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Nicolás Carcelén J, Potes Rodríguez H, González-Gago A, Marchante-Gayón JM, Ballesteros A, González JM, García Alonso JI, Rodríguez-González P. Evaluation of different isotope dilution mass spectrometry strategies for the characterization of naturally abundant and isotopically labelled peptide standards. Anal Bioanal Chem 2024; 416:1717-1731. [PMID: 38363304 PMCID: PMC10899365 DOI: 10.1007/s00216-024-05176-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Natural abundance and isotopically labelled tryptic peptides are routinely employed as standards in quantitative proteomics. The certification of the peptide content is usually carried out by amino acid analysis using isotope dilution mass spectrometry (IDMS) after the acid hydrolysis of the peptide. For the validation and traceability of the amino acid analysis procedure, expensive certified peptides must be employed. In this work we evaluate different IDMS alternatives which will reduce the amount of certified peptide required for validation of the amino acid analysis procedure. In this context, the characterization of both natural and isotopically labelled synthetic angiotensin I peptides was carried out. First, we applied a fast procedure for peptide hydrolysis based on microwave-assisted digestion and employed two certified peptide reference materials SRM 998 angiotensin I and CRM 6901-b C-peptide for validation of the hydrolysis procedure. The amino acids proline, leucine, isoleucine, valine, tyrosine, arginine and phenylalanine were evaluated for their suitability for peptide certification by IDMS by both liquid chromatography with tandem mass spectrometry (LC-MS/MS) and gas chromatography with mass spectrometry (GC)-MS/MS. Then, natural angiotensin I and 13C1-labelled angiotensin I were synthesized in-house and purified by preparative liquid chromatography. The concentration of the 13C1-labelled angiotensin I peptide was established by reverse IDMS in its native form using SRM 998 angiotensin I as reference. The concentration of the natural synthesized peptide was determined by IDMS both using the 13C1-labelled peptide in its native form and by amino acid analysis showing comparable results. Finally, the synthetic naturally abundant angiotensin I peptide was employed as "in-house" standard for the validation of subsequent peptide characterization procedures. Therefore, the novelty of this work relies on, first, the development of a faster hydrolysis procedure assisted by focused microwaves, providing complete hydrolysis in 150 min, and secondly, a validation strategy combining GC-MS and LC-MS/MS that allowed us to certify the purity of an in-house-synthesized peptide standard that can be employed as quality control in further experiments.
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Affiliation(s)
- Jesús Nicolás Carcelén
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Helí Potes Rodríguez
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Adriana González-Gago
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | | | - Alfredo Ballesteros
- Department of Organic and Inorganic Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - José Manuel González
- Department of Organic and Inorganic Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - José Ignacio García Alonso
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
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Optimization and Identification of Single Mutation in Hemoglobin Variants with 2,2,2 Trifluoroethanol Modified Digestion Method and Nano-LC Coupled MALDI MS/MS. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196357. [PMID: 36234894 PMCID: PMC9572498 DOI: 10.3390/molecules27196357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/21/2022] [Indexed: 12/30/2022]
Abstract
Background: Hemoglobin (Hb) variants arise due to point mutations in globin chains and their pathological treatments rely heavily on the identification of the nature and location of the mutation in the globin chains. Traditional methods for diagnosis such as HPLC and electrophoresis have their own limitations. Therefore, the present study aims to develop and optimize a specific method of sample processing that could lead to improved sequence coverage and analysis of Hb variants by nano LC-MALDI MS/MS. Methods: In our study, we primarily standardized various sample processing methods such as conventional digestion with trypsin followed by 10% acetonitrile treatment, digestion with multiple proteases like trypsin, Glu-C, Lys-C, and trypsin digestion subsequent to 2,2,2 trifluoroethanol (TFE) treatment. Finally, the peptides were identified by LC-MALDI MS/MS. All of these sample processing steps were primarily tested with recombinant Hb samples. After initial optimization, we found that the TFE method was the most suitable one and the efficiency of this method was applied in Hb variant identification based on high sequence coverage. Results: We developed and optimized a method using an organic solvent TFE and heat denaturation prior to digestion, resulting in 100% sequence coverage in the β-chains and 95% sequence coverage in the α-chains, which further helped in the identification of Hb mutations. A Hb variant protein sequence database was created to specify the search and reduce the search time. Conclusion: All of the mutations were identified using a bottom-up non-target approach. Therefore, a sensitive, robust and reproducible method was developed to identify single substitution mutations in the Hb variants from the sequence of the entire globin chains. Biological Significance: Over 330,000 infants are born annually with hemoglobinopathies and it is the major cause of morbidity and mortality in early childhood. Hb variants generally arise due to point mutation in the globin chains. There is high sequence homology between normal Hb and Hb variant chains. Due to this high homology between the two forms, identification of variants by mass spectrometry is very difficult and requires the full sequence coverage of α- and β-chains. As such, there is a need for a suitable method that provides 100% sequence coverage of globin chains for variant analysis by mass spectrometry. Our study provides a simple, robust, and reproducible method that is suitable for LC-MALDI and provides nearly complete sequence coverage in the globin chains. This method may be used in the near future in routine diagnosis for Hb variant analysis.
