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Mansuri MS, Bathla S, Lam TT, Nairn AC, Williams KR. Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells. J Proteomics 2024; 297:105109. [PMID: 38325732 PMCID: PMC10939724 DOI: 10.1016/j.jprot.2024.105109] [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: 11/13/2023] [Revised: 01/10/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
To identify proteins by the bottom-up mass spectrometry workflow, enzymatic digestion is essential to break down proteins into smaller peptides amenable to both chromatographic separation and mass spectrometric analysis. Trypsin is the most extensively used protease due to its high cleavage specificity and generation of peptides with desirable positively charged N- and C-terminal amino acid residues that are amenable to reverse phase HPLC separation and MS/MS analyses. However, trypsin can yield variable digestion profiles and its protein cleavage activity is interdependent on trypsin source and quality, digestion time and temperature, pH, denaturant, trypsin and substrate concentrations, composition/complexity of the sample matrix, and other factors. There is therefore a need for a more standardized, general-purpose trypsin digestion protocol. Based on a review of the literature we delineate optimal conditions for carrying out trypsin digestions of complex proteomes from bulk samples to limiting amounts of protein extracts. Furthermore, we highlight recent developments and technological advances used in digestion protocols to quantify complex proteomes from single cells. SIGNIFICANCE: Currently, bottom-up MS-based proteomics is the method of choice for global proteome analysis. Since trypsin is the most utilized protease in bottom-up MS proteomics, delineating optimal conditions for carrying out trypsin digestions of complex proteomes in samples ranging from tissues to single cells should positively impact a broad range of biomedical research.
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Affiliation(s)
- M Shahid Mansuri
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | - Shveta Bathla
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Department of Psychiatry, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA; Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA; Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT 06511, USA.
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Pavón-Pérez J, Henriquez-Aedo K, Salazar R, Herrero M, Aranda M. Chemometric optimization of trypsin digestion method applying infrared, microwave and ultrasound energies for determination of caseins and ovalbumin in wines. JOURNAL OF FOOD SCIENCE AND TECHNOLOGY 2021; 58:2914-2923. [PMID: 34294953 PMCID: PMC8249656 DOI: 10.1007/s13197-020-04793-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 08/20/2020] [Accepted: 09/12/2020] [Indexed: 06/13/2023]
Abstract
Caseins and ovalbumin are frequently used as wine fining agents to remove undesirable compounds like polymeric phenols. Their presence in wines is a subject of concern because may cause adverse effects on susceptible consumers, especially when their presence is not labeled. A key step for its determination is trypsin digestion, which is considered the bottleneck of bottom-up approach workflow because usually requires several hours. To reduce this time, the objective of this work was to carry out a chemometric optimization of trypsin digestion method applying infrared, microwave and ultrasound energies to determine caseins and ovalbumin in wines. The conditions of each accelerated digestion method were optimized using a Response Surface Methodology based on central composite design. The parameters optimized were digestion time and trypsin: protein ratio. The response variable evaluated was digestion yield, which was determined through the peak area of each protein transition determined by liquid chromatography-mass spectrometry. The most effective technique was microwave followed by ultrasound and infrared. Since optimal values of microwave and ultrasound-assisted digestion were the same, the later was chosen considering sample preparation and cost. Applying the proposed approach, a reduction of ca. 140 and 240-fold on digestion time was achieved compared with optimized and non-optimized conventional methods, respectively. With this workflow, both proteins were digested in a single 3 min process allowing its detection by liquid chromatography-mass spectrometry at µg L-1 level, which is ca. 60 times lower than the current limit of 0.25 mg L-1.
