1
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Venter AR. Protein analysis by desorption electrospray ionization mass spectrometry. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39056172 DOI: 10.1002/mas.21900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 05/22/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024]
Abstract
This review presents progress made in the ambient analysis of proteins, in particular by desorption electrospray ionization-mass spectrometry (DESI-MS). Related ambient ionization techniques are discussed in comparison to DESI-MS only to illustrate the larger context of protein analysis by ambient ionization mass spectrometry. The review describes early and current approaches for the analysis of undigested proteins, native proteins, tryptic digests, and indirect protein determination through reporter molecules. Applications to mass spectrometry imaging for protein spatial distributions, the identification of posttranslational modifications, determination of binding stoichiometries, and enzymatic transformations are discussed. The analytical capabilities of other ambient ionization techniques such as LESA and nano-DESI currently exceed those of DESI-MS for in situ surface sampling of intact proteins from tissues. This review shows, however, that despite its many limitations, DESI-MS is making valuable contributions to protein analysis. The challenges in sensitivity, spatial resolution, and mass range are surmountable obstacles and further development and improvements to DESI-MS is justified.
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Affiliation(s)
- Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, Michigan, USA
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2
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Surface-sampling mass spectrometry to study proteins and protein complexes. Essays Biochem 2023; 67:229-241. [PMID: 36748325 PMCID: PMC10070487 DOI: 10.1042/ebc20220191] [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: 10/11/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 02/08/2023]
Abstract
This review aims to summarise the current capabilities of surface mass spectrometry (MS) approaches that offer intact protein analysis, and that of non-covalent complexes. Protein analysis is largely achieved via matrix-assisted laser desorption/ionisation (MALDI), which is in itself a surface analysis approach or solvent-based electrospray ionisation (ESI). Several surface sampling approaches have been developed based on ESI, and those that have been used for intact protein analysis will be discussed below. The extent of protein coverage, top-down elucidation, and probing of protein structure for native proteins and non-covalent complexes will be discussed for each approach. Strategies for improving protein analysis, ranging from sample preparation, and sampling methods to instrument modifications and the inclusion of ion mobility separation in the workflow will also be discussed. The relative benefits and drawbacks of each approach will be summarised, providing an overview of current capabilities.
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3
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Villacob RA, Egbejiogu BC, Feizi N, Hogan C, Murray KK, Solouki T. Native Mass Spectrometry and Collision-Induced Unfolding of Laser-Ablated Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:2215-2225. [PMID: 36346890 DOI: 10.1021/jasms.2c00184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Infrared laser ablation sample transfer (LAST) was used to collect samples from solid surfaces for mass spectrometry under native spray conditions. Native mass spectrometry was utilized to probe the charge states and collision-induced unfolding (CIU) characteristics of bovine serum albumin (BSA), bovine hemoglobin (BHb), and jack-bean concanavalin A (ConA) via direct injection electrospray, after liquid extraction surface sampling, and after LAST. Each protein was deposited from solution on solid surfaces and laser-ablated for off-line analysis or sampled for online analysis. It was found that the protein ion gas-phase charge-state distributions were comparable for direct infusion, liquid extraction, and laser ablation experiments. Moreover, calculated average collision cross section (CCS) values from direct injection, liquid extraction, and laser ablation experiments were consistent with previously reported literature values. Additionally, an equivalent number of mobility features and conformational turnovers were identified from unfolding pathways from all three methods for all charge states of each protein analyzed in this work. The presented work suggests that laser ablation yields intact proteins (BSA, BHb, and ConA), is compatible with native mass spectrometry, and could be suitable for spatially resolved interrogation of unfolding pathways of proteins.
