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Liang LH, Ma YD, Yang Y, Yu HL, Xia JM, Zhang T, Liu CC, Liu SL. A protein standard absolute quantification strategy for enhanced absolute quantification of ricin in complex matrices using in vitro synthesized mutant holoprotein as internal standard by ultra-high-performance liquid chromatography-tandem mass spectrometry. J Chromatogr A 2023; 1708:464373. [PMID: 37717454 DOI: 10.1016/j.chroma.2023.464373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/19/2023]
Abstract
Ricin is a highly toxic protein toxin that poses a potential bioterrorism threat due to its potency and widespread availability. However, the accurate quantification of ricin through absolute mass spectrometry (MS) using a protein standard absolute quantification (PSAQ) strategy is not widely practiced. This limitation primarily arises from the presence of interchain disulfide bonds, which hinder the production of full-length isotope-labeled ricin as an internal standard (IS) in vitro. In this study, we have developed a novel approach for the absolute quantification of ricin in complex matrices using recombinant single-chain and full-length mutant ricin as the protein IS, instead of isotope-labeled ricin, in conjunction with ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). The amino acid sequence of the ricin mutant internal standard (RMIS) was designed by introducing site mutations in specific amino acids of trypsin/Glu-C enzymatic digestion marker peptides of ricin. To simplify protein expression, the A-chain and B-chain of RMIS were directly linked to replace the original interchain disulfide bonds. The RMISs were synthesized using an Escherichia coli expression system. An appropriate RMIS was selected as the protein IS based on consistent digestion efficiency, UHPLC-MS/MS behavior, antibody recognition function, lectin activity, and proper depurination activity with intact ricin. The RMIS was utilized to simultaneously quantify A- and B-chain marker peptides of ricin through UHPLC-MS/MS. This method was thoroughly validated using a milk matrix. By employing internal protein standards, this quantitative strategy overcomes the challenges posed by variations in extraction recoveries, matrix effects, and digestion efficiency encountered when working with different matrices. Consequently, calibration curves generated from milk matrix-spiked samples were utilized to accurately and precisely quantify ricin in river water and plasma samples. Moreover, the established method successfully detected intact ricin in samples obtained from the sixth Organization for the Prohibition of Chemical Weapons (OPCW) exercise on biotoxin analysis. This study presents a novel PSAQ strategy that enables the accurate quantification of ricin in complex matrices.
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Affiliation(s)
- Long-Hui Liang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Yang-De Ma
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Yang Yang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Hui-Lan Yu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Jun-Mei Xia
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Tao Zhang
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China
| | - Chang-Cai Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
| | - Shi-Lei Liu
- State Key Laboratory of NBC Protection for Civilian, Beijing 102205, China.
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Sun X, Wang W, Chai Y, Zheng Z, Wang Y, Bi J, Wang Q, Hu Y, Gao Z. A DNA walker triggered isothermal amplification method based on freezing construction of AuNP probes and its application in ricin detection. Analyst 2023; 148:690-699. [PMID: 36632708 DOI: 10.1039/d2an01793h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA molecular machines are widely used in the fields of biosensors and biological detection. Among them, DNA walkers have attracted much attention due to their simple design and controllability. Herein, we attempt to develop a DNA walker triggered exponential amplification method and explore its application. The AuNP probes in the DNA walker are constructed by a freezing technology, instead of the time-consuming and complex synthesis process of the traditional method. Meanwhile, after the "recognition-cleavage-relative motion" cycle of this DNA walker reaction, the exponential amplification reaction is initiated, and leads to the fluorescence recovery of the molecular beacon. Taking ricin as a target, this new method shows a limit of detection of 2.25 pM by selecting aptamers with strong binding affinity, and exhibits a wide detection range, satisfactory specificity, and excellent stability in practical application. Therefore, our method provides a universal sensing platform and has great prospects in the fields of biosensors, food safety detection, and clinical diagnostics.
