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Rosas-Román I, Guillén-Alonso H, Moreno-Pedraza A, Winkler R. Technical Note: mzML and imzML Libraries for Processing Mass Spectrometry Data with the High-Performance Programming Language Julia. Anal Chem 2024; 96:3999-4004. [PMID: 38427332 PMCID: PMC10938284 DOI: 10.1021/acs.analchem.3c05853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Julia combines the virtues of high-level and low-level programming languages: The code is human-readable, and the performance of the created binaries competes with machine-orientated compilers. Thus, Julia is popular in "Big Data" sciences. Reading mass spectrometry (MS) data with Julia was impossible until now due to missing libraries. Here, we present a Julia library for importing mass spectrometry (MS) data in HUPO standard mzML and imzML formats and demonstrate its function with direct and ambient ionization MS, liquid chromatography-MS, and MS imaging data on standard platforms (Windows, Linux, and Mac OS). The processing speed of Julia for reading imzML MS imaging files was up to 214 times faster than the comparable code in R. Julia can remove bottlenecks for computationally demanding tasks in large-scale MS-Omics and MS imaging data processing workflows and supports their agile development. In addition, time-critical and complex data evaluation tasks become possible, such as following the real-time monitoring of biological processes and pattern recognition in large MS imaging projects. Our mzML/imzML libraries and code examples are available under the terms of the MIT license from https://github.com/CINVESTAV-LABI/julia_mzML_imzML.
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Affiliation(s)
- Ignacio Rosas-Román
- Universidad
de Guanajuato, División de Ciencias e Ingenierías, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, Mexico
| | - Héctor Guillén-Alonso
- Center
for Research and Advanced Studies (CINVESTAV) Irapuato, UGA-Langebio, Km.
9.6 Libramiento Norte Carr. Irapuato-León, 36824 Irapuato, Guanajuato, Mexico
- Department
of Biochemical Engineering, National Technological
Institute, 38010 Celaya, Guanajuato, Mexico
| | - Abigail Moreno-Pedraza
- Leibniz
Institute for Vegetable and Ornamental Crops (IGZ) e.V., Theodor-Echtermeyer-Weg 1, 14979, Großbeeren, Germany
- Institute
of Biodiversity, Friedrich Schiller University
Jena, Dornburger-Str.
159, 07743, Jena, Germany
| | - Robert Winkler
- Center
for Research and Advanced Studies (CINVESTAV) Irapuato, UGA-Langebio, Km.
9.6 Libramiento Norte Carr. Irapuato-León, 36824 Irapuato, Guanajuato, Mexico
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2
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Yue H, He F, Zhao Z, Duan Y. Plasma-based ambient mass spectrometry: Recent progress and applications. MASS SPECTROMETRY REVIEWS 2023; 42:95-130. [PMID: 34128567 DOI: 10.1002/mas.21712] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 06/12/2023]
Abstract
Ambient mass spectrometry (AMS) has grown as a group of advanced analytical techniques that allow for the direct sampling and ionization of the analytes in different statuses from their native environment without or with minimum sample pretreatments. As a significant category of AMS, plasma-based AMS has gained a lot of attention due to its features that allow rapid, real-time, high-throughput, in vivo, and in situ analysis in various fields, including bioanalysis, pharmaceuticals, forensics, food safety, and mass spectrometry imaging. Tens of new methods have been developed since the introduction of the first plasma-based AMS technique direct analysis in real-time. This review first provides a comprehensive overview of the established plasma-based AMS techniques from their ion source configurations, mechanisms, and developments. Then, the progress of the representative applications in various scientific fields in the past 4 years (January 2017 to January 2021) has been summarized. Finally, we discuss the current challenges and propose the future directions of plasma-based AMS from our perspective.