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Affiliation(s)
| | | | - Neda Feizi
- Baylor University, Waco, Texas 76706, United States
| | - Cole Hogan
- Baylor University, Waco, Texas 76706, United States
| | - Kermit K Murray
- Louisiana State University, Baton Rouge, Louisiana 70803, United States
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4
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Shi L, Habib A, Bi L, Hong H, Begum R, Wen L. Ambient Ionization Mass Spectrometry: Application and Prospective. Crit Rev Anal Chem 2022; 54:1584-1633. [PMID: 36206159 DOI: 10.1080/10408347.2022.2124840] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Abstract
Mass spectrometry (MS) is a formidable analytical tool for the analysis of non-polar to polar compounds individually and/or from mixtures, providing information on the molecular weights and chemical structures of the analytes. During the last more than one-decade, ambient ionization mass spectrometry (AIMS) has developed quickly, producing a wide range of platforms and proving scientific improvements in a variety of domains, from biological imaging to quick quality control. These methods have made it possible to detect target analytes in real time without sample preparation in an open environment, and they can be connected to any MS system with an atmospheric pressure interface. They also have the ability to analyze explosives, illicit drugs, disease diagnostics, drugs in biological samples, adulterants in food and agricultural products, reaction progress, and environmental monitoring. The development of novel ambient ionization techniques, such as probe electrospray ionization, paper spray ionization, and fiber spray ionization, employed even at picolitre to femtolitre solution levels to provide femtogram to attogram levels of the target analytes. The special characteristic of this ambient ion source, which has been extensively used, is the noninvasive property of PESI of examination of biological real samples. The results in the current review supports the idea that AIMS has emerged as a pioneer in MS-based approaches and that methods will continue to be developed along with improvements to existing ones in the near future.
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Affiliation(s)
- Lulu Shi
- Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
| | - Ahsan Habib
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
- Department of Chemistry, University of Dhaka, Dhaka, Bangladesh
| | - Lei Bi
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
| | - Huanhuan Hong
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
| | - Rockshana Begum
- Department of Chemistry, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Luhong Wen
- China Innovation Instrument Co., Ltd, Ningbo, Zhejiang, China
- The Research Institute of Advanced Technologies, Ningbo University, Ningbo, Zhejiang, China
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5
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Luo Y, Song C, Mao J, Peng Z, Sun S, Zhang Y, Yu A, Zhang W, Zhao W, Ouyang G. Developing a Noncontact Heating Matrix Spraying Apparatus with Controllable Matrix Film Formation for MALDI Mass Spectrometry Imaging. Anal Chem 2022; 94:12136-12143. [PMID: 35993787 DOI: 10.1021/acs.analchem.2c02192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Matrix deposition plays an important role in obtaining high-quality and reliable molecular spatial location information for matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). To control the matrix film formation, an automatic matrix spraying apparatus was developed with the introduction of a noncontact heating lamp. Compared with the unheated condition, the noncontact heating lamp suppressed the coffee-ring effect and the diffusion phenomenon of the analyte effectively by controllable matrix film formation. Meanwhile, the signal intensity was increased by 2-5 fold. To prove the ability of the matrix deposition apparatus, the apparatus combined with metabolomics analysis was used to show the spatial distribution of the substance in sprouted potato tubers. The potential biomarkers at m/z 868.5049 and m/z 852.5101 were identified as α-solanine and α-chaconine, and the synthesis pathways were further searched. To further demonstrate the quality of MALDI images including localization and spatial resolution, lipid distribution in rat brain tissue was investigated by the developed noncontact heating matrix spraying apparatus. An excellent match with distinguishable compartments of lipids in the rat brain was obtained between the H&E-stained sections and MALDI-MSI images. These results indicate that the developed noncontact heating matrix spraying apparatus is reliable and provides a low-cost, high-quality, rapid approach for MALDI-MSI.
