurements, Faculty of Medicine and Health Technology, Tampere University, Hervanta Campus, Sähkötalo Building, Korkeakoulunkatu 3, FI-33720 Tampere, Finland
| | - Roine Antti
- Surgery, Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Building, Arvo Ylpön katu 34, 33520 Tampere, Finland; Olfactomics Ltd, Kampusareena, Korkeakoulunkatu 7, FI-33720 Tampere, Finland
| | - Oksala Niku
- Surgery, Faculty of Medicine and Health Technology, Tampere University, Kauppi Campus, Arvo Building, Arvo Ylpön katu 34, 33520 Tampere, Finland; Olfactomics Ltd, Kampusareena, Korkeakoulunkatu 7, FI-33720 Tampere, Finland; Vascular Centre, Tampere University Hospital, Central Hospital, P.O. Box 2000, FI-33521 Tampere, Finland
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21
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Ogrinc N, Attencourt C, Colin E, Boudahi A, Tebbakha R, Salzet M, Testelin S, Dakpé S, Fournier I. Mass Spectrometry-Based Differentiation of Oral Tongue Squamous Cell Carcinoma and Nontumor Regions With the SpiderMass Technology. FRONTIERS IN ORAL HEALTH 2022; 3:827360. [PMID: 35309279 PMCID: PMC8929397 DOI: 10.3389/froh.2022.827360] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/26/2022] [Indexed: 12/14/2022] Open
Abstract
Oral cavity cancers are the 15th most common cancer with more than 350,000 new cases and ~178,000 deaths each year. Among them, squamous cell carcinoma (SCC) accounts for more than 90% of tumors located in the oral cavity and on oropharynx. For the oral cavity SCC, the surgical resection remains the primary course of treatment. Generally, surgical margins are defined intraoperatively using visual and tactile elements. However, in 15–30% of cases, positive margins are found after histopathological examination several days postsurgery. Technologies based on mass spectrometry (MS) were recently developed to help guide surgical resection. The SpiderMass technology is designed for in-vivo real-time analysis under minimally invasive conditions. This instrument achieves tissue microsampling and real-time molecular analysis with the combination of a laser microprobe and a mass spectrometer. It ultimately acts as a tool to support histopathological decision-making and diagnosis. This pilot study included 14 patients treated for tongue SCC (T1 to T4) with the surgical resection as the first line of treatment. Samples were first analyzed by a pathologist to macroscopically delineate the tumor, dysplasia, and peritumoral areas. The retrospective and prospective samples were sectioned into three consecutive sections and thaw-mounted on slides for H&E staining (7 μm), SpiderMass analysis (20 μm), and matrix-assisted laser desorption ionization (MALDI) MS imaging (12 μm). The SpiderMass microprobe collected lipidometabolic profiles of the dysplasia, tumor, and peritumoral regions annotated by the pathologist. The MS spectra were then subjected to the multivariate statistical analysis. The preliminary data demonstrate that the lipidometabolic molecular profiles collected with the SpiderMass are significantly different between the tumor and peritumoral regions enabling molecular classification to be established by linear discriminant analysis (LDA). MALDI images of the different samples were submitted to segmentation for cross instrument validation and revealed additional molecular discrimination within the tumor and nontumor regions. These very promising preliminary results show the applicability of the SpiderMass to SCC of the tongue and demonstrate its interest in the surgical treatment of head and neck cancers.
