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Guo X, Wang X, Tian C, Dai J, Zhao Z, Duan Y. Development of mass spectrometry imaging techniques and its latest applications. Talanta 2023; 264:124721. [PMID: 37271004 DOI: 10.1016/j.talanta.2023.124721] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 05/03/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
Mass spectrometry imaging (MSI) is a novel molecular imaging technology that collects molecular information from the surface of samples in situ. The spatial distribution and relative content of various compounds can be visualized simultaneously with high spatial resolution. The prominent advantages of MSI promote the active development of ionization technology and its broader applications in diverse fields. This article first gives a brief introduction to the vital parts of the processes during MSI. On this basis, provides a comprehensive overview of the most relevant MS-based imaging techniques from their mechanisms, pros and cons, and applications. In addition, a critical issue in MSI, matrix effects is also discussed. Then, the representative applications of MSI in biological, forensic, and environmental fields in the past 5 years have been summarized, with a focus on various types of analytes (e.g., proteins, lipids, polymers, etc.) Finally, the challenges and further perspectives of MSI are proposed and concluded.
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Affiliation(s)
- Xing Guo
- College of Chemistry and Material Science, Northwest University, Xi'an, 710069, PR China
| | - Xin Wang
- College of Chemistry and Material Science, Northwest University, Xi'an, 710069, PR China
| | - Caiyan Tian
- College of Life Science, Sichuan University, Chengdu, 610064, PR China
| | - Jianxiong Dai
- Aliben Science and Technology Company Limited, Chengdu, 610064, PR China
| | | | - Yixiang Duan
- College of Chemistry and Material Science, Northwest University, Xi'an, 710069, PR China; Research Center of Analytical Instrumentation, Sichuan University, Chengdu, 610064, PR China.
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2
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Spanov B, Baartmans B, Olaleye O, Nicolardi S, Govorukhina N, Wuhrer M, van de Merbel NC, Bischoff R. Revealing charge heterogeneity of stressed trastuzumab at the subunit level. Anal Bioanal Chem 2023; 415:1505-1513. [PMID: 36693954 PMCID: PMC9974696 DOI: 10.1007/s00216-023-04547-4] [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: 11/09/2022] [Revised: 12/24/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023]
Abstract
Trastuzumab is known to be heterogeneous in terms of charge. Stressing trastuzumab under physiological conditions (pH 7.4 and 37 °C) increases charge heterogeneity further. Separation of charge variants of stressed trastuzumab at the intact protein level is challenging due to increasing complexity making it difficult to obtain pure charge variants for further characterization. Here we report an approach for revealing charge heterogeneity of stressed trastuzumab at the subunit level by pH gradient cation-exchange chromatography. Trastuzumab subunits were generated after limited proteolytic cleavage with papain, IdeS, and GingisKHAN®. The basic pI of Fab and F(ab)2 fragments allowed to use the same pH gradient for intact protein and subunit level analysis. Baseline separation of Fab subunits was obtained after GingisKHAN® and papain digestion and the corresponding modifications were determined by LC-MS/MS peptide mapping and middle-down MALDI-ISD FT-ICR MS. The described approach allows a comprehensive charge variant analysis of therapeutic antibodies that have two or more modification sites in the Fab region.
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Affiliation(s)
- Baubek Spanov
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Bas Baartmans
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Oladapo Olaleye
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Simone Nicolardi
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Nico C van de Merbel
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Bioanalytical Laboratory, ICON, Amerikaweg 18, 9407 TK, Assen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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3
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Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, Neumann EK, Allen JL, Drown BS, Butun FA, Greer JB, Early BP, Fellers RT, Spraggins JM, Laskin J, Camarillo JM, Kafader JO, Kelleher NL. Highly multiplexed, label-free proteoform imaging of tissues by individual ion mass spectrometry. SCIENCE ADVANCES 2022; 8:eabp9929. [PMID: 35947651 PMCID: PMC9365283 DOI: 10.1126/sciadv.abp9929] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/24/2022] [Indexed: 05/25/2023]
Abstract
Imaging of proteoforms in human tissues is hindered by low molecular specificity and limited proteome coverage. Here, we introduce proteoform imaging mass spectrometry (PiMS), which increases the size limit for proteoform detection and identification by fourfold compared to reported methods and reveals tissue localization of proteoforms at <80-μm spatial resolution. PiMS advances proteoform imaging by combining ambient nanospray desorption electrospray ionization with ion detection using individual ion mass spectrometry. We demonstrate highly multiplexed proteoform imaging of human kidney, annotating 169 of 400 proteoforms of <70 kDa using top-down MS and a database lookup of ~1000 kidney candidate proteoforms, including dozens of key enzymes in primary metabolism. PiMS images reveal distinct spatial localizations of proteoforms to both anatomical structures and cellular neighborhoods in the vasculature, medulla, and cortex regions of the human kidney. The benefits of PiMS are poised to increase proteome coverage for label-free protein imaging of tissues.