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Affiliation(s)
- Hanlu Yue
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Feiyao He
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhongjun Zhao
- School of Chemical Engineering, Sichuan University, Chengdu, China
| | - Yixiang Duan
- College of Life Sciences, Sichuan University, Chengdu, China
- School of Manufacturing Science and Engineering, Sichuan University, Chengdu, China
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García-Rojas NS, Guillén-Alonso H, Martínez-Jarquín S, Moreno-Pedraza A, Soto-Rodríguez LD, Winkler R. Build, Share and Remix: 3D Printing for Speeding Up the Innovation Cycles in Ambient Ionisation Mass Spectrometry (AIMS). Metabolites 2022; 12:185. [PMID: 35208258 PMCID: PMC8874637 DOI: 10.3390/metabo12020185] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 02/01/2023] Open
Abstract
Ambient ionisation mass spectrometry (AIMS) enables studying biological systems in their native state and direct high-throughput analyses. The ionisation occurs in the physical conditions of the surrounding environment. Simple spray or plasma-based AIMS devices allow the desorption and ionisation of molecules from solid, liquid and gaseous samples. 3D printing helps to implement new ideas and concepts in AIMS quickly. Here, we present examples of 3D printed AIMS sources and devices for ion transfer and manipulation. Further, we show the use of 3D printer parts for building custom AIMS sampling robots and imaging systems. Using 3D printing technology allows upgrading existing mass spectrometers with relatively low cost and effort.
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Affiliation(s)
- Nancy Shyrley García-Rojas
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV) Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Mexico; (N.S.G.-R.); (H.G.-A.); (A.M.-P.); (L.D.S.-R.)
| | - Héctor Guillén-Alonso
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV) Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Mexico; (N.S.G.-R.); (H.G.-A.); (A.M.-P.); (L.D.S.-R.)
- Department of Biochemical Engineering, Nacional Technological Institute, Celaya 38010, Mexico
| | | | - Abigail Moreno-Pedraza
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV) Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Mexico; (N.S.G.-R.); (H.G.-A.); (A.M.-P.); (L.D.S.-R.)
| | - Leonardo D. Soto-Rodríguez
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV) Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Mexico; (N.S.G.-R.); (H.G.-A.); (A.M.-P.); (L.D.S.-R.)
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV) Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León, Irapuato 36824, Mexico; (N.S.G.-R.); (H.G.-A.); (A.M.-P.); (L.D.S.-R.)
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4
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Moreno-Pedraza A, Garcia-Rojas NS, Winkler R. Analyzing the Distribution of Specialized Metabolites from Plant Native Tissues with Laser Desorption Low-Temperature Plasma Mass Spectrometry Imaging. Methods Mol Biol 2022; 2469:145-154. [PMID: 35508836 DOI: 10.1007/978-1-0716-2185-1_12] [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: 06/14/2023]
Abstract
The localization of metabolites in plant tissues is often related to their biological function and biosynthesis. Mass spectrometry imaging (MSI) provides comprehensive information about the distribution of known and unknown compounds in tissues. In this protocol, we describe the use of laser desorption low-temperature plasma (LD-LTP) ionization MSI. This technology enables the direct analysis of native tissues under ambient conditions.
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Affiliation(s)
- Abigail Moreno-Pedraza
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV), Irapuato, Gto, Mexico
| | - Nancy Shyrley Garcia-Rojas
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV), Irapuato, Gto, Mexico
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV), Irapuato, Gto, Mexico.
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Rosas-Román I, Winkler R. Contrast optimization of mass spectrometry imaging (MSI) data visualization by threshold intensity quantization (TrIQ). PeerJ Comput Sci 2021; 7:e585. [PMID: 34179452 PMCID: PMC8205298 DOI: 10.7717/peerj-cs.585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Mass spectrometry imaging (MSI) enables the unbiased characterization of surfaces with respect to their chemical composition. In biological MSI, zones with differential mass profiles hint towards localized physiological processes, such as the tissue-specific accumulation of secondary metabolites, or diseases, such as cancer. Thus, the efficient discovery of 'regions of interest' (ROI) is of utmost importance in MSI. However, often the discovery of ROIs is hampered by high background noise and artifact signals. Especially in ambient ionization MSI, unmasking biologically relevant information from crude data sets is challenging. Therefore, we implemented a Threshold Intensity Quantization (TrIQ) algorithm for augmenting the contrast in MSI data visualizations. The simple algorithm reduces the impact of extreme values ('outliers') and rescales the dynamic range of mass signals. We provide an R script for post-processing MSI data in the imzML community format (https://bitbucket.org/lababi/msi.r) and implemented the TrIQ in our open-source imaging software RmsiGUI (https://bitbucket.org/lababi/rmsigui/). Applying these programs to different biological MSI data sets demonstrated the universal applicability of TrIQ for improving the contrast in the MSI data visualization. We show that TrIQ improves a subsequent detection of ROIs by sectioning. In addition, the adjustment of the dynamic signal intensity range makes MSI data sets comparable.