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Affiliation(s)
- Yake Luo
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Chenchen Song
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Jian Mao
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Zifang Peng
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Shihao Sun
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Yanhao Zhang
- College of Ecology and Environment, Zhengzhou University, Zhengzhou, 450001, China.,State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong 999077, China
| | - Ajuan Yu
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China
| | - Wenfen Zhang
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.,College of Ecology and Environment, Zhengzhou University, Zhengzhou, 450001, China
| | - Wuduo Zhao
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.,College of Ecology and Environment, Zhengzhou University, Zhengzhou, 450001, China
| | - Gangfeng Ouyang
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China.,MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
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6
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Liu R, Xia S, Li H. Native top-down mass spectrometry for higher-order structural characterization of proteins and complexes. MASS SPECTROMETRY REVIEWS 2022:e21793. [PMID: 35757976 DOI: 10.1002/mas.21793] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Progress in structural biology research has led to a high demand for powerful and yet complementary analytical tools for structural characterization of proteins and protein complexes. This demand has significantly increased interest in native mass spectrometry (nMS), particularly native top-down mass spectrometry (nTDMS) in the past decade. This review highlights recent advances in nTDMS for structural research of biological assemblies, with a particular focus on the extra multi-layers of information enabled by TDMS. We include a short introduction of sample preparation and ionization to nMS, tandem fragmentation techniques as well as mass analyzers and software/analysis pipelines used for nTDMS. We highlight unique structural information offered by nTDMS and examples of its broad range of applications in proteins, protein-ligand interactions (metal, cofactor/drug, DNA/RNA, and protein), therapeutic antibodies and antigen-antibody complexes, membrane proteins, macromolecular machineries (ribosome, nucleosome, proteosome, and viruses), to endogenous protein complexes. The challenges, potential, along with perspectives of nTDMS methods for the analysis of proteins and protein assemblies in recombinant and biological samples are discussed.
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Affiliation(s)
- Ruijie Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shujun Xia
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
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7
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Nguyen MT, Halvorsen TG, Thiede B, Reubsaet L. Smart proteolysis samplers for pre‐lab bottom‐up protein analysis – Performance of on‐paper digestion compared to conventional digestion. SEPARATION SCIENCE PLUS 2022. [DOI: 10.1002/sscp.202100062] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Minh Thao Nguyen
- Section of Pharmaceutical Chemistry, Department of Pharmacy University of Oslo Oslo Norway
| | | | - Bernd Thiede
- Section of Biochemistry and Molecular Biology, Department of Biosciences University of Oslo Oslo Norway
| | - Léon Reubsaet
- Section of Pharmaceutical Chemistry, Department of Pharmacy University of Oslo Oslo Norway
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8
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9
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Gerbasi VR, Melani RD, Abbatiello SE, Belford MW, Huguet R, McGee JP, Dayhoff D, Thomas PM, Kelleher NL. Deeper Protein Identification Using Field Asymmetric Ion Mobility Spectrometry in Top-Down Proteomics. Anal Chem 2021; 93:6323-6328. [PMID: 33844503 DOI: 10.1021/acs.analchem.1c00402] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Field asymmetric ion mobility spectrometry (FAIMS), when used in proteomics studies, provides superior selectivity and enables more proteins to be identified by providing additional gas-phase separation. Here, we tested the performance of cylindrical FAIMS for the identification and characterization of proteoforms by top-down mass spectrometry of heterogeneous protein mixtures. Combining FAIMS with chromatographic separation resulted in a 62% increase in protein identifications, an 8% increase in proteoform identifications, and an improvement in proteoform identification compared to samples analyzed without FAIMS. In addition, utilization of FAIMS resulted in the identification of proteins encoded by lower-abundance mRNA transcripts. These improvements were attributable, in part, to improved signal-to-noise for proteoforms with similar retention times. Additionally, our results show that the optimal compensation voltage of any given proteoform was correlated with the molecular weight of the analyte. Collectively these results suggest that the addition of FAIMS can enhance top-down proteomics in both discovery and targeted applications.