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Affiliation(s)
- Nina Ogrinc
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse – PRISM, Lille, France
- *Correspondence: Nina Ogrinc
| | - Christophe Attencourt
- Department of Pathology, CHU Amiens-Picardie, Amiens, France
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
| | - Emilien Colin
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
- Department of Maxillofacial Surgery, CHU Amiens-Picardie, Amiens, France
- Institut Faire Faces, Amiens, France
| | - Ahmed Boudahi
- Department of Pathology, CHU Amiens-Picardie, Amiens, France
| | - Riad Tebbakha
- Tumorothèque de Picardie, CHU Amiens-Picardie, Amiens, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse – PRISM, Lille, France
- Institut Universitaire de France (IUF), Paris, France
| | - Sylvie Testelin
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
- Department of Maxillofacial Surgery, CHU Amiens-Picardie, Amiens, France
- Institut Faire Faces, Amiens, France
| | - Stéphanie Dakpé
- UR7516 CHIMERE, Université de Picardie Jules Verne, Amiens, France
- Department of Maxillofacial Surgery, CHU Amiens-Picardie, Amiens, France
- Institut Faire Faces, Amiens, France
- Stéphanie Dakpé
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse – PRISM, Lille, France
- Institut Universitaire de France (IUF), Paris, France
- Isabelle Fournier
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22
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Santilli AML, Ren K, Oleschuk R, Kaufmann M, Rudan J, Fichtinger G, Mousavi P. Application of Intraoperative Mass Spectrometry and Data Analytics for Oncological Margin Detection, A Review. IEEE Trans Biomed Eng 2022; 69:2220-2232. [PMID: 34982670 DOI: 10.1109/tbme.2021.3139992] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE A common phase of early-stage oncological treatment is the surgical resection of cancerous tissue. The presence of cancer cells on the resection margin, referred to as positive margin, is correlated with the recurrence of cancer and may require re-operation, negatively impacting many facets of patient outcomes. There exists a significant gap in the surgeons ability to intraoperatively delineate between tissues. Mass spectrometry methods have shown considerable promise as intraoperative tissue profiling tools that can assist with the complete resection of cancer. To do so, the vastness of the information collected through these modalities must be digested, relying on robust and efficient extraction of insights through data analysis pipelines. METHODS We review clinical mass spectrometry literature and prioritize intraoperatively applied modalities. We also survey the data analysis methods employed in these studies. RESULTS Our review outlines the advantages and shortcomings of mass spectrometry imaging and point-based tissue probing methods. For each modality, we identify statistical, linear transformation and machine learning techniques that demonstrate high performance in classifying cancerous tissues across several organ systems. A limited number of studies presented results captured intraoperatively. CONCLUSION Through continued research of data centric techniques, like mass spectrometry, and the development of robust analysis approaches, intraoperative margin assessment is becoming feasible. SIGNIFICANCE By establishing the relatively short history of mass spectrometry techniques applied to surgical studies, we hope to inform future applications and aid in the selection of suitable data analysis frameworks for the development of intraoperative margin detection technologies.
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Ogrinc N, Kruszewski A, Chaillou P, Saudemont P, Lagadec C, Salzet M, Duriez C, Fournier I. Robot-Assisted SpiderMass for In Vivo Real-Time Topography Mass Spectrometry Imaging. Anal Chem 2021; 93:14383-14391. [PMID: 34670081 DOI: 10.1021/acs.analchem.1c01692] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mass spectrometry imaging (MSI) has shown to bring invaluable information for biological and clinical applications. However, conventional MSI is generally performed ex vivo from tissue sections. Here, we developed a novel MS-based method for in vivo mass spectrometry imaging. By coupling the SpiderMass technology, that provides in vivo minimally invasive analysis-to a robotic arm of high accuracy, we demonstrate that images can be acquired from any surface by moving the laser probe above the surface. By equipping the robotic arm with a sensor, we are also able to both get the topography image of the sample surface and the molecular distribution, and then and plot back the molecular data, directly to the 3D topographical image without the need for image fusion. This is shown for the first time with the 3D topographic MS-based whole-body imaging of a mouse. Enabling fast in vivo MSI bridged to topography paves the way for surgical applications to excision margins.