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Verbeeck N, Caprioli RM, Van de Plas R. Unsupervised machine learning for exploratory data analysis in imaging mass spectrometry. MASS SPECTROMETRY REVIEWS 2020; 39:245-291. [PMID: 31602691 PMCID: PMC7187435 DOI: 10.1002/mas.21602] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 08/27/2018] [Indexed: 05/20/2023]
Abstract
Imaging mass spectrometry (IMS) is a rapidly advancing molecular imaging modality that can map the spatial distribution of molecules with high chemical specificity. IMS does not require prior tagging of molecular targets and is able to measure a large number of ions concurrently in a single experiment. While this makes it particularly suited for exploratory analysis, the large amount and high-dimensional nature of data generated by IMS techniques make automated computational analysis indispensable. Research into computational methods for IMS data has touched upon different aspects, including spectral preprocessing, data formats, dimensionality reduction, spatial registration, sample classification, differential analysis between IMS experiments, and data-driven fusion methods to extract patterns corroborated by both IMS and other imaging modalities. In this work, we review unsupervised machine learning methods for exploratory analysis of IMS data, with particular focus on (a) factorization, (b) clustering, and (c) manifold learning. To provide a view across the various IMS modalities, we have attempted to include examples from a range of approaches including matrix assisted laser desorption/ionization, desorption electrospray ionization, and secondary ion mass spectrometry-based IMS. This review aims to be an entry point for both (i) analytical chemists and mass spectrometry experts who want to explore computational techniques; and (ii) computer scientists and data mining specialists who want to enter the IMS field. © 2019 The Authors. Mass Spectrometry Reviews published by Wiley Periodicals, Inc. Mass SpecRev 00:1-47, 2019.
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Affiliation(s)
- Nico Verbeeck
- Delft Center for Systems and ControlDelft University of Technology ‐ TU DelftDelftThe Netherlands
- Aspect Analytics NVGenkBelgium
- STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, Department of Electrical Engineering (ESAT)KU LeuvenLeuvenBelgium
| | - Richard M. Caprioli
- Mass Spectrometry Research CenterVanderbilt UniversityNashvilleTN
- Department of BiochemistryVanderbilt UniversityNashvilleTN
- Department of ChemistryVanderbilt UniversityNashvilleTN
- Department of PharmacologyVanderbilt UniversityNashvilleTN
- Department of MedicineVanderbilt UniversityNashvilleTN
| | - Raf Van de Plas
- Delft Center for Systems and ControlDelft University of Technology ‐ TU DelftDelftThe Netherlands
- Mass Spectrometry Research CenterVanderbilt UniversityNashvilleTN
- Department of BiochemistryVanderbilt UniversityNashvilleTN
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7
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Alexandrov T. Spatial Metabolomics and Imaging Mass Spectrometry in the Age of Artificial Intelligence. Annu Rev Biomed Data Sci 2020; 3:61-87. [PMID: 34056560 DOI: 10.1146/annurev-biodatasci-011420-031537] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Spatial metabolomics is an emerging field of omics research that has enabled localizing metabolites, lipids, and drugs in tissue sections, a feat considered impossible just two decades ago. Spatial metabolomics and its enabling technology-imaging mass spectrometry-generate big hyper-spectral imaging data that have motivated the development of tailored computational methods at the intersection of computational metabolomics and image analysis. Experimental and computational developments have recently opened doors to applications of spatial metabolomics in life sciences and biomedicine. At the same time, these advances have coincided with a rapid evolution in machine learning, deep learning, and artificial intelligence, which are transforming our everyday life and promise to revolutionize biology and healthcare. Here, we introduce spatial metabolomics through the eyes of a computational scientist, review the outstanding challenges, provide a look into the future, and discuss opportunities granted by the ongoing convergence of human and artificial intelligence.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, USA