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Affiliation(s)
- Vincent R Gerbasi
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States.,Pacific Northwest National Laboratories, Richland, Washington 99352, United States
| | - Rafael D Melani
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Susan E Abbatiello
- Northeastern University, Boston, Massachusetts 02115, United States.,Thermo Fisher Scientific, San Jose, California 98665, United States
| | | | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 98665, United States
| | - John P McGee
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Dawson Dayhoff
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Paul M Thomas
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Northwestern University, National Resource for Translational and Developmental Proteomics, Evanston, Illinois 60208, United States
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10
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Yan B, Bunch J. Probing Folded Proteins and Intact Protein Complexes by Desorption Electrospray Ionization Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:690-699. [PMID: 33605725 DOI: 10.1021/jasms.0c00417] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Native mass spectrometry (MS) enables the study of intact proteins as well as noncovalent protein-protein and protein-ligand complexes in their biological state. In this work, we present the application of a Waters desorption electrospray ionization (DESI) source with a prototype spray emitter for rapid surface measurements of folded and native protein structures. A comparison of DESI spray solvent shows that adding 50% methanol to 200 mM ammonium acetate solution does not reduce its performance in preserving folded protein structures. Instead, improved signal-to-noise (S/N) ratio is obtained, and less adducted peaks are detected by using this uncommon native MS solvent system. The standard DESI design with an inlet tube allows optimization of sampling temperature conditions to improve desolvation and therefore S/N ratio. Furthermore, tuning the inlet temperature enables the control and study of unfolding behavior of proteins from surface samples. The optimized condition for native DESI has been applied to several selected proteins and protein complexes with the molecular weight ranging from 8.6 to 66.4 kDa. Ions of folded proteins with narrow charge state distribution (CSD), or peaks showing noncovalent-bond-assembled intact protein complexes, are observed in the spectra. Evidence for the structural refolding of denatured proteins and protein complexes sampled with native solvent highlights the need for care when interpreting DESI native MS data, particularly for proteins with stable native structures.
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Affiliation(s)
- Bin Yan
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
| | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington TW11 0LW, U.K
- Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, U.K
- Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0FA, U.K
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11
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Giampà M, Sgobba E. Insight to Functional Conformation and Noncovalent Interactions of Protein-Protein Assembly Using MALDI Mass Spectrometry. Molecules 2020; 25:E4979. [PMID: 33126406 PMCID: PMC7662314 DOI: 10.3390/molecules25214979] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/22/2020] [Accepted: 10/24/2020] [Indexed: 11/16/2022] Open
Abstract
Noncovalent interactions are the keys to the structural organization of biomolecule e.g., proteins, glycans, lipids in the process of molecular recognition processes e.g., enzyme-substrate, antigen-antibody. Protein interactions lead to conformational changes, which dictate the functionality of that protein-protein complex. Besides biophysics techniques, noncovalent interaction and conformational dynamics, can be studied via mass spectrometry (MS), which represents a powerful tool, due to its low sample consumption, high sensitivity, and label-free sample. In this review, the focus will be placed on Matrix-Assisted Laser Desorption Ionization Mass Spectrometry (MALDI-MS) and its role in the analysis of protein-protein noncovalent assemblies exploring the relationship within noncovalent interaction, conformation, and biological function.
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Affiliation(s)
- Marco Giampà
- MR Cancer Group, Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Olav Kyrres Gate 9, 7030 Trondheim, Norway
| | - Elvira Sgobba
- Genetics and Plant Physiology, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden;
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12
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Abstract
Analysis of intact proteins by native mass spectrometry has emerged as a powerful tool for obtaining insight into subunit diversity, post-translational modifications, stoichiometry, structural arrangement, stability, and overall architecture. Typically, such an analysis is performed following protein purification procedures, which are time consuming, costly, and labor intensive. As this technology continues to move forward, advances in sample handling and instrumentation have enabled the investigation of intact proteins in situ and in crude samples, offering rapid analysis and improved conservation of the biological context. This emerging field, which involves various ion source platforms such as matrix-assisted laser desorption ionization (MALDI) and electrospray ionization (ESI) for both spatial imaging and solution-based analysis, is expected to impact many scientific fields, including biotechnology, pharmaceuticals, and clinical sciences. In this Perspective, we discuss the information that can be retrieved by such experiments as well as the current advantages and technical challenges associated with the different sampling strategies. Furthermore, we present future directions of these MS-based methods, including current limitations and efforts that should be made to make these approaches more accessible. Considering the vast progress we have witnessed in recent years, we anticipate that the advent of further innovations enabling minimal handling of MS samples will make this field more robust, user friendly, and widespread.