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Affiliation(s)
- Xuan Sun
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Weiya Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin 300050, China
| | - Yanyan Chai
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhou Zheng
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Yu Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin 300050, China
| | - Jing Bi
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Qian Wang
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, China.
| | - Yonggang Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhixian Gao
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environment and Operational Medicine, Tianjin 300050, China
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Kandasamy K, Selvaprakash K, Chen YC. Functional magnetic nanoparticle-based affinity probe for MALDI mass spectrometric detection of ricin B. Mikrochim Acta 2021; 188:339. [PMID: 34510288 DOI: 10.1007/s00604-021-04991-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/17/2021] [Indexed: 11/30/2022]
Abstract
The use of lactosylated Fe3O4 magnetic nanoparticles (MNP@LAC) has been explored as affinity probes against ricin B based on galactose-ricin B binding interactions. Lactose was bound onto the surface of aminated MNPs through the Maillard reaction. The enrichment of ricin B took ~1 h by incubating MNP@LAC with samples under shaking at room temperature, followed by magnetic isolation. The resultant MNP@LAC-ricin B conjugates were characterized by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The limit of detection toward ricin B was ~3 nM by using the developed method. It was possible to detect the peptides derived from the tryptic digest of trace ricin B (~0.39 nM) enriched by the MNP@LAC probes followed by tryptic digestion and MALDI-MS analysis. The feasibility of using the developed method for detection of ricin B from complex white corn starch samples spiked with trace ricin B was demonstrated.
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Affiliation(s)
- Karthikeyan Kandasamy
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Karuppuchamy Selvaprakash
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yu-Chie Chen
- Department of Applied Chemistry, National Chiao Tung University, Hsinchu, 300, Taiwan. .,Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan.
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O'Bryon I, Jenson SC, Merkley ED. Flying blind, or just flying under the radar? The underappreciated power of de novo methods of mass spectrometric peptide identification. Protein Sci 2020; 29:1864-1878. [PMID: 32713088 PMCID: PMC7454419 DOI: 10.1002/pro.3919] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/15/2022]
Abstract
Mass spectrometry-based proteomics is a popular and powerful method for precise and highly multiplexed protein identification. The most common method of analyzing untargeted proteomics data is called database searching, where the database is simply a collection of protein sequences from the target organism, derived from genome sequencing. Experimental peptide tandem mass spectra are compared to simplified models of theoretical spectra calculated from the translated genomic sequences. However, in several interesting application areas, such as forensics, archaeology, venomics, and others, a genome sequence may not be available, or the correct genome sequence to use is not known. In these cases, de novo peptide identification can play an important role. De novo methods infer peptide sequence directly from the tandem mass spectrum without reference to a sequence database, usually using graph-based or machine learning algorithms. In this review, we provide a basic overview of de novo peptide identification methods and applications, briefly covering de novo algorithms and tools, and focusing in more depth on recent applications from venomics, metaproteomics, forensics, and characterization of antibody drugs.
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Affiliation(s)
- Isabelle O'Bryon
- Chemical and Biological SignaturesPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Sarah C. Jenson
- Chemical and Biological SignaturesPacific Northwest National LaboratoryRichlandWashingtonUSA
| | - Eric D. Merkley
- Chemical and Biological SignaturesPacific Northwest National LaboratoryRichlandWashingtonUSA
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Merkley ED, Burnum-Johnson KE, Anderson LN, Jenson SC, Wahl KL. Uniformly 15N-Labeled Recombinant Ricin A-Chain as an Internal Retention Time Standard for Increased Confidence in Forensic Identification of Ricin by Untargeted Nanoflow Liquid Chromatography-Tandem Mass Spectrometry. Anal Chem 2019; 91:13372-13376. [PMID: 31596564 DOI: 10.1021/acs.analchem.9b03389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ricin, a toxic protein from the castor plant, is of forensic and biosecurity interest because of its high toxicity and common occurrence in crimes and attempted crimes. Qualitative methods to detect ricin are therefore needed. Untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics methods are well suited because of their high specificity. Specificity in LC-MS/MS comes from both the LC and MS components. However, modern untargeted proteomics methods often use nanoflow LC, which has less reproducible retention times than standard-flow LC, making it challenging to use retention time as a point of identification in a forensic assay. We address this challenge by using retention times relative to a standard, namely, the uniformly 15N-labeled ricin A-chain produced recombinantly in a bacterial expression system. This material, added as an internal standard prior to trypsin digestion, produces a stable-isotope-labeled standard for every ricin tryptic peptide in the sample. We show that the MS signals for 15N and natural isotopic abundance ricin peptides are distinct, with mass shifts that correspond to the numbers of nitrogen atoms in each peptide or fragment. We also show that, as expected, labeled and unlabeled peptides coelute, with relative retention time differences of less than 0.2%.
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Affiliation(s)
- Eric D Merkley
- Chemical and Biological Signature Sciences Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Kristin E Burnum-Johnson
- Integrative Omics Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Lindsey N Anderson
- Biological Systems Science Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Sarah C Jenson
- Chemical and Biological Signature Sciences Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
| | - Karen L Wahl
- Integrative Omics Group , Pacific Northwest National Laboratory , Richland , Washington 99354 , United States
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