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Föll MC, Moritz L, Wollmann T, Stillger MN, Vockert N, Werner M, Bronsert P, Rohr K, Grüning BA, Schilling O. Accessible and reproducible mass spectrometry imaging data analysis in Galaxy. Gigascience 2019; 8:giz143. [PMID: 31816088 PMCID: PMC6901077 DOI: 10.1093/gigascience/giz143] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Revised: 09/10/2019] [Accepted: 11/10/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Mass spectrometry imaging is increasingly used in biological and translational research because it has the ability to determine the spatial distribution of hundreds of analytes in a sample. Being at the interface of proteomics/metabolomics and imaging, the acquired datasets are large and complex and often analyzed with proprietary software or in-house scripts, which hinders reproducibility. Open source software solutions that enable reproducible data analysis often require programming skills and are therefore not accessible to many mass spectrometry imaging (MSI) researchers. FINDINGS We have integrated 18 dedicated mass spectrometry imaging tools into the Galaxy framework to allow accessible, reproducible, and transparent data analysis. Our tools are based on Cardinal, MALDIquant, and scikit-image and enable all major MSI analysis steps such as quality control, visualization, preprocessing, statistical analysis, and image co-registration. Furthermore, we created hands-on training material for use cases in proteomics and metabolomics. To demonstrate the utility of our tools, we re-analyzed a publicly available N-linked glycan imaging dataset. By providing the entire analysis history online, we highlight how the Galaxy framework fosters transparent and reproducible research. CONCLUSION The Galaxy framework has emerged as a powerful analysis platform for the analysis of MSI data with ease of use and access, together with high levels of reproducibility and transparency.
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Affiliation(s)
- Melanie Christine Föll
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
| | - Lennart Moritz
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
| | - Thomas Wollmann
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Maren Nicole Stillger
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Stefan-Meier-Straße 17, 79104 Freiburg, Germany
| | - Niklas Vockert
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Martin Werner
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Faculty of Medicine - University of Freiburg, Breisacher Straße 153, 79110 Freiburg, Germany
- Tumorbank Comprehensive Cancer Center Freiburg, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Peter Bronsert
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Faculty of Medicine - University of Freiburg, Breisacher Straße 153, 79110 Freiburg, Germany
- Tumorbank Comprehensive Cancer Center Freiburg, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Karl Rohr
- Biomedical Computer Vision Group, BioQuant, IPMB, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Björn Andreas Grüning
- Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Oliver Schilling
- Institute of Surgical Pathology, Medical Center – University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Faculty of Medicine - University of Freiburg, Breisacher Straße 153, 79110 Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Hugstetter Straße 55, 79106 Freiburg, Germany
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Placenta, Pericarp, and Seeds of Tabasco Chili Pepper Fruits Show a Contrasting Diversity of Bioactive Metabolites. Metabolites 2019; 9:metabo9100206. [PMID: 31569403 PMCID: PMC6835813 DOI: 10.3390/metabo9100206] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/21/2019] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
Chili pepper (Capsicum spp.) is one of the most important horticultural crops worldwide, and its unique organoleptic properties and health benefits have been established for centuries. However, there is little knowledge about how metabolites are distributed throughout fruit parts. This work focuses on the use of liquid chromatography coupled with high resolution mass spectrometry (UHPLC-ESI-HRMS) to estimate the global metabolite profiles of the pericarp, placenta, and seeds of Tabasco pepper fruits (Capsicum frutescens L.) at the red mature stage of ripening. Our main results putatively identified 60 differential compounds between these tissues and seeds. Firstly, we found that pericarp has a higher content of glycosides, showing on average a fold change of 5 and a fold change of 14 for terpenoids when compared with other parts of the fruit. While placenta was the richest tissue in capsaicinoid-related compounds, alkaloids, and tocopherols, with a 35, 3, and 7 fold change, respectively. However, the seeds were richer in fatty acids and saponins with fold changes of 86 and 224, respectively. Therefore, our study demonstrates that a non-targeted metabolomic approach may help to improve our understanding of unexplored areas of plant metabolism and also may be the starting point for a detailed analysis in complex plant parts, such as fruits.