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Affiliation(s)
- Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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13
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Specker JT, Van Orden SL, Ridgeway ME, Prentice BM. Identification of Phosphatidylcholine Isomers in Imaging Mass Spectrometry Using Gas-Phase Charge Inversion Ion/Ion Reactions. Anal Chem 2020; 92:13192-13201. [PMID: 32845134 DOI: 10.1021/acs.analchem.0c02350] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Gas-phase ion/ion reactions have been enabled on a commercial dual source, hybrid QhFT-ICR mass spectrometer for use during imaging mass spectrometry experiments. These reactions allow for the transformation of the ion type most readily generated from the tissue surface to an ion type that gives improved chemical structural information upon tandem mass spectrometry (MS/MS) without manipulating the tissue sample. This process is demonstrated via the charge inversion reaction of phosphatidylcholine (PC) lipid cations generated from rat brain tissue via matrix-assisted laser desorption/ionization (MALDI) with 1,4-phenylenedipropionic acid (PDPA) reagent dianions generated via electrospray ionization (ESI). Collision-induced dissociation (CID) of the resulting demethylated PC product anions allows for the determination of the lipid fatty acyl tail identities and positions, which is not possible via CID of the precursor lipid cations. The abundance of lipid isomers revealed by this workflow is found to vary significantly in different regions of the brain. As each isoform may have a unique cellular function, these results underscore the importance of accurately separating and identifying the many isobaric and isomeric lipids and metabolites that can complicate image interpretation and spectral analysis.
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Affiliation(s)
- Jonathan T Specker
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | | | - Mark E Ridgeway
- Bruker Daltonics, Billerica, Massachusetts 01821, United States
| | - Boone M Prentice
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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14
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15
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Kocurek KI, Havlikova J, Buchan E, Tanner A, May RC, Cooper HJ. Electroporation and Mass Spectrometry: A New Paradigm for In Situ Analysis of Intact Proteins Direct from Living Yeast Colonies. Anal Chem 2020; 92:2605-2611. [PMID: 31922714 PMCID: PMC7145282 DOI: 10.1021/acs.analchem.9b04365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Yeasts
constitute an oft-neglected class of pathogens among which the resistance
to first-line treatments, attributed in part to mutations in efflux
pumps, is rapidly emerging. Their thick, chitin-reinforced cell walls
render cell lysis difficult, complicating their analysis and identification
by methods routinely used for bacteria, including matrix-assisted
laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS).
Liquid extraction surface analysis mass spectrometry (LESA-MS) has
previously been applied to the analysis of intact proteins from Gram-positive
and Gram-negative bacterial colonies sampled directly on solid nutrient
media. To date, a similar analysis of yeast colonies has not proved
possible. Here we demonstrate the rapid release of intact yeast proteins
for LESA-MS by electroporation using a home-built high-voltage device
designed to lyse cells grown in colonies on agar media. Detection
and identification of previously inaccessible proteins from baker’s
yeast Saccharomyces cerevisiae, as well as two clinically
relevant yeast species (Candida glabrata and Cryptococcus neoformans), is shown. The electroporation
approach also has the potential to be translated to other mass spectrometric
analysis techniques, including MALDI and various ambient ionization
methods.