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Abstract
Accurate full-length sequencing of a purified unknown protein is still challenging nowadays due to the error-prone mass-spectrometry (MS)-based methods. De novo identified peptide sequence largely contain errors, undermining the accuracy of assembly. Bias on the detectability of the peptides also makes low-coverage regions, resulting in gaps. Although recent advances on multi-enzyme hydrolysis and algorithms showed complete assembly of full-length protein sequences in a few examples, the robustness in practical application is still to be improved. Here, inspired by genome assembly strategies, we demonstrate a contig-scaffolding strategy to assemble protein sequences with high robustness and accuracy. This strategy integrates multiple unspecific hydrolysis methods to minimize the bias in the hydrolysis process. After de novo identification of the peptides, our assembly algorithm, named Multiple Contigs & Scaffolding (MuCS), assembles the peptide sequences in a multistep, i.e., contig-scaffold manner, with error correction in each step. MS data from different hydrolysis experiments complement each other for robust contig extension and error correction. We demonstrated that our strategy on three proteins and three replications all reached 100% coverage (except one with 98.85%) and 98.69-100% accuracy. It can also efficiently deal with the membrane protein, although the transmembrane region was missing due to the limitation of the MS. The three replicates reached 88.85-92.57% coverage and 97.57-100% accuracy. In sum, we provided a practical, robust, and accurate solution for full-length protein sequencing. The MuCS software is available at http://chi-biotech.com/mucs/.
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Affiliation(s)
- Zhi-Biao Mai
- Big Data Decision Institute, Jinan University, Guangzhou 510632, China.,Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Zhong-Hua Zhou
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes and MOE Key Laboratory of Tumor Molecular Biology, Institute of Life and Health Engineering, Jinan University, Guangzhou 510632, China
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Lopez R, Escudero L, D’Amato R, Businelli D, Trabalza-Marinucci M, Cerutti S, Pacheco P. Optimisation of microwave-assisted acid hydrolysis for the determination of seleno-amino acids bound to proteins in powdered milk, lyophilized milk and infant formula. J Food Compost Anal 2019. [DOI: 10.1016/j.jfca.2019.03.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Gao J, Yao S, Wang Y, Hou Z, Yang C, Song H. Hydrolysis of trichosanthin (TCS) catalyzed by imidazolium-based ionic liquids in heating and microwave-assisted modes. NEW J CHEM 2018. [DOI: 10.1039/c8nj01876f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two modes of TCS hydrolysis based on ILs were compared and a higher degree of hydrolysis can be obtained compared to common catalysts.
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Affiliation(s)
- Jing Gao
- Department of Pharmaceutical and Biological Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Shun Yao
- Department of Pharmaceutical and Biological Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Yu Wang
- Department of Pharmaceutical and Biological Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Zhengbo Hou
- Department of Pharmaceutical and Biological Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Chang Yang
- Inner Mongolia Mengniu Dairy Industry (Group) Co., LTD
- Shengle Economical District
- Helingeer
- Huhhot Inner Mongolia
- China
| | - Hang Song
- Department of Pharmaceutical and Biological Engineering
- Sichuan University
- Chengdu 610065
- China
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Jiang H, Liu Z, Wang S. Microwave processing: Effects and impacts on food components. Crit Rev Food Sci Nutr 2017; 58:2476-2489. [PMID: 28613917 DOI: 10.1080/10408398.2017.1319322] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
As an efficient heating method, microwave processing has attracted attention both in academic research and industry. However, the mechanism of dielectric heating is quite distinct from that of the traditional conduction heating, and is widely applied as polar molecules and charged ions interaction with the alternative electromagnetic fields, resulting in fast and volumetric heating through their friction losses. Such a heating pattern would cause a certain change in microwave treatment, which is an unarguable reality. In this review, we made a retrospect of the essential knowledge about dielectric properties and summarized the concept of microwave heating, and the impact of microwave application on the main components of foods and agricultural products, which are classified as carbohydrates, lipids, proteins, chromatic/flavor substances, and vitamins. Finally, we offered a way to resolve the drawbacks of relevant microwave treatment and outlined the directions for future research.
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Affiliation(s)
- Hao Jiang
- a College of Food Science and Engineering , Northwest A&F University , Yangling , Shaanxi , China
| | - Zhigang Liu
- a College of Food Science and Engineering , Northwest A&F University , Yangling , Shaanxi , China
| | - Shaojin Wang
- b College of Mechanical and Electronic Engineering , Northwest A&F University , Yangling , Shaanxi , China.,c Department of Biological Systems Engineering , Washington State University , Pullman , WA , USA
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