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Perez CJ, Bagga AK, Prova SS, Yousefi Taemeh M, Ifa DR. Review and perspectives on the applications of mass spectrometry imaging under ambient conditions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 3:27-53. [PMID: 29698560 DOI: 10.1002/rcm.8145] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 04/06/2018] [Accepted: 04/12/2018] [Indexed: 05/18/2023]
Abstract
Ambient mass spectrometry (AMS)-based techniques are performed under ambient conditions in which the ionization and desorption occur in the open environment allowing the direct analysis of molecules with minimal or no sample preparation. A selected group of AMS techniques demonstrate imaging capabilities that can provide information about the localization of molecules on complex sample surfaces such as biological tissues. 2D, 3D, and multimodal imaging have unlocked an array of applications to systematically address complex problems in many areas of research such as drug monitoring, natural products, forensics, and cancer diagnostics. In the present review, we summarize recent advances in the field with respect to the implementation of new ambient ionization techniques and current applications in the last 5 years. In more detail, we mainly focus on imaging applications in topics related to animal whole bodies and tissues, single cells, cancer diagnostics and biomarkers, microbial cultures and co-cultures, plant and natural product metabolomics, and forensic applications. Finally, we discuss new areas of research, future perspectives, and the overall direction that the field may take in the years to come.
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Affiliation(s)
- Consuelo J Perez
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Aafreen K Bagga
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Shamina S Prova
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Maryam Yousefi Taemeh
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
| | - Demian R Ifa
- Centre for Research in Mass Spectrometry, Department of Chemistry, York University, 4700 Keele Street, Toronto, ON, M3J 1P3, Canada
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11
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Moreno-Pedraza A, Rosas-Román I, Garcia-Rojas NS, Guillén-Alonso H, Ovando-Vázquez C, Díaz-Ramírez D, Cuevas-Contreras J, Vergara F, Marsch-Martínez N, Molina-Torres J, Winkler R. Elucidating the Distribution of Plant Metabolites from Native Tissues with Laser Desorption Low-Temperature Plasma Mass Spectrometry Imaging. Anal Chem 2019; 91:2734-2743. [PMID: 30636413 DOI: 10.1021/acs.analchem.8b04406] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Secondary metabolites of plants have important biological functions, which often depend on their localization in tissues. Ideally, a fresh untreated material should be directly analyzed to obtain a realistic view of the true sample chemistry. Therefore, there is a large interest for ambient mass-spectrometry-based imaging (MSI) methods. Our aim was to simplify this technology and to find an optimal combination of desorption/ionization principles for a fast ambient MSI of macroscopic plant samples. We coupled a 405 nm continuous wave (CW) ultraviolet (UV) diode laser to a three-dimensionally (3D) printed low-temperature plasma (LTP) probe. By moving the sample with a RepRap-based sampling stage, we could perform imaging of samples up to 16 × 16 cm2. We demonstrate the system performance by mapping mescaline in a San Pedro cactus ( Echinopsis pachanoi) cross section, tropane alkaloids in jimsonweed ( Datura stramonium) fruits and seeds, and nicotine in tobacco ( Nicotiana tabacum) seedlings. In all cases, the anatomical regions of enriched compound concentrations were correctly depicted. The modular design of the laser desorption (LD)-LTP MSI platform, which is mainly assembled from commercial and 3D-printed components, facilitates its adoption by other research groups. The use of the CW-UV laser for desorption enables fast imaging measurements. A complete tobacco seedling with an image size of 9.2 × 15.0 mm2 was analyzed at a pixel size of 100 × 100 μm2 (14 043 mass scans), in less than 2 h. Natural products can be measured directly from native tissues, which inspires a broad use of LD-LTP MSI in plant chemistry studies.