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Affiliation(s)
- Klaudia I Kocurek
- School of Biosciences , University of Birmingham , Edgbaston , Birmingham B15 2TT , U.K
| | - Jana Havlikova
- School of Biosciences , University of Birmingham , Edgbaston , Birmingham B15 2TT , U.K
| | - Emma Buchan
- School of Biosciences , University of Birmingham , Edgbaston , Birmingham B15 2TT , U.K
| | - Andrew Tanner
- School of Biosciences , University of Birmingham , Edgbaston , Birmingham B15 2TT , U.K
| | - Robin C May
- Institute of Microbiology and Infection , University of Birmingham , Edgbaston , Birmingham B15 2TT , U.K
| | - Helen J Cooper
- School of Biosciences , University of Birmingham , Edgbaston , Birmingham B15 2TT , U.K
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16
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Illes-Toth E, Cooper HJ. Probing the Fundamentals of Native Liquid Extraction Surface Analysis Mass Spectrometry of Proteins: Can Proteins Refold during Extraction? Anal Chem 2019; 91:12246-12254. [PMID: 31490666 PMCID: PMC7006963 DOI: 10.1021/acs.analchem.9b02075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Native ambient mass spectrometry has the potential for simultaneous analysis of native protein structure and spatial distribution within thin tissue sections. Notwithstanding sensitivity, this information can, in principle, be obtained for any protein present with no requirement for a priori knowledge of protein identity. To date, native ambient mass spectrometry has primarily made use of the liquid extraction surface analysis (LESA) sampling technique. Here, we address a fundamental question: Are the protein structures observed following native liquid extraction surface analysis representative of the protein structures within the substrate, or does the extraction process facilitate refolding (or unfolding)? Specifically, our aim was to determine whether protein-ligand complexes observed following LESA are indicative of complexes present in the substrate, or an artifact of the sampling process. The systems investigated were myoglobin and its noncovalently bound heme cofactor, and the Zn-binding protein carbonic anhydrase and its binding with ethoxzolamide. Charge state distributions, drift time profiles, and collision cross sections were determined by liquid extraction surface analysis ion mobility mass spectrometry of native and denatured proteins and compared with those obtained by direct infusion electrospray. The results show that it was not possible to refold denatured proteins with concomitant ligand binding (neither heme, zinc, nor ethoxzolamide) simply by use of native-like LESA solvents. That is, protein-ligand complexes were only observed by LESA MS when present in the substrate.
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Affiliation(s)
- Eva Illes-Toth
- School of Biosciences , University of Birmingham , Birmingham , B15 2TT , U.K
| | - Helen J Cooper
- School of Biosciences , University of Birmingham , Birmingham , B15 2TT , U.K
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17
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Yan B, Taylor AJ, Bunch J. Cryo-LESA Mass Spectrometry-a Step Towards Truly Native Surface Sampling of Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1179-1189. [PMID: 30927181 DOI: 10.1007/s13361-019-02178-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/12/2019] [Accepted: 03/03/2019] [Indexed: 06/09/2023]
Abstract
Liquid extraction surface analysis (LESA) is a powerful method for measuring proteins from surfaces. In this work, we present development and initial testing of a cryo-platform for LESA mass spectrometry of proteins. We explore the use of native sampling solutions for probing proteins directly from frozen surfaces. Our initial results from analysis of ubiquitin and hemoglobin standards showed that protein and protein complex refolding or unfolding occurs during the liquid solvent extraction stage of routine room temperature LESA. However, by employing the cryo-sampling method, the refolding or unfolding of protein ubiquitin can be dramatically reduced, while for the protein complex of hemoglobin, its native structures can be better preserved compared with room temperature sampling. This indicates that a truly native LESA sampling method of proteins is feasible. We also present detection of proteins directly from a frozen tissue section. Interestingly, slight conformational differences are observed from different regions of the frozen tissue surface. Further development of this strategy should be considered as a method for preserving, maintaining, and studying proteins in their native states, directly from tissue. Graphical Abstract.
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Affiliation(s)
- Bin Yan
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Adam J Taylor
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
| | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
- Department of Surgery and Cancer, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK.