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Affiliation(s)
- Jessy Pavón-Pérez
- Departamento de Ciencia Y Tecnología de Los Alimentos, Facultad de Farmacia, Universidad de Concepción. Barrio Universitario S/N, Concepción, Chile
| | - Karem Henriquez-Aedo
- Laboratorio de Biotecnología Y Genética de Alimentos, Departamento de Ciencia Y Tecnología de Los Alimentos, Facultad de Farmacia, Universidad de Concepción. Barrio Universitario S/N, Concepción, Chile
- Laboratorio de Alimentos Funcionales, Centro de Biotecnología, Universidad de Concepción. Barrio Universitario S/N, Concepción, Chile
| | - Ricardo Salazar
- Laboratorio de Electroquímica del Medio Ambiente, LEQMA, Departamento de Química de Los Materiales, Universidad de Santiago de Chile, USACH, Casilla 40, C.P. 33, Av. Libertador Bernardo O’Higgins, 3363, Estación Central, Santiago, Chile
| | - Miguel Herrero
- Instituto de Investigación en Ciencias de La Alimentación CIAL (CSIC-UAM), Calle Nicolás Cabrera, 9, 28049 Madrid, Spain
| | - Mario Aranda
- Laboratorio de Investigación en Fármacos Y Alimentos, Departamento de Farmacia, Facultad de Química Y de Farmacia, Pontificia Universidad Católica de Chile, Avda. Vicuña Mackenna Casilla 306, Correo 22, 4860 Macul, Santiago, Chile
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Ultrasonic-Based Filter Aided Sample Preparation as the General Method to Sample Preparation in Proteomics. Anal Chem 2020; 92:9164-9171. [PMID: 32484334 DOI: 10.1021/acs.analchem.0c01470] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We propose a new high-throughput ultrafast method for large-scale proteomics approaches by speeding up the classic filter aided sample preparation protocol, FASP, from overnight to 2.5 h. Thirty-six samples can be treated in 2.5 h, and the method is scalable to 96-well plate-based pipelines. After a modification of the FASP-tube, the steps of protein reduction, protein alkylation, and protein digestion of complex proteomes are done in just 5.25 min, each one under the effects of an ultrasonic field (7 cycles: 30 s on and 15 s off). The new method was compared to the standard overnight digestion FASP protocol, and no statistical differences were found for more than 92.4%, 92%, and 93.3% of the proteins identified by studying the proteome of E. coli, mouse brain, and mouse liver tissue samples, respectively. Furthermore, the successful relative label-free quantification of four spiked proteins in E. coli samples, BSA, β-lactoglobulin, α-casein, and α-lactalbumin, was achieved, using either the ultrasonic-based FASP protocol or the classic overnight one. The new US-FASP method matches the analytical minimalism rules as time, cost, sample requirement, reagent consumption, energy requirements, and production of waste products are reduced to a minimum while maintaining high sample throughput in a robust manner as all of the advantages of the filter aided sample preparation protocol are maintained.
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Pavón-Pérez J, Henriquez-Aedo K, Herrero M, Aranda M. Occurrence of allergen proteins in wines from Chilean market. FOOD ADDITIVES & CONTAMINANTS PART B-SURVEILLANCE 2020; 13:268-274. [DOI: 10.1080/19393210.2020.1769194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jessy Pavón-Pérez
- Departamento de Ciencia y Tecnología de los Alimentos, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Karem Henriquez-Aedo
- Laboratorio de Biotecnología y Genética de Alimentos, Departamento de Ciencia y Tecnología de Los Alimentos, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
- Laboratorio de Alimentos Funcionales, Centro de Biotecnología, Universidad de Concepción, Concepción, Chile
| | - Miguel Herrero
- Foodomics Laboratory, Institute of Food Science Research (CIAL, CSIC), Madrid, Spain
| | - Mario Aranda
- Laboratorio de Investigación en Fármacos y Alimentos, Departamento de Farmacia, Facultad de Química y de Farmacia, Pontificia Universidad Católica de Chile, Santiago, Chile
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Label-free protein quantification after ultrafast digestion of complex proteomes using ultrasonic energy and immobilized-trypsin magnetic nanoparticles. Talanta 2019; 196:262-270. [DOI: 10.1016/j.talanta.2018.12.066] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/27/2022]
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López-Fernández H, Araújo JE, Jorge S, Glez-Peña D, Reboiro-Jato M, Santos HM, Fdez-Riverola F, Capelo JL. S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2018; 155:1-9. [PMID: 29512488 DOI: 10.1016/j.cmpb.2017.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND OBJECTIVE 2D-gel electrophoresis is widely used in combination with MALDI-TOF mass spectrometry in order to analyze the proteome of biological samples. For instance, it can be used to discover proteins that are differentially expressed between two groups (e.g. two disease conditions, case vs. control, etc.) thus obtaining a set of potential biomarkers. This procedure requires a great deal of data processing in order to prepare data for analysis or to merge and integrate data from different sources. This kind of work is usually done manually (e.g. copying and pasting data into spreadsheet files), which is highly time consuming and distracts the researcher from other important, core tasks. Moreover, engaging in a repetitive process in a non-automated, handling-based manner is prone to error, thus threatening reliability and reproducibility. The objective of this paper is to present S2P, an open source software to overcome these drawbacks. METHODS S2P is implemented in Java on top of the AIBench framework, and relies on well-established open source libraries to accomplish different tasks. RESULTS S2P is an AIBench based desktop multiplatform application, specifically aimed to process 2D-gel and MALDI-mass spectrometry protein identification-based data in a computer-aided, reproducible manner. Different case studies are presented in order to show the usefulness of S2P. CONCLUSIONS S2P is open source and free to all users at http://www.sing-group.org/s2p. Through its user-friendly GUI interface, S2P dramatically reduces the time that researchers need to invest in order to prepare data for analysis.