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Affiliation(s)
- Pei Su
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - John P. McGee
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Kenneth R. Durbin
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Michael A. R. Hollas
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Manxi Yang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Elizabeth K. Neumann
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Jamie L. Allen
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - Bryon S. Drown
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | | | - Joseph B. Greer
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Bryan P. Early
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Ryan T. Fellers
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
| | - Jeffrey M. Spraggins
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
- Departments of Chemistry and Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Jeannie M. Camarillo
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Jared O. Kafader
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Neil L. Kelleher
- Departments of Molecular Biosciences, Chemistry, and Chemical and Biological Engineering and the Feinberg School of Medicine, Northwestern University, Evanston, IL, USA
- Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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Nicolardi S, Joseph AA, Zhu Q, Shen Z, Pardo-Vargas A, Chiodo F, Molinaro A, Silipo A, van der Burgt YEM, Yu B, Seeberger PH, Wuhrer M. Analysis of Synthetic Monodisperse Polysaccharides by Wide Mass Range Ultrahigh-Resolution MALDI Mass Spectrometry. Anal Chem 2021; 93:4666-4675. [PMID: 33667082 PMCID: PMC8034773 DOI: 10.1021/acs.analchem.1c00239] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 02/19/2021] [Indexed: 12/13/2022]
Abstract
Carbohydrates, such as oligo- and polysaccharides, are highly abundant biopolymers that are involved in numerous processes. The study of their structure and functions is commonly based on a material that is isolated from complex natural sources. However, a more precise analysis requires pure compounds with well-defined structures that can be obtained from chemical or enzymatic syntheses. Novel synthetic strategies have increased the accessibility of larger monodisperse polysaccharides, posing a challenge to the analytical methods used for their molecular characterization. Here, we present wide mass range ultrahigh-resolution matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) as a powerful platform for the analysis of synthetic oligo- and polysaccharides. Synthetic carbohydrates 16-, 64-, 100-, and 151-mers were mass analyzed and characterized by MALDI in-source decay FT-ICR MS. Detection of fragment ions generated from glycosidic bond cleavage (or cross-ring cleavage) provided information of the monosaccharide content and the linkage type, allowing for the corroboration of the carbohydrate compositions and structures.
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Affiliation(s)
- Simone Nicolardi
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - A. Abragam Joseph
- Department
of Biomolecular Systems, Max-Planck-Institute
of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Qian Zhu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, University of Chinese Academy
of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Zhengnan Shen
- School
of Physical Science and Technology, ShanghaiTech
University, 393 Huaxia Middle Road, Shanghai 201210, China
| | - Alonso Pardo-Vargas
- Department
of Biomolecular Systems, Max-Planck-Institute
of Colloids and Interfaces, 14476 Potsdam, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Fabrizio Chiodo
- Institute
of Biomolecular Chemistry (ICB), Italian
National Research Council (CNR), Via Campi Flegrei, 34, Pozzuoli, Napoli 80078, Italy
- Amsterdam
UMC-Locatie VUMC, Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam 1081 HZ, The Netherlands
| | - Antonio Molinaro
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cintia 4, Napoli 80126, Italy
| | - Alba Silipo
- Department
of Chemical Sciences, University of Naples
Federico II, Via Cintia 4, Napoli 80126, Italy
| | - Yuri E. M. van der Burgt
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
| | - Biao Yu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Center
for Excellence in Molecular Synthesis, Shanghai Institute of Organic
Chemistry, University of Chinese Academy
of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
- School
of Chemistry and Materials Science, Hangzhou Institute for Advanced
Study, University of Chinese Academy of
Sciences, 1 Sub-lane
Xiangshan, Hangzhou 310024, China
| | - Peter H. Seeberger
- Department
of Biomolecular Systems, Max-Planck-Institute