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18
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Griffiths RL, Konijnenberg A, Viner R, Cooper HJ. Direct Mass Spectrometry Analysis of Protein Complexes and Intact Proteins up to >70 kDa from Tissue. Anal Chem 2019; 91:6962-6966. [PMID: 31062957 PMCID: PMC7006965 DOI: 10.1021/acs.analchem.9b00971] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Native liquid extraction surface analysis (LESA) mass spectrometry allows direct analysis of folded proteins and protein complexes from biological substrates, such as dried blood spots and thin tissue sections, by use of native-like extraction/ionization solvents. Previously, we have demonstrated native LESA mass spectrometry of folded proteins up to 16 kDa as well as the 64 kDa hemoglobin tetramer, from mouse tissues. With denaturing LESA solvents, the highest mass protein detected in tissue to date is ∼37 kDa. Here, we demonstrate native LESA mass spectrometry by use of a Q Exactive UHMR Hybrid Quadrupole-Orbitrap (QE-UHMR) mass spectrometer, pushing the upper mass limit of proteins detected in tissue to >70 kDa. Moreover, a protein trimer of 42 kDa was detected and its stoichiometry confirmed by higher energy collision dissociation (HCD). The benefits of inclusion of detergents in the LESA sampling solvent are also demonstrated.
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Affiliation(s)
- Rian L Griffiths
- School of Biosciences , University of Birmingham , Edgbaston , Birmingham B15 2TT , U.K
| | - Albert Konijnenberg
- Thermo Fisher Scientific , Achtseweg Noord 5 , 5651 GG Eindhoven , The Netherlands
| | - Rosa Viner
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Helen J Cooper
- School of Biosciences , University of Birmingham , Edgbaston , Birmingham B15 2TT , U.K
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19
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Feider CL, Krieger A, DeHoog RJ, Eberlin LS. Ambient Ionization Mass Spectrometry: Recent Developments and Applications. Anal Chem 2019; 91:4266-4290. [PMID: 30790515 PMCID: PMC7444024 DOI: 10.1021/acs.analchem.9b00807] [Citation(s) in RCA: 262] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Clara L. Feider
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Anna Krieger
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Rachel J. DeHoog
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Livia S. Eberlin
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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20
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Abstract
Direct sampling mass spectrometry (MS) has been advancing aggressively, showing immense potential in translating MS into the clinical field. Unlike traditional MS analysis involving extensive sample preparation and chromatographic separation, quick and simple procedures with minimal sample pretreatment or purification became available with direct sampling. An overview of the development in this field is provided, including some representative ambient ionization and fast extraction methods. Quantitative applications of these methods are emphasized and their efficacy are highlighted from a clinical aspect; non-quantitative applications in clinical analysis are also discussed. This review also discusses the integration of direct sampling MS with miniature mass spectrometers and its future outlook as an emerging clinical tool for point-of-care analysis.
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Affiliation(s)
- Fan Pu
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Spencer Chiang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Wenpeng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Zheng Ouyang
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
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21
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Xu G, Li J. Recent advances in mass spectrometry imaging for multiomics application in neurology. J Comp Neurol 2018; 527:2158-2169. [DOI: 10.1002/cne.24571] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/14/2018] [Accepted: 10/24/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Guang Xu
- Hubei Education Cloud Service Engineering Technology Research CenterHubei University of Education Wuhan China
| | - Jianjun Li
- Human Health TherapeuticsNational Research Council Canada Ottawa Ontario
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22
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Griffiths RL, Simmonds AL, Swales JG, Goodwin RJA, Cooper HJ. LESA MS Imaging of Heat-Preserved and Frozen Tissue: Benefits of Multistep Static FAIMS. Anal Chem 2018; 90:13306-13314. [DOI: 10.1021/acs.analchem.8b02739] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Rian L. Griffiths
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - Anna L. Simmonds
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
| | - John G. Swales
- Pathology, Drug Safety & Metabolism, IMED Biotech Unit, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Richard J. A. Goodwin
- Pathology, Drug Safety & Metabolism, IMED Biotech Unit, AstraZeneca, Darwin Building, Cambridge Science Park, Milton Road, Cambridge CB4 0WG, U.K
| | - Helen J. Cooper
- School of Biosciences, University of Birmingham, Edgbaston B15 2TT, U.K
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23