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Affiliation(s)
- Nina Ogrinc
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Alexandre Kruszewski
- UMR 9189 - CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille, University of Lille, INRIA, CNRS, F-59000 Lille, France
| | - Paul Chaillou
- UMR 9189 - CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille, University of Lille, INRIA, CNRS, F-59000 Lille, France
| | - Philippe Saudemont
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Chann Lagadec
- University of Lille, CNRS, Inserm, CHU Lille, Centre Oscar Lambret, UMR9020 - UMR-S 1277 - Canther - Cancer Heterogeneity, Plasticity and Resistance to Therapies, F-59000 Lille, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.,Institut Universitaire de France (IUF), Paris 75231, France
| | - Christian Duriez
- UMR 9189 - CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille, University of Lille, INRIA, CNRS, F-59000 Lille, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France.,Institut Universitaire de France (IUF), Paris 75231, France
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24
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Ogrinc N, Caux PD, Robin YM, Bouchaert E, Fatou B, Ziskind M, Focsa C, Bertin D, Tierny D, Takats Z, Salzet M, Fournier I. Direct Water-Assisted Laser Desorption/Ionization Mass Spectrometry Lipidomic Analysis and Classification of Formalin-Fixed Paraffin-Embedded Sarcoma Tissues without Dewaxing. Clin Chem 2021; 67:1513-1523. [PMID: 34586394 DOI: 10.1093/clinchem/hvab160] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Formalin-fixed paraffin-embedded (FFPE) tissue has been the gold standard for routine pathology for general and cancer postoperative diagnostics. Despite robust histopathology, immunohistochemistry, and molecular methods, accurate diagnosis remains difficult for certain cases. Overall, the entire process can be time consuming, labor intensive, and does not reach over 90% diagnostic sensitivity and specificity. There is a growing need in onco-pathology for adjunct novel rapid, accurate, reliable, diagnostically sensitive, and specific methods for high-throughput biomolecular identification. Lipids have long been considered only as building blocks of cell membranes or signaling molecules, but have recently been introduced as central players in cancer. Due to sample processing, which limits their detection, lipid analysis directly from unprocessed FFPE tissues has never been reported. METHODS We present a proof-of-concept with direct analysis of tissue-lipidomic signatures from FFPE tissues without dewaxing and minimal sample preparation using water-assisted laser desorption ionization mass spectrometry and deep-learning. RESULTS On a cohort of difficult canine and human sarcoma cases, classification for canine sarcoma subtyping was possible with 99.1% accuracy using "5-fold" and 98.5% using "leave-one-patient out," and 91.2% accuracy for human sarcoma using 5-fold and 73.8% using leave-one-patient out. The developed classification model enabled stratification of blind samples in <5 min and showed >95% probability for discriminating 2 human sarcoma blind samples. CONCLUSION It is possible to create a rapid diagnostic platform to screen clinical FFPE tissues with minimal sample preparation for molecular pathology.
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Affiliation(s)
- Nina Ogrinc
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Pierre-Damien Caux
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Yves-Marie Robin
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Unité de Pathologie Morphologique et Moléculaire, Centre Oscar Lambret, Lille, France
| | - Emmanuel Bouchaert
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,OCR (Oncovet Clinical Research), Parc Eurasante Lille Metropole, Loos, France
| | - Benoit Fatou
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Michael Ziskind
- University of Lille, CNRS, UMR 8523, PhLAM-Physique des Lasers, Atomes et Molécules, Lille, France
| | - Cristian Focsa
- University of Lille, CNRS, UMR 8523, PhLAM-Physique des Lasers, Atomes et Molécules, Lille, France
| | - Delphine Bertin
- Unité de Pathologie Morphologique et Moléculaire, Centre Oscar Lambret, Lille, France
| | - Dominique Tierny
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,OCR (Oncovet Clinical Research), Parc Eurasante Lille Metropole, Loos, France
| | - Zoltan Takats
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France (IUF), Paris, France
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse-PRISM, Lille, France.,Institut Universitaire de France (IUF), Paris, France
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25
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Hahn J, Moritz M, Voß H, Pelczar P, Huber S, Schlüter H. Tissue Sampling and Homogenization in the Sub-Microliter Scale with a Nanosecond Infrared Laser (NIRL) for Mass Spectrometric Proteomics. Int J Mol Sci 2021; 22:ijms221910833. [PMID: 34639174 PMCID: PMC8509473 DOI: 10.3390/ijms221910833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022] Open
Abstract
It was recently shown that ultrashort pulse infrared (IR) lasers, operating at the wavelength of the OH vibration stretching band of water, are highly efficient for sampling and homogenizing biological tissue. In this study we utilized a tunable nanosecond infrared laser (NIRL) for tissue sampling and homogenization with subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis for mass spectrometric proteomics. For the first time, laser sampling was performed with murine spleen and colon tissue. An ablation volume of 1.1 × 1.1 × 0.4 mm³ (approximately 0.5 µL) was determined with optical coherence tomography (OCT). The results of bottom-up proteomics revealed proteins with significant abundance differences for both tissue types, which are in accordance with the corresponding data of the Human Protein Atlas. The results demonstrate that tissue sampling and homogenization of small tissue volumes less than 1 µL for subsequent mass spectrometric proteomics is feasible with a NIRL.
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Affiliation(s)
- Jan Hahn
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (M.M.); (H.V.); (H.S.)
- Correspondence: ; Tel.: +49-1522-2827-168
| | - Manuela Moritz
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (M.M.); (H.V.); (H.S.)
| | - Hannah Voß
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (M.M.); (H.V.); (H.S.)
| | - Penelope Pelczar
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (P.P.); (S.H.)
| | - Samuel Huber
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (P.P.); (S.H.)