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Affiliation(s)
- Hugo López-Fernández
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain; UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal.
| | - José E Araújo
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Susana Jorge
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Daniel Glez-Peña
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - Miguel Reboiro-Jato
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - Hugo M Santos
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Florentino Fdez-Riverola
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - José L Capelo
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
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Jorge S, Araújo J, Pimentel-Santos F, Branco JC, Santos HM, Lodeiro C, Capelo J. Unparalleled sample treatment throughput for proteomics workflows relying on ultrasonic energy. Talanta 2018; 178:1067-1076. [DOI: 10.1016/j.talanta.2017.07.079] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 07/22/2017] [Accepted: 07/26/2017] [Indexed: 10/19/2022]
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Guo Z, Cheng J, Sun H, Sun W. A qualitative and quantitative evaluation of the peptide characteristics of microwave- and ultrasound-assisted digestion in discovery and targeted proteomic analyses. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1353-1362. [PMID: 28557149 DOI: 10.1002/rcm.7913] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 05/22/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE Fast digestion methods can dramatically accelerate enzyme digestion and increase the throughput of proteomic analysis. However, the peptide characteristics of fast digestion methods and their performance in discovery and targeted proteomic analysis must be systematically evaluated. METHODS Three digestion methods, including overnight digestion, microwave-assisted protein enzymatic digestion (MAPED), and high-intensity focused ultrasonic-assisted enzymatic digestion (HIFUSAED), in trypsin or in trypsin/Lys-C were comprehensively compared in both discovery and targeted proteomics analysis using the HeLa cell proteome. In discovery proteomic analysis, the highest numbers of peptides and proteins were identified when the sample was digested via the MAPED method with trypsin/Lys-C. RESULTS The fast digestion methods showed a higher mis-cleavage rate and a lower semi-tryptic rate than the overnight digestion method. In both label-free quantitative analysis and targeted proteomic analysis, both fully cleaved peptides (FCPs) and mis-cleaved peptides (MCPs) from the fast digestion methods and the overnight digestion method showed good reproducibility if they showed good abundance. CONCLUSIONS When both the FCPs and MCPs were included in the analysis, the MAPED with trypsin/Lys-C method showed the best results for both discovery proteomic analysis and relative quantitative targeted proteomic analysis. These results will be beneficial for the application of fast digestion methods to proteomics.
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Affiliation(s)
- Zhengguang Guo
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jie Cheng
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Haidan Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Institute of Basic Medicine, Chinese Academy of Medical Sciences, Beijing, China
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Branco P, Kemsawasd V, Santos L, Diniz M, Caldeira J, Almeida MG, Arneborg N, Albergaria H. Saccharomyces cerevisiae accumulates GAPDH-derived peptides on its cell surface that induce death of non-Saccharomyces yeasts by cell-to-cell contact. FEMS Microbiol Ecol 2017; 93:3753550. [DOI: 10.1093/femsec/fix055] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/21/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Patrícia Branco
- Unit of Bioenergy, Laboratório Nacional de Energia e Geologia (LNEG), Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal
- LEAF, Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda 1349-017 Lisboa, Portugal
| | - Varongsiri Kemsawasd
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Lara Santos
- Instituto Superior de Saúde Egas Moniz, Campus Universitário, Quinta da Granja, 2829-511 Monte Caparica, Portugal
| | - Mário Diniz
- Instituto Superior de Saúde Egas Moniz, Campus Universitário, Quinta da Granja, 2829-511 Monte Caparica, Portugal
| | - Jorge Caldeira
- Instituto Superior de Saúde Egas Moniz, Campus Universitário, Quinta da Granja, 2829-511 Monte Caparica, Portugal
- REQUIMTE- Dept. Química, Faculdade de Ciências e Tecnologia (UNL), 2829-516 Monte Caparica, Portugal
| | - Maria Gabriela Almeida
- Instituto Superior de Saúde Egas Moniz, Campus Universitário, Quinta da Granja, 2829-511 Monte Caparica, Portugal
- REQUIMTE- Dept. Química, Faculdade de Ciências e Tecnologia (UNL), 2829-516 Monte Caparica, Portugal
| | - Nils Arneborg
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Helena Albergaria
- Unit of Bioenergy, Laboratório Nacional de Energia e Geologia (LNEG), Estrada do Paço do Lumiar 22, 1649-038 Lisboa, Portugal
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Devi S, Wu BH, Chu PY, Liu YP, Wu HL, Ho YP. Studying the effect of microwave heating on the digestion process and identification of proteins. Electrophoresis 2016; 38:429-440. [PMID: 27770443 DOI: 10.1002/elps.201600392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 11/07/2022]
Abstract
The impact of microwave irradiation on the in-solution digestion processes and the detection limit of proteins are systematically studied. Kinetic processes of many peptides produced through the trypsin digestion of various proteins under microwave heating at 50°C were investigated with MALDI-MS. This study also examines the detection limits and digestion completeness of individual proteins under microwave heating at 50°C and at different time intervals (1, 5 and 30 min) using LC-MS. We conclude that if the peptides without missed cleavage dictate the detection limit, conventional digestion will lead to a better detection limit. The detection limit may not differ between the microwave and conventional heating if the peptides with missed cleavage sites and strong intensity are formed at the very early stage (i.e., less than 1 min) and are not further digested throughout the entire digestion process. The digestion of Escherichia coli lysate was compared under conventional and short time (microwave) conditions. The number of proteins identified under conventional heating exceeded that obtained from microwave heating over heating periods less than 5 min. The overall results show that the microwave-assisted digestion is not complete. Although the sequence coverage might be better, the detection limit might be worse than that under conventional heating.