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Affiliation(s)
- Abigail Moreno-Pedraza
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Ignacio Rosas-Román
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Nancy Shyrley Garcia-Rojas
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Héctor Guillén-Alonso
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Cesaré Ovando-Vázquez
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
- CONACYT Potosino Institute of Scientific and Technological Research, National Supercomputing Center , Camino a la Presa San José 2055 , Colonia Lomas 4ta Sección, 78216 San Luis Potosí , Mexico
| | - David Díaz-Ramírez
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Jessica Cuevas-Contreras
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Fredd Vergara
- German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig , Deutscher Platz 5e , 04103 Leipzig , Germany
| | - Nayelli Marsch-Martínez
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Jorge Molina-Torres
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
| | - Robert Winkler
- Department of Biochemistry and Biotechnology , Center for Research and Advanced Studies Irapuato , Kilómetro 9.6 Libramiento Norte Carretera Irapuato-León , 36824 Irapuato , Guanajuato , Mexico
- Mass Spectrometry Group , Max Planck Institute for Chemical Ecology , Beutenberg Campus, Hans-Knoell-Strasse 8 , 07745 Jena , Germany
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Weiskirchen R, Weiskirchen S, Kim P, Winkler R. Software solutions for evaluation and visualization of laser ablation inductively coupled plasma mass spectrometry imaging (LA-ICP-MSI) data: a short overview. J Cheminform 2019; 11:16. [PMID: 30778692 PMCID: PMC6690067 DOI: 10.1186/s13321-019-0338-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/09/2019] [Indexed: 12/19/2022] Open
Abstract
Mass spectrometry imaging (MSI) using laser ablation (LA) inductively coupled plasma (ICP) is an innovative and exciting methodology to perform highly sensitive elemental analyses. LA-ICP-MSI of metals, trace elements or isotopes in tissues has been applied to a range of biological samples. Several LA-ICP-MSI studies have shown that metals have a highly compartmentalized distribution in some organs, which might be altered in consequence of genetic diseases, intoxication, or malnutrition. Although metal imaging by LA-ICP-MSI is an established methodology, potential pitfalls in the determination of metal concentrations might result from erroneous calibration, standardization, and normalization. In addition, for simple display of final imaging results, most LA-ICP-MSI users prefer to process their measurements by commercial processing software. Such programs typically visualize the regional metal differences in colorful and vivid imaging maps, but might not represent the actual signal densities correctly. There is a great abundance of such MSI data processing programs available differing in quality, usability, integrated features, workflow, reliability, system requirements, speed of data processing, and price. Some software packages contain a multitude of features which are superfluous for most users. In contrast, often only few data formats are used, in case of commercial programs even only the instrument provider’s own raw data format. Therefore, first time and average users are often confused and helpless in choosing the correct software for processing their data. Here we have briefly summarized software packages, data routines, macros, programming tools, scripts, algorithms, or self-written patches and updates for existing programs presently in use for mining LA-ICP-MSI data.![]()
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Affiliation(s)
- Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, 52074, Aachen, Germany.
| | - Sabine Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, 52074, Aachen, Germany
| | - Philipp Kim
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, 52074, Aachen, Germany
| | - Robert Winkler
- Department of Biochemistry and Biotechnology, Center for Research and Advanced Studies (CINVESTAV) Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León, 36824, Irapuato, Gto., Mexico. .,Mass Spectrometry Group, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany.
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Martínez-Jarquín S, Winkler R. Low-temperature plasma (LTP) jets for mass spectrometry (MS): Ion processes, instrumental set-ups, and application examples. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.01.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Spatial Metabolite Profiling by Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 965:291-321. [DOI: 10.1007/978-3-319-47656-8_12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Martínez-Jarquín S, Moreno-Pedraza A, Guillén-Alonso H, Winkler R. Template for 3D Printing a Low-Temperature Plasma Probe. Anal Chem 2016; 88:6976-80. [PMID: 27302654 DOI: 10.1021/acs.analchem.6b01019] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Low-temperature plasma (LTP) ionization represents an emerging technology in ambient mass spectrometry. LTP enables the solvent-free direct detection of a broad range of molecules and mass spectrometry imaging (MSI). The low energy consumption and modest technical requirements of these ion sources favors their employment in mobile applications and as a means to upgrade existing mass analyzers. However, the broad adoption of LTP is hindered by the lack of commercial devices, and constructing personal devices is tricky. Improper setup can result in equipment malfunction or may cause serious damage to instruments due to strong electromagnetic fields or arcing. With this in mind, we developed a reproducible LTP probe, which is designed exclusively from commercial and 3D printed components. The plasma jet generated by the device has a diameter of about 200 μm, which is satisfactory for the ambient imaging of macroscopic samples. We coupled the 3D-LTP probe to an ion trap analyzer and demonstrated the functionality of the ion source by detecting organic and chemical compounds from pure reference standards, biological substances, and pharmaceutical samples. Molecules were primarily detected in their protonated form or as water/ammonium adducts. The identification of compounds was possible by standard collision-induced dissociation (CID) fragmentation spectra. The files necessary to reproduce the 3D parts are available from the project page ( http://lababi.bioprocess.org/index.php/3d-ltp ) under a dual license model, which permits reproduction of the probe and further community-driven development for noncommercial use ("peer production"). Our reproducible probe design thus contributes to a facilitated adaption and evolution of low-temperature plasma technologies in analytical chemistry.
