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Wamer N, Morse CN, Gadient JN, Dodson TA, Carlson EA, Prestwich EG. Comparison of Small Biomolecule Ionization and Fragmentation in Pseudomonas aeruginosa Using Common MALDI Matrices. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:355-365. [PMID: 36696681 PMCID: PMC9983012 DOI: 10.1021/jasms.2c00157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/05/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Different bacterial cell surface associated biomolecules can be analyzed by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry and coupled with collision induced dissociation (CID) for identification. Pseudomonas aeruginosa is an opportunistic, Gram-negative bacterium that causes acute or chronic biofilm infections. Cells of P. aeruginosa communicate through a system of signaling biomolecules known as quorum sensing (QS). The QS system can result in the production of biosurfactant rhamnolipids known to associate and alter the cellular membrane. MALDI-TOF utilizes a variety of matrices that can interact differently with biomolecules for selective ionization. We examined six common matrices to determine the optimal matrix specific to different molecule classes in P. aeruginosa associated with cell surfaces. Three major molecule classes (quinolones, rhamnolipids, and phospholipids) were observed to ionize selectively with the different matrices tested. Sodiated and protonated adducts differed between matrices utilized in our study. Isobaric ions were identified as different molecule classes depending on the matrix used. We highlight the role of matrix selection in MALDI-TOF identification of molecules within a complex biological mixture.
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Affiliation(s)
- Nathan
C. Wamer
- Department
of Medicinal and Biological Chemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Chase N. Morse
- Department
of Medicinal and Biological Chemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Jennifer N. Gadient
- The
College of Natural Sciences and Mathematics, NSM Instrumentation Center, University of Toledo, Toledo, Ohio 43606, United States
| | - Taylor A. Dodson
- Department
of Medicinal and Biological Chemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Eric A. Carlson
- Department
of Medicinal and Biological Chemistry, University
of Toledo, Toledo, Ohio 43606, United States
| | - Erin G. Prestwich
- Department
of Medicinal and Biological Chemistry, University
of Toledo, Toledo, Ohio 43606, United States
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2
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Jiang X, Gao F, Chen X, Yu Y, Ding G, Wu J. Ultrasensitive and High Reproducible Detection of Urinary Metabolites Using the Tip-Contact Extraction Method Coupled with Negative LDI-MS. J Proteome Res 2021; 20:4022-4030. [PMID: 34279957 DOI: 10.1021/acs.jproteome.1c00340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
More and more evidence has proved that urinary metabolites can instantly reflect disease state. Therefore, ultra-sensitive and reproducible detection of urinary metabolites in a high-throughput way is urgently desirable for clinical diagnosis. Matrix-free laser desorption/ionization mass spectrometry (LDI-MS) is a high-throughput platform for metabolites detection, but it is encountered by severe interference from numerous salts in urine samples, because the crystallized urine salt on dried samples could result in poor reproducibility in LDI-MS detection. The present work proposed a tip-contact extraction (TCE) technique to eliminate interference from the urine salt. Vertical silicon nanowire arrays decorated with the fluorinated ethylene propylene film (FEP@VSiNWs) could effectively extract metabolites from the urine sample dropping on its surface. High salt tolerance was observed in the subsequent LDI-MS detection of the metabolites extracted on the tip of FEP@VSiNWs even in the presence of 1 M urea. Stable and reproducible mass spectra for non-target metabolic analysis were obtained in real urine samples with different dilution folds. Urinary metabolites collected from bladder cancer (BC) patients were reliably profiled by the TCE method coupled with negative LDI-MS. Based on this platform, potential metabolic biomarkers that can distinguish BC patients and normal controls were uncovered.
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Affiliation(s)
- Xinrong Jiang
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, P. R. China
| | - Fengbin Gao
- Department of Urology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Xiaoming Chen
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, P. R. China.,Well-healthcare Technologies Co., Hangzhou 310051, China
| | - Yanlan Yu
- Department of Urology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Guoqing Ding
- Department of Urology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Jianmin Wu
- Institute of Analytical Chemistry, Department of Chemistry, Zhejiang University, Hangzhou 310058, P. R. China
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AlMasoud N, Muhamadali H, Chisanga M, AlRabiah H, Lima CA, Goodacre R. Discrimination of bacteria using whole organism fingerprinting: the utility of modern physicochemical techniques for bacterial typing. Analyst 2021; 146:770-788. [DOI: 10.1039/d0an01482f] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review compares and contrasts MALDI-MS, FT-IR spectroscopy and Raman spectroscopy for whole organism fingerprinting and bacterial typing.