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (M.M.); (H.V.); (H.S.)
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26
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Chen R, Brown HM, Cooks RG. Metabolic profiles of human brain parenchyma and glioma for rapid tissue diagnosis by targeted desorption electrospray ionization mass spectrometry. Anal Bioanal Chem 2021; 413:6213-6224. [PMID: 34373931 PMCID: PMC8522078 DOI: 10.1007/s00216-021-03593-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/23/2021] [Accepted: 07/30/2021] [Indexed: 12/19/2022]
Abstract
Desorption electrospray ionization mass spectrometry (DESI-MS) is well suited for intraoperative tissue analysis since it requires little sample preparation and offers rapid and sensitive molecular diagnostics. Currently, intraoperative assessment of the tumor cell percentage of glioma biopsies can be made by measuring a single metabolite, N-acetylaspartate (NAA). The inclusion of additional biomarkers will likely improve the accuracy when distinguishing brain parenchyma from glioma by DESI-MS. To explore this possibility, mass spectra were recorded for extracts from 32 unmodified human brain samples with known pathology. Statistical analysis of data obtained from full-scan and multiple reaction monitoring (MRM) profiles identified discriminatory metabolites, namely gamma-aminobutyric acid (GABA), creatine, glutamic acid, carnitine, and hexane-1,2,3,4,5,6-hexol (abbreviated as hexol), as well as the established biomarker NAA. Brain parenchyma was readily differentiated from glioma based on these metabolites as measured both in full-scan mass spectra and by the intensities of their characteristic MRM transitions. New DESI-MS methods (5 min acquisition using full scans and MS/MS), developed to measure ion abundance ratios among these metabolites, were tested using smears of 29 brain samples. Ion abundance ratios based on signals for GABA, creatine, carnitine, and hexol all had sensitivities > 90%, specificities > 80%, and accuracies > 85%. Prospectively, the implementation of diagnostic ion abundance ratios should strengthen the discriminatory power of individual biomarkers and enhance method robustness against signal fluctuations, resulting in an improved DESI-MS method of glioma diagnosis.
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Affiliation(s)
- Rong Chen
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Hannah Marie Brown
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - R Graham Cooks
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA.
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27
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Zhang J, Sans M, Garza KY, Eberlin LS. MASS SPECTROMETRY TECHNOLOGIES TO ADVANCE CARE FOR CANCER PATIENTS IN CLINICAL AND INTRAOPERATIVE USE. MASS SPECTROMETRY REVIEWS 2021; 40:692-720. [PMID: 33094861 DOI: 10.1002/mas.21664] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
Developments in mass spectrometry technologies have driven a widespread interest and expanded their use in cancer-related research and clinical applications. In this review, we highlight the developments in mass spectrometry methods and instrumentation applied to direct tissue analysis that have been tailored at enhancing performance in clinical research as well as facilitating translation and implementation of mass spectrometry in clinical settings, with a focus on cancer-related studies. Notable studies demonstrating the capabilities of direct mass spectrometry analysis in biomarker discovery, cancer diagnosis and prognosis, tissue analysis during oncologic surgeries, and other clinically relevant problems that have the potential to substantially advance cancer patient care are discussed. Key challenges that need to be addressed before routine clinical implementation including regulatory efforts are also discussed. Overall, the studies highlighted in this review demonstrate the transformative potential of mass spectrometry technologies to advance clinical research and care for cancer patients. © 2020 Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Jialing Zhang
- Department of Chemistry, University of Texas at Austin, Austin, TX
| | - Marta Sans
- Department of Chemistry, University of Texas at Austin, Austin, TX
| | - Kyana Y Garza
- Department of Chemistry, University of Texas at Austin, Austin, TX
| | - Livia S Eberlin
- Department of Chemistry, University of Texas at Austin, Austin, TX
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28
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Plekhova V, Van Meulebroek L, De Graeve M, Perdones-Montero A, De Spiegeleer M, De Paepe E, Van de Walle E, Takats Z, Cameron SJS, Vanhaecke L. Rapid ex vivo molecular fingerprinting of biofluids using laser-assisted rapid evaporative ionization mass spectrometry. Nat Protoc 2021; 16:4327-4354. [PMID: 34341579 DOI: 10.1038/s41596-021-00580-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 05/31/2021] [Indexed: 01/29/2023]
Abstract
Of the many metabolites involved in any clinical condition, only a narrow range of biomarkers is currently being used in the clinical setting. A key to personalized medicine would be to extend this range. Metabolic fingerprinting provides a more comprehensive insight, but many methods used for metabolomics analysis are too complex and time-consuming to be diagnostically useful. Here, a rapid evaporative ionization mass spectrometry (REIMS) system for direct ex vivo real-time analysis of biofluids with minor sample pretreatment is detailed. The REIMS can be linked to various laser wavelength systems (such as optical parametric oscillator or CO2 laser) and with automation for high-throughput analysis. Laser-induced sample evaporation occurs within seconds through radiative heating with the plume guided to the MS instrument. The presented procedure includes (i) laser setup with automation, (ii) analysis of biofluids (blood/urine/stool/saliva/sputum/breast milk) and (iii) data analysis. We provide the optimal settings for biofluid analysis and quality control, enabling sensitive, precise and robust analysis. Using the automated setup, 96 samples can be analyzed in ~35-40 min per ionization mode, with no intervention required. Metabolic fingerprints are made up of 2,000-4,000 features, for which relative quantification can be achieved at high repeatability when total ion current normalization is applied. With saliva and feces as example matrices, >70% of features had a coefficient of variance ≤30%. However, to achieve acceptable long-term reproducibility, additional normalizations by, e.g., LOESS are recommended, especially for positive ionization.