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Affiliation(s)
- Sandra Martínez-Jarquín
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato , Irapuato, 36821, Mexico
| | - Abigail Moreno-Pedraza
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato , Irapuato, 36821, Mexico
| | - Héctor Guillén-Alonso
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato , Irapuato, 36821, Mexico
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato , Irapuato, 36821, Mexico
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Winkler R. An evolving computational platform for biological mass spectrometry: workflows, statistics and data mining with MASSyPup64. PeerJ 2015; 3:e1401. [PMID: 26618079 PMCID: PMC4655102 DOI: 10.7717/peerj.1401] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/22/2015] [Indexed: 01/25/2023] Open
Abstract
In biological mass spectrometry, crude instrumental data need to be converted into meaningful theoretical models. Several data processing and data evaluation steps are required to come to the final results. These operations are often difficult to reproduce, because of too specific computing platforms. This effect, known as 'workflow decay', can be diminished by using a standardized informatic infrastructure. Thus, we compiled an integrated platform, which contains ready-to-use tools and workflows for mass spectrometry data analysis. Apart from general unit operations, such as peak picking and identification of proteins and metabolites, we put a strong emphasis on the statistical validation of results and Data Mining. MASSyPup64 includes e.g., the OpenMS/TOPPAS framework, the Trans-Proteomic-Pipeline programs, the ProteoWizard tools, X!Tandem, Comet and SpiderMass. The statistical computing language R is installed with packages for MS data analyses, such as XCMS/metaXCMS and MetabR. The R package Rattle provides a user-friendly access to multiple Data Mining methods. Further, we added the non-conventional spreadsheet program teapot for editing large data sets and a command line tool for transposing large matrices. Individual programs, console commands and modules can be integrated using the Workflow Management System (WMS) taverna. We explain the useful combination of the tools by practical examples: (1) A workflow for protein identification and validation, with subsequent Association Analysis of peptides, (2) Cluster analysis and Data Mining in targeted Metabolomics, and (3) Raw data processing, Data Mining and identification of metabolites in untargeted Metabolomics. Association Analyses reveal relationships between variables across different sample sets. We present its application for finding co-occurring peptides, which can be used for target proteomics, the discovery of alternative biomarkers and protein-protein interactions. Data Mining derived models displayed a higher robustness and accuracy for classifying sample groups in targeted Metabolomics than cluster analyses. Random Forest models do not only provide predictive models, which can be deployed for new data sets, but also the variable importance. We demonstrate that the later is especially useful for tracking down significant signals and affected pathways in untargeted Metabolomics. Thus, Random Forest modeling supports the unbiased search for relevant biological features in Metabolomics. Our results clearly manifest the importance of Data Mining methods to disclose non-obvious information in biological mass spectrometry . The application of a Workflow Management System and the integration of all required programs and data in a consistent platform makes the presented data analyses strategies reproducible for non-expert users. The simple remastering process and the Open Source licenses of MASSyPup64 (http://www.bioprocess.org/massypup/) enable the continuous improvement of the system.
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Affiliation(s)
- Robert Winkler
- Department of Biotechnology and Biochemistry, CINVESTAV Unidad Irapuato , Mexico
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