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Affiliation(s)
- Najla AlMasoud
- Department of Chemistry
- College of Science
- Princess Nourah bint Abdulrahman University
- Riyadh 11671
- Saudi Arabia
| | - Howbeer Muhamadali
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Malama Chisanga
- School of Chemistry and Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Haitham AlRabiah
- Department of Pharmaceutical Chemistry
- College of Pharmacy
- King Saud University
- Riyadh
- Saudi Arabia
| | - Cassio A. Lima
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology
- Institute of Systems
- Molecular and Integrative Biology
- University of Liverpool
- Liverpool L69 7ZB
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Li N, Dou S, Feng L, Zhu Q, Lu N. Eliminating sweet spot in MALDI-MS with hydrophobic ordered structure as target for quantifying biomolecules. Talanta 2020; 218:121172. [PMID: 32797923 DOI: 10.1016/j.talanta.2020.121172] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 12/13/2022]
Abstract
In matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), the analyte is usually distributed unevenly throughout the sample spot. The area with aggregated analyte molecules contributing abundant signal, is termed as "sweet spot", which results in poor detection reproducibility and makes it impossible to quantify analytes without internal standards. We proposed a strategy to eliminate sweet spot in MALDI-MS by using a hydrophobic ordered structure as target. The target is fabricated by creating a hydrophobic silicon nanopillar array and subsequently decorating it uniformly with poly(methyl methacrylate) nanodots for capturing analytes. The sweet spot is eliminated by distributing analyte molecules uniformly on this target, and then result in a uniform MS image, which demonstrates an ideal reproducibility. Finally, with the target assisted MALDI-MS as biosensor was suitable to analyze practical sample such as bacitracin A in milk. Horse heart myoglobin and, angiotensin III molecules can be quantified without internal standard using α-cyano-4-hydroxycinnamic acid as matrix. This biosensor presented good linearity, high salts tolerance and high signal-to-noise ratio (up to 271.8), even the 1 mol/L salt concentration. This strategy could provide an alternative for improving the performance of MALDI-MS.
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Affiliation(s)
- Ning Li
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Shuzhen Dou
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Lei Feng
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Qunyan Zhu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China
| | - Nan Lu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, PR China.
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Jacyna J, Kordalewska M, Markuszewski MJ. Design of Experiments in metabolomics-related studies: An overview. J Pharm Biomed Anal 2019; 164:598-606. [DOI: 10.1016/j.jpba.2018.11.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/09/2018] [Accepted: 11/11/2018] [Indexed: 02/05/2023]
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Maes E, Clerens S, Dyer JM, Deb-Choudhury S. Improved Detection and Fragmentation of Disulphide-Linked Peptides. Methods Protoc 2018; 1:mps1030033. [PMID: 31164574 PMCID: PMC6481087 DOI: 10.3390/mps1030033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 08/24/2018] [Accepted: 08/28/2018] [Indexed: 12/04/2022] Open
Abstract
Characterisation of peptides containing intact disulphide bonds (DSBs) via mass spectrometry is challenging. Our study demonstrates that the addition of aniline to alpha-cyano-4-hydroxycinnamic acid improves detection and fragmentation of complex DSB peptides by matrix-assisted laser desorption/ionization, tandem time-of-flight mass spectrometry (MALDI-TOF-TOF MS). This improved assignment will be a significant new tool when a simple screening to confirm the DSB existence is required.
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Affiliation(s)
- Evelyne Maes
- Food & Bio-Based Products, AgResearch Ltd., 1365 Springs Road, Lincoln 7674, New Zealand.
| | - Stefan Clerens
- Food & Bio-Based Products, AgResearch Ltd., 1365 Springs Road, Lincoln 7674, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.
| | - Jolon M Dyer
- Food & Bio-Based Products, AgResearch Ltd., 1365 Springs Road, Lincoln 7674, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch 8140, New Zealand.
- Riddet Institute, Massey University, Palmerston North 4442, New Zealand.
- Wine, Food & Molecular Biosciences, Lincoln University, Lincoln 7674, New Zealand.
| | - Santanu Deb-Choudhury
- Food & Bio-Based Products, AgResearch Ltd., 1365 Springs Road, Lincoln 7674, New Zealand.