of Colloids and Interfaces, 14476 Potsdam, Germany
- Institute
of Chemistry and Biochemistry, Freie Universität
Berlin, Arnimallee 22, Berlin 14195, Germany
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, Leiden 2333 ZA, The Netherlands
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Nicolardi S, Kilgour DPA, van der Burgt YEM, Wuhrer M. Improved N- and C-Terminal Sequencing of Proteins by Combining Positive and Negative Ion MALDI In-Source Decay Mass Spectrometry. Anal Chem 2020; 92:12429-12436. [PMID: 32803948 PMCID: PMC7498143 DOI: 10.1021/acs.analchem.0c02198] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 08/17/2020] [Indexed: 01/10/2023]
Abstract
The development of various ionization and fragmentation techniques has been of key importance for establishing mass spectrometry (MS) as a powerful tool for protein characterization. One example of this is matrix-assisted laser desorption/ionization (MALDI) combined with in-source decay (ISD) fragmentation that allows mapping of N- and C-terminal regions of large proteins without the need for proteolysis. Positive ion mode ISD fragments are commonly assigned in the mass region above m/z 1000, while MALDI matrix ions generally hamper the detection of smaller singly charged fragments. The ultrahigh resolving power provided by Fourier transform ion cyclotron resonance (FT-ICR) MS partially overcomes this limitation, but to further increase the detection of smaller fragments we have revisited the application of negative ion mode MALDI-ISD and found good coverage of the peptide chain termini starting from c'2 and z'2 fragment ions. For the first time, we demonstrate that the combination of negative and positive ion MALDI FT-ICR MS is a useful tool to improve the characterization of mAbs. The different specificities of the two ion modes allowed us to selectively cover the sequence of the light and heavy chains of mAbs at increased sensitivity. A comprehensive evaluation of positive and negative ion mode MALDI-ISD FT-ICR MS in the m/z range 46-13 500 showed an increased sequence coverage for three standard proteins, namely, myoglobin, SiLuLite mAb, and NIST mAb. The data obtained in the two ion modes were, in part, complementary.
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Affiliation(s)
- Simone Nicolardi
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - David P A Kilgour
- Department of Chemistry, Nottingham Trent University, Nottingham NG11 0JN, U.K
| | - Yuri E M van der Burgt
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics & Metabolomics, Leiden University Medical Center, Albinusdreef 2, Leiden 2333 ZA, The Netherlands
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Asakawa D. Ultraviolet-Laser-Induced Electron Transfer from Peptides to an Oxidizing Matrix: Study of the First Step of MALDI In-Source Decay Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1918-1926. [PMID: 32687357 DOI: 10.1021/jasms.0c00186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Although the N-H bond in peptide backbones is stronger than the C-H bond, hydrogen abstraction from the amide nitrogen is considered to be the initial step in the Cα-C bond cleavage of peptide backbones by matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) when using an oxidizing matrix. MALDI-ISD induces Cα-C bond cleavage in most amino acid residues, whereas the N-terminal sides of proline (Pro) residues preferentially undergo peptide bond cleavage, which cannot be explained by the previously proposed mechanism involving hydrogen abstraction from peptides. To explain the whole MALDI-ISD process, electron abstraction from peptides by the oxidizing matrix is proposed as the initial step in the MALDI-ISD process. The electron abstraction occurs from either nitrogen or oxygen in the peptide backbone and induces the cleavage of both Cα-C and N-H bonds in most amino acid residues, except for those on the N-terminal sides of Pro residues. Electron abstraction from the Pro residues induces the cleavage of both peptide and Cα-C bonds, which is consistent with MALDI-ISD experimental results. The electron transfer from the peptide to the oxidizing matrix occurs simultaneously with the formation of matrix ions, which is considered to be the initial ion formation process in MALDI. The resultant peptide radical cation produces protonated and neutral molecules/radicals, which undergo subsequent ion-molecule reactions in the MALDI plume, finally yielding the ions that are observed in MALDI-ISD spectrum. As a result, the fragment ions formed by MALDI-ISD are observed as both positive and negative ions.
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Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan
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