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Affiliation(s)
- Vera Plekhova
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium.,ProDigest BV, Zwijnaarde, Belgium
| | - Marilyn De Graeve
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | | | | | - Ellen De Paepe
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Emma Van de Walle
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium
| | - Zoltan Takats
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Simon J S Cameron
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Lynn Vanhaecke
- Laboratory of Chemical Analysis, Ghent University, Merelbeke, Belgium. .,School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, Northern Ireland, UK.
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29
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Zhang J, Sans M, DeHoog RJ, Garza KY, King ME, Feider CL, Bensussan A, Keating MF, Lin JQ, Povilaitis SC, Katta N, Milner TE, Yu W, Nagi C, Dhingra S, Pirko C, Brahmbhatt KA, Van Buren G, Carter S, Thompson A, Grogan RH, Suliburk J, Eberlin LS. Clinical Translation and Evaluation of a Handheld and Biocompatible Mass Spectrometry Probe for Surgical Use. Clin Chem 2021; 67:1271-1280. [PMID: 34263289 DOI: 10.1093/clinchem/hvab098] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/05/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Intraoperative tissue analysis and identification are critical to guide surgical procedures and improve patient outcomes. Here, we describe the clinical translation and evaluation of the MasSpec Pen technology for molecular analysis of in vivo and freshly excised tissues in the operating room (OR). METHODS An Orbitrap mass spectrometer equipped with a MasSpec Pen interface was installed in an OR. A "dual-path" MasSpec Pen interface was designed and programmed for the clinical studies with 2 parallel systems that facilitated the operation of the MasSpec Pen. The MasSpec Pen devices were autoclaved before each surgical procedure and were used by surgeons and surgical staff during 100 surgeries over a 12-month period. RESULTS Detection of mass spectral profiles from 715 in vivo and ex vivo analyses performed on thyroid, parathyroid, lymph node, breast, pancreatic, and bile duct tissues during parathyroidectomies, thyroidectomies, breast, and pancreatic neoplasia surgeries was achieved. The MasSpec Pen enabled gentle extraction and sensitive detection of various molecular species including small metabolites and lipids using a droplet of sterile water without causing apparent tissue damage. Notably, effective molecular analysis was achieved while no limitations to sequential histologic tissue analysis were identified and no device-related complications were reported for any of the patients. CONCLUSIONS This study shows that the MasSpec Pen system can be successfully incorporated into the OR, allowing direct detection of rich molecular profiles from tissues with a seconds-long turnaround time that could be used to inform surgical and clinical decisions without disrupting tissue analysis workflows.