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Affiliation(s)
- Shobha Devi
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Bo-Hung Wu
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Pei-Yu Chu
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Yue-Pei Liu
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Hsin-Lin Wu
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
| | - Yen-Peng Ho
- Department of Chemistry, National Dong Hwa University, Hualien, Taiwan
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Changes in metabolic pathways of Desulfovibrio alaskensis G20 cells induced by molybdate excess. J Biol Inorg Chem 2014; 20:311-22. [PMID: 25488518 DOI: 10.1007/s00775-014-1224-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/25/2014] [Indexed: 01/06/2023]
Abstract
The activity of sulfate-reducing bacteria (SRB) intensifies the problems associated to corrosion of metals and the solution entails significant economic costs. Although molybdate can be used to control the negative effects of these organisms, the mechanisms triggered in the cells exposed to Mo-excess are poorly understood. In this work, the effects of molybdate ions on the growth and morphology of the SRB Desulfovibrio alaskensis G20 (DaG20) were investigated. In addition, the cellular localization, ion uptake and regulation of protein expression were studied. We found that molybdate concentrations ranging between 50 and 150 µM produce a twofold increase in the doubling time with this effect being more significant at 200 µM molybdate (five times increase in the doubling time). It was also observed that 500 µM molybdate completely inhibits the cellular growth. On the context of protein regulation, we found that several enzymes involved in energy metabolism, cellular division and metal uptake processes were particularly influenced under the conditions tested. An overall description of some of the mechanisms involved in the DaG20 adaptation to molybdate-stress conditions is discussed.
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Fernández-Costa C, Reboiro-Jato M, Fdez-Riverola F, Ruiz-Romero C, Blanco FJ, Capelo-Martínez JL. Sequential depletion coupled to C18 sequential extraction as a rapid tool for human serum multiple profiling. Talanta 2014; 125:189-95. [DOI: 10.1016/j.talanta.2014.02.050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/15/2014] [Accepted: 02/20/2014] [Indexed: 01/01/2023]
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13
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Araújo J, Oliveira E, Kouvonen P, Corthals G, Lodeiro C, Santos H, Capelo J. A journey through PROTEOSONICS. Talanta 2014; 121:71-80. [DOI: 10.1016/j.talanta.2013.12.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 10/25/2022]
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14
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Nunes-Miranda JD, Núñez C, Santos HM, Vale G, Reboiro-Jato M, Fdez-Riverola F, Lodeiro C, Miró M, Capelo JL. A mesofluidic platform integrating on-chip probe ultrasonication for multiple sample pretreatment involving denaturation, reduction, and digestion in protein identification assays by mass spectrometry. Analyst 2014; 139:992-5. [DOI: 10.1039/c3an02178e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel mesofluidic platform integrating on-chip probe ultrasonication for automated high-throughput shotgun proteomic assays.