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Schröter J, Fülöp A, Hopf C, Schiller J. The combination of 2,5-dihydroxybenzoic acid and 2,5-dihydroxyacetophenone matrices for unequivocal assignment of phosphatidylethanolamine species in complex mixtures. Anal Bioanal Chem 2018; 410:2437-2447. [PMID: 29445834 DOI: 10.1007/s00216-018-0926-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/19/2018] [Accepted: 01/29/2018] [Indexed: 12/13/2022]
Abstract
Unequivocal assignment of phospholipid peaks in complex mixtures is difficult if only the m/z values but no tandem mass spectrometry (MS/MS) data are available. This is usually the case for matrix-assisted laser/desorption ionization time-of-flight (MALDI-TOF) MS imaging experiments and the analysis has normally to be performed without prior separation. Another problem might be the often matrix-induced loss of one methyl group in phosphatidylcholine (PC) species, which makes them detectable as negative ions becoming isomers of some phosphatidylethanolamines (PEs). Selected lipid mixtures of known compositions were investigated by negative ion MALDI-TOF MS and various imaging experiments. In addition to common matrices such as 2,5-dihydroxybenzoic acid (DHB) and 9-aminoacridine (9-AA), different binary matrices, including 2,5-dihydroxyacetophenone (2,5-DHAP) as matrix additive to DHB, were tested to probe their performance in both ionization modes. Beside artificial PC and PE mixtures of known compositions, egg yolk and liver extracts as well as cryosections from liver and pancreas tissue were selected as biologically relevant systems. The majority of the binary MALDI matrices used here leads to the loss of a methyl group from PC in the negative ion mode, which makes the clear identification of PE species ambiguous. However, this problem does not apply if a mixture of DHB and 2,5-DHAP is used. Therefore, the application of DHB/2,5-DHAP as matrix is a simple method to unequivocally identify PEs even in complex mixtures and tissue sections as negative ions and without the necessity to separate the individual lipid classes prior to MS detection. Graphical abstract Many common MALDI matrices (such as 9-AA) induce the loss of a methyl group from PC rendering the PC detectable as negative ion. These ions (m/z 744.6 in the upper trace) represent isomers of typical PE species. It will be shown that this problem can be avoided if mixtures between DHB and 2,5-DHAP are applied. At these conditions, POPC is exclusively detectable as a matrix adduct with DHB (at m/z 912.6, lower trace) and does not interfere with PE. This approach can also be used in MALDI MS imaging.
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Affiliation(s)
- Jenny Schröter
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107, Leipzig, Germany.
| | - Annabelle Fülöp
- Center for Biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Strasse 10, 68163, Mannheim, Germany
| | - Carsten Hopf
- Center for Biomedical Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Paul-Wittsack-Strasse 10, 68163, Mannheim, Germany
| | - Jürgen Schiller
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Leipzig University, Härtelstr. 16-18, 04107, Leipzig, Germany
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AlMasoud N, Xu Y, Trivedi DK, Salivo S, Abban T, Rattray NJW, Szula E, AlRabiah H, Sayqal A, Goodacre R. Classification of Bacillus and Brevibacillus species using rapid analysis of lipids by mass spectrometry. Anal Bioanal Chem 2016; 408:7865-7878. [PMID: 27604269 PMCID: PMC5061856 DOI: 10.1007/s00216-016-9890-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/16/2016] [Indexed: 01/02/2023]
Abstract
Bacillus are aerobic spore-forming bacteria that are known to lead to specific diseases, such as anthrax and food poisoning. This study focuses on the characterization of these bacteria by the detection of lipids extracted from 33 well-characterized strains from the Bacillus and Brevibacillus genera, with the aim to discriminate between the different species. For the purpose of analysing the lipids extracted from these bacterial samples, two rapid physicochemical techniques were used: matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF-MS) and liquid chromatography in conjunction with mass spectrometry (LC-MS). The findings of this investigation confirmed that MALDI-TOF-MS could be used to identify different bacterial lipids and, in combination with appropriate chemometrics, allowed for the discrimination between these different bacterial species, which was supported by LC-MS. The average correct classification rates for the seven species of bacteria were 62.23 and 77.03 % based on MALDI-TOF-MS and LC-MS data, respectively. The Procrustes distance for the two datasets was 0.0699, indicating that the results from the two techniques were very similar. In addition, we also compared these bacterial lipid MALDI-TOF-MS profiles to protein profiles also collected by MALDI-TOF-MS on the same bacteria (Procrustes distance, 0.1006). The level of discrimination between lipids and proteins was equivalent, and this further indicated the potential of MALDI-TOF-MS analysis as a rapid, robust and reliable method for the classification of bacteria based on different bacterial chemical components. Graphical abstract MALDI-MS has been successfully developed for the characterization of bacteria at the subspecies level using lipids and benchmarked against HPLC.
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Affiliation(s)
- Najla AlMasoud
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Yun Xu
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Drupad K Trivedi
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Simona Salivo
- Shimadzu, Kratos Analytical Ltd. Wharfside, Trafford Wharf Road, Manchester, M17 1GP, UK
| | - Tom Abban
- Shimadzu, Kratos Analytical Ltd. Wharfside, Trafford Wharf Road, Manchester, M17 1GP, UK
| | - Nicholas J W Rattray
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Ewa Szula
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Haitham AlRabiah
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh, 11451, Saudi Arabia
| | - Ali Sayqal
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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