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Affiliation(s)
- Jialing Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - Marta Sans
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - Rachel J DeHoog
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - Kyana Y Garza
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - Mary E King
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - Clara L Feider
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - Alena Bensussan
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - Michael F Keating
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | - John Q Lin
- Department of Chemistry, The University of Texas at Austin, Austin, TX
| | | | - Nitesh Katta
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX
| | - Thomas E Milner
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX
| | - Wendong Yu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Chandandeep Nagi
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | - Sadhna Dhingra
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX
| | | | | | | | - Stacey Carter
- Department of Surgery, Baylor College of Medicine, Houston, TX
| | | | - Raymon H Grogan
- Department of Surgery, Baylor College of Medicine, Houston, TX
| | - James Suliburk
- Department of Surgery, Baylor College of Medicine, Houston, TX
| | - Livia S Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, TX
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30
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Cameron SJS, Perdones-Montero A, Van Meulebroek L, Burke A, Alexander-Hardiman K, Simon D, Schaffer R, Balog J, Karancsi T, Rickards T, Rebec M, Stead S, Vanhaecke L, Takáts Z. Sample Preparation Free Mass Spectrometry Using Laser-Assisted Rapid Evaporative Ionization Mass Spectrometry: Applications to Microbiology, Metabolic Biofluid Phenotyping, and Food Authenticity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1393-1401. [PMID: 33980015 DOI: 10.1021/jasms.0c00452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Mass spectrometry has established itself as a powerful tool in the chemical, biological, medical, environmental, and agricultural fields. However, experimental approaches and potential application areas have been limited by a traditional reliance on sample preparation, extraction, and chromatographic separation. Ambient ionization mass spectrometry methods have addressed this challenge but are still somewhat restricted in requirements for sample manipulation to make it suitable for analysis. These limitations are particularly restrictive in view of the move toward high-throughput and automated analytical workflows. To address this, we present what we consider to be the first automated sample-preparation-free mass spectrometry platform utilizing a carbon dioxide (CO2) laser for sample thermal desorption linked to the rapid evaporative ionization mass spectrometry (LA-REIMS) methodology. We show that the pulsatile operation of the CO2 laser is the primary factor in achieving high signal-to-noise ratios. We further show that the LA-REIMS automated platform is suited to the analysis of three diverse biological materials within different application areas. First, clinical microbiology isolates were classified to species level with an accuracy of 97.2%, the highest accuracy reported in current literature. Second, fecal samples from a type 2 diabetes mellitus cohort were analyzed with LA-REIMS, which allowed tentative identification of biomarkers which are potentially associated with disease pathogenesis and a disease classification accuracy of 94%. Finally, we showed the ability of the LA-REIMS system to detect instances of adulteration of cooking oil and determine the geographical area of production of three protected olive oil products with 100% classification accuracy.
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Affiliation(s)
- Simon J S Cameron
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
| | - Alvaro Perdones-Montero
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Lieven Van Meulebroek
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Ghent University, Ghent B-9820, Belgium
| | - Adam Burke
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Kate Alexander-Hardiman
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
| | - Daniel Simon
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Waters Research Center, Budapest 1031, Hungary
| | | | - Julia Balog
- Waters Research Center, Budapest 1031, Hungary
| | | | - Tony Rickards
- Department of Microbiology, Imperial College Healthcare NHS Trust, London W6 8RD, U.K
| | - Monica Rebec
- Department of Microbiology, Imperial College Healthcare NHS Trust, London W6 8RD, U.K
| | - Sara Stead
- Waters Corporation, Wilmslow SK9 4AX, U.K
| | - Lynn Vanhaecke
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
- Laboratory of Chemical Analysis, Department of Veterinary Public Health and Food Safety, Ghent University, Ghent B-9820, Belgium
| | - Zoltán Takáts
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London SW7 2AZ, U.K
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, Belfast BT9 5DL, U.K
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31
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Ogrinc N, Saudemont P, Takats Z, Salzet M, Fournier I. Cancer Surgery 2.0: Guidance by Real-Time Molecular Technologies. Trends Mol Med 2021; 27:602-615. [PMID: 33965341 DOI: 10.1016/j.molmed.2021.04.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 12/14/2022]
Abstract
In vivo cancer margin delineation during surgery remains a major challenge. Despite the availability of several image guidance techniques and intraoperative assessment, clear surgical margins and debulking efficiency remain scarce. For this reason, there is particular interest in developing rapid intraoperative tools with high sensitivity and specificity to help guide cancer surgery in vivo. Recently, several emerging technologies including intraoperative mass spectrometry have paved the way for molecular guidance in a clinical setting. We evaluate these techniques and assess their relevance for intraoperative surgical guidance and how they can transform the future of molecular cancer surgery, diagnostics, patient management and care.
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Affiliation(s)
- Nina Ogrinc
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Philippe Saudemont
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Zoltan Takats
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France
| | - Michel Salzet
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France; Institut Universitaire de France (IUF), Paris, France.
| | - Isabelle Fournier
- University of Lille, Inserm, CHU Lille, U1192 - Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, F-59000 Lille, France; Institut Universitaire de France (IUF), Paris, France.