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Affiliation(s)
- J. D. Nunes-Miranda
- Department of Genetics and Biotechnology
- University of Trás-os-Montes and Alto Douro
- Vila Real, Portugal
- Institute for Biotechnology and Bioengineering
- Centre of Genomics and Biotechnology
| | - Cristina Núñez
- REQUIMTE
- Departamento de Química
- Faculdade de Ciencias e Tecnologia
- FCT
- Universidade Nova de Lisboa
| | - Hugo M. Santos
- Institute for Biotechnology and Bioengineering
- Centre of Genomics and Biotechnology
- University of Trás-os-Montes and Alto Douro
- Vila Real, Portugal
- REQUIMTE
| | - G. Vale
- REQUIMTE
- Departamento de Química
- Faculdade de Ciencias e Tecnologia
- FCT
- Universidade Nova de Lisboa
| | - Miguel Reboiro-Jato
- SING Group
- Informatics Department
- Higher Technical School of Computer Engineering
- University of Vigo
- Ourense, Spain
| | - Florentino Fdez-Riverola
- SING Group
- Informatics Department
- Higher Technical School of Computer Engineering
- University of Vigo
- Ourense, Spain
| | - Carlos Lodeiro
- REQUIMTE
- Departamento de Química
- Faculdade de Ciencias e Tecnologia
- FCT
- Universidade Nova de Lisboa
| | - Manuel Miró
- FI-TRACE Group
- Department of Chemistry
- University of the Balearic Islands
- Palma de Mallorca, Spain
| | - J. L. Capelo
- REQUIMTE
- Departamento de Química
- Faculdade de Ciencias e Tecnologia
- FCT
- Universidade Nova de Lisboa
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López-Cortés R, Oliveira E, Núñez C, Lodeiro C, Páez de la Cadena M, Fdez-Riverola F, López-Fernández H, Reboiro-Jato M, Glez-Peña D, Luis Capelo J, Santos HM. Fast human serum profiling through chemical depletion coupled to gold-nanoparticle-assisted protein separation. Talanta 2012; 100:239-45. [DOI: 10.1016/j.talanta.2012.08.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2012] [Revised: 08/09/2012] [Accepted: 08/13/2012] [Indexed: 01/23/2023]
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16
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Seike T, Yamagishi Y, Iio H, Nakamura T, Shimoda C. Remarkably simple sequence requirement of the M-factor pheromone of Schizosaccharomyces pombe. Genetics 2012; 191:815-25. [PMID: 22542965 PMCID: PMC3389977 DOI: 10.1534/genetics.112.140483] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 04/16/2012] [Indexed: 11/18/2022] Open
Abstract
The mating reaction is triggered by specific pheromones in a wide variety of organisms. Small peptides are used as mating pheromones in yeasts and fungi. In the fission yeast Schizosaccharomyces pombe, M-factor is a C terminally farnesylated nonapeptide secreted from M-cells, and its counterpart, P-factor, is a simple peptide composed of 23 amino acids. The primary structure requirements for the biological activity of pheromone peptides remain to be elucidated. Here, we conducted comprehensive substitution of each of the amino acids in M-factor peptide and inspected the mating ability of these missense mutants. Thirty-five sterile mutants were found among an array of 152 mutants with single amino acid substitutions. Mapping of the mutation sites clearly indicated that the sterile mutants were associated exclusively with four amino acid residues (VPYM) in the carboxyl-terminal half. In contrast, the substitution of four amino-terminal residues (YTPK) with any amino acid had no or only a slightly deleterious effect on mating. Furthermore, deletion of the three N-terminal residues caused no sterility, although truncation of a fourth residue had a marked effect. We conclude that a farnesylated hexapeptide (KVPYMC(Far)-OCH(3)) is the minimal M-factor that retains pheromone activity. At least 15 nonfunctional peptides were found to be secreted, suggesting that these mutant M-factor peptides are no longer recognized by the cognate receptor.
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Affiliation(s)
| | - Yoshikazu Yamagishi
- Department of Material Science and Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Hideo Iio
- Department of Material Science and Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka 558-8585, Japan
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Effects of temperature on ultrasound-assisted tryptic protein digestion. Anal Biochem 2011; 414:125-30. [DOI: 10.1016/j.ab.2011.02.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 02/10/2011] [Accepted: 02/17/2011] [Indexed: 11/20/2022]
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Accelerated sample treatment for screening of banned doping substances by GC–MS: ultrasonication versus microwave energy. Anal Bioanal Chem 2010; 399:861-75. [DOI: 10.1007/s00216-010-4319-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 09/15/2010] [Accepted: 10/10/2010] [Indexed: 10/18/2022]
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19
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Galesio M, Rial-Otero R, Simal-Gándara J, de la Torre X, Botrè F, Capelo-Martínez JL. Improved ultrasonic-based sample treatment for the screening of anabolic steroids by gas chromatography/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:2375-2385. [PMID: 20635322 DOI: 10.1002/rcm.4654] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A rapid sample treatment procedure