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Kocurek KI, Griffiths RL, Cooper HJ. Ambient ionisation mass spectrometry for in situ analysis of intact proteins. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:565-578. [PMID: 29607564 PMCID: PMC6001466 DOI: 10.1002/jms.4087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 05/05/2023]
Abstract
Ambient surface mass spectrometry is an emerging field which shows great promise for the analysis of biomolecules directly from their biological substrate. In this article, we describe ambient ionisation mass spectrometry techniques for the in situ analysis of intact proteins. As a broad approach, the analysis of intact proteins offers unique advantages for the determination of primary sequence variations and posttranslational modifications, as well as interrogation of tertiary and quaternary structure and protein-protein/ligand interactions. In situ analysis of intact proteins offers the potential to couple these advantages with information relating to their biological environment, for example, their spatial distributions within healthy and diseased tissues. Here, we describe the techniques most commonly applied to in situ protein analysis (liquid extraction surface analysis, continuous flow liquid microjunction surface sampling, nano desorption electrospray ionisation, and desorption electrospray ionisation), their advantages, and limitations and describe their applications to date. We also discuss the incorporation of ion mobility spectrometry techniques (high field asymmetric waveform ion mobility spectrometry and travelling wave ion mobility spectrometry) into ambient workflows. Finally, future directions for the field are discussed.
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Affiliation(s)
- Klaudia I. Kocurek
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Rian L. Griffiths
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Helen J. Cooper
- School of BiosciencesUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
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24
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Meurs J, Alexander MR, Levkin PA, Widmaier S, Bunch J, Barrett DA, Kim DH. Improved Extraction Repeatability and Spectral Reproducibility for Liquid Extraction Surface Analysis–Mass Spectrometry Using Superhydrophobic–Superhydrophilic Patterning. Anal Chem 2018; 90:6001-6005. [DOI: 10.1021/acs.analchem.8b00973] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Joris Meurs
- Advanced Materials and Healthcare Technology Division, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Morgan R. Alexander
- Advanced Materials and Healthcare Technology Division, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Pavel A. Levkin
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen, 76344, Germany
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Simon Widmaier
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz Platz 1, Eggenstein-Leopoldshafen, 76344, Germany
| | - Josephine Bunch
- National Centre of Excellence in Mass Spectrometry Imaging, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - David A. Barrett
- Advanced Materials and Healthcare Technology Division, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Dong-Hyun Kim
- Advanced Materials and Healthcare Technology Division, School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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25
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Ambient surface mass spectrometry–ion mobility spectrometry of intact proteins. Curr Opin Chem Biol 2018; 42:67-75. [DOI: 10.1016/j.cbpa.2017.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/31/2017] [Accepted: 11/02/2017] [Indexed: 11/18/2022]
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26
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Griffiths RL, Randall EC, Race AM, Bunch J, Cooper HJ. Raster-Mode Continuous-Flow Liquid Microjunction Mass Spectrometry Imaging of Proteins in Thin Tissue Sections. Anal Chem 2017; 89:5683-5687. [DOI: 10.1021/acs.analchem.7b00977] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rian L. Griffiths
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Elizabeth C. Randall
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
- PSIBS
Doctoral Training Centre, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Alan M. Race
- National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, U.K
| | - Josephine Bunch
- National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, U.K
- School
of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Helen J. Cooper
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
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27
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Griffiths RL, Creese AJ, Race AM, Bunch J, Cooper HJ. LESA FAIMS Mass Spectrometry for the Spatial Profiling of Proteins from Tissue. Anal Chem 2016; 88:6758-66. [DOI: 10.1021/acs.analchem.6b01060] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rian L. Griffiths
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Andrew J. Creese
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
| | - Alan M. Race
- National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, U.K
| | - Josephine Bunch
- National Physical Laboratory, Hampton Road, Teddington, Middlesex, TW11 0LW, U.K
- School
of Pharmacy, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Helen J. Cooper
- School
of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K
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