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32
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Pekov SI, Bormotov DS, Nikitin PV, Sorokin AA, Shurkhay VA, Eliferov VA, Zavorotnyuk DS, Potapov AA, Nikolaev EN, Popov IA. Rapid estimation of tumor cell percentage in brain tissue biopsy samples using inline cartridge extraction mass spectrometry. Anal Bioanal Chem 2021; 413:2913-2922. [PMID: 33751161 DOI: 10.1007/s00216-021-03220-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/28/2021] [Accepted: 02/03/2021] [Indexed: 10/21/2022]
Abstract
Tumor cell percentage (TCP) is an essential characteristic of biopsy samples that directly affects the sensitivity of molecular testing in clinical practice. Apart from clarifying diagnoses, rapid evaluation of TCP combined with various neuronavigation systems can be used to support decision making in neurosurgery. It is known that ambient mass spectrometry makes it possible to rapidly distinguish healthy from malignant tissues. In connection with this, here we demonstrate the possibility of using non-imaging ambient mass spectrometry to evaluate TCP in glial tumor tissues with a high degree of confidence. Molecular profiles of histologically annotated human glioblastoma tissue samples were obtained using the inline cartridge extraction ambient mass spectrometry approach. XGBoost regressors were trained to evaluate tumor cell percentage. Using cross-validation, it was estimated that the TCP was determined by the regressors with a precision of approximately 90% using only low-resolution data. This result demonstrates that ambient mass spectrometry provides an accurate method todetermine TCP in dissected tissues even without implementing mass spectrometry imaging. The application of such techniques offers the possibility to automate routine tissue screening and TCP evaluation to boost the throughput of pathology laboratories. Rapid estimation of tumor cell percentage during neurosurgery.
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Affiliation(s)
- Stanislav I Pekov
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143026, Russian Federation.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Denis S Bormotov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Pavel V Nikitin
- N.N. Burdenko National Scientific and Practical Center for Neurosurgery, Moscow, 125047, Russian Federation
| | - Anatoly A Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Vsevolod A Shurkhay
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation.,N.N. Burdenko National Scientific and Practical Center for Neurosurgery, Moscow, 125047, Russian Federation
| | - Vasiliy A Eliferov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Denis S Zavorotnyuk
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation
| | - Alexander A Potapov
- N.N. Burdenko National Scientific and Practical Center for Neurosurgery, Moscow, 125047, Russian Federation
| | - Eugene N Nikolaev
- Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143026, Russian Federation
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russian Federation.
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33
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Yan B, Murta T, Elia EA, Steven RT, Bunch J. Direct Tissue Mass Spectrometry Imaging by Atmospheric Pressure UV-Laser Desorption Plasma Postionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:429-435. [PMID: 33289553 DOI: 10.1021/jasms.0c00315] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Matrix-assisted laser desorption ionization (MALDI) operated at atmospheric pressure has been shown to be a promising technique for mass spectrometry imaging of biological tissues at high spatial resolution. Recent studies have shown several orders of magnitude improvement in sensitivity afforded by coupling with a low-temperature plasma (LTP) for postionization. In this work we report the first results from "matrix-free" imaging using our atmospheric pressure (AP) transmission mode (TM) (MA)LDI source with LTP postionization. Direct MSI analysis of murine testis with no sample preparation after tissue sectioning enabled imaging of a range of lipid classes at pixel sizes of 25 μm. We compared results from the matrix-free methods with MALDI experiments in which the matrix was applied on top, underneath, or layered as a sandwich. The sandwich preparation was found to lead to ion yields approximately 2- or 3-fold higher than the other methods, indicating that the addition of a light absorbing matrix remains beneficial. Nonetheless, LDI methods confer a range of advantages, and the sensitivity improvements provided by postionization strategies are a promising step toward high-efficiency laser sampling under ambient conditions.
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Affiliation(s)
- Bin Yan
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington TW11 0LW, United Kingdom
| | - Teresa Murta
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington TW11 0LW, United Kingdom
| | - Efstathios A Elia
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington TW11 0LW, United Kingdom
| | - Rory T Steven
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington TW11 0LW, United Kingdom
| | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging (NiCE-MSI), National Physical Laboratory, Teddington TW11 0LW, United Kingdom
- Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0FA, United Kingdom
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34
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Drake RR, Scott DA, Angel PM. Imaging Mass Spectrometry. Mol Imaging 2021. [DOI: 10.1016/b978-0-12-816386-3.00017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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35
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Cumulative learning enables convolutional neural network representations for small mass spectrometry data classification. Nat Commun 2020; 11:5595. [PMID: 33154370 PMCID: PMC7644674 DOI: 10.1038/s41467-020-19354-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
Rapid and accurate clinical diagnosis remains challenging. A component of diagnosis tool development is the design of effective classification models with Mass spectrometry (MS) data. Some Machine Learning approaches have been investigated but these models require time-consuming preprocessing steps to remove artifacts, making them unsuitable for rapid analysis. Convolutional Neural Networks (CNNs) have been found to perform well under such circumstances since they can learn representations from raw data. However, their effectiveness decreases when the number of available training samples is small, which is a common situation in medicine. In this work, we investigate transfer learning on 1D-CNNs, then we develop a cumulative learning method when transfer learning is not powerful enough. We propose to train the same model through several classification tasks over various small datasets to accumulate knowledge in the resulting representation. By using rat brain as the initial training dataset, a cumulative learning approach can have a classification accuracy exceeding 98% for 1D clinical MS-data. We show the use of cumulative learning using datasets generated in different biological contexts, on different organisms, and acquired by different instruments. Here we show a promising strategy for improving MS data classification accuracy when only small numbers of samples are available. Convolutional Neural Networks are powerful tools for clinical diagnosis but their effectiveness decreases when the number of available samples is small. Here, the authors develop a cumulative learning method by training the same model through several classification tasks over various small Mass Spectrometry datasets.
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36
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Domenick TM, Gill EL, Vedam-Mai V, Yost RA. Mass Spectrometry-Based Cellular Metabolomics: Current Approaches, Applications, and Future Directions. Anal Chem 2020; 93:546-566. [PMID: 33146525 DOI: 10.1021/acs.analchem.0c04363] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Taylor M Domenick
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Emily L Gill
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104-4283, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-4283, United States
| | - Vinata Vedam-Mai
- Department of Neurology, University of Florida, Gainesville, Florida 32610, United States
| | - Richard A Yost
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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37
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Keating MF, Zhang J, Feider CL, Retailleau S, Reid R, Antaris A, Hart B, Tan G, Milner TE, Miller K, Eberlin LS. Integrating the MasSpec Pen to the da Vinci Surgical System for In Vivo Tissue Analysis during a Robotic Assisted Porcine Surgery. Anal Chem 2020; 92:11535-11542. [PMID: 32786489 DOI: 10.1021/acs.analchem.0c02037] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Minimally invasive robotic-assisted surgeries have been increasingly used as a first-line of treatment for patients undergoing oncologic surgeries. In-situ tissue identification is critical to guide tissue resection and assist decision-making. Traditional intraoperative histopathologic analysis of frozen tissue sections can be time-consuming and present logistical challenges which interrupt surgical workflows. We report the development and implementation of a laparoscopic, drop-in version of the MasSpec Pen device integrated into the da Vinci Xi Surgical system for in vivo tissue analysis in a robotic-assisted porcine surgery. We evaluated the performance of the drop-in MasSpec Pen during surgery by introducing the device into the animal upper gastrointestinal system and performing in vivo analyses of the stomach and liver, including charred and bloody tissues after electrocauterization. The molecular profiles obtained included ions tentatively identified as metabolites and lipids typically observed with MasSpec Pen analysis, without causing observable tissue damage. Statistical classifiers built to distinguish porcine liver and stomach tissues using the in vivo data yielded an overall tissue identification accuracy of 98% (n = 53 analyses). The results provide evidence that the drop-in MasSpec Pen developed can be used to acquire mass spectra in vivo during a robotic-assisted surgery and might be used as an in vivo tissue assessment tool to help guide surgical resections and streamline surgical workflows.
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Affiliation(s)
- Michael F Keating
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78751, United States
| | - Jialing Zhang
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78751, United States
| | - Clara L Feider
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78751, United States
| | | | - Robert Reid
- Intuitive Surgical, Sunnyvale, California 94086, United States
| | | | - Bradley Hart
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Gina Tan
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Thomas E Milner
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78751, United States
| | - Kyle Miller
- Intuitive Surgical, Sunnyvale, California 94086, United States
| | - Livia S Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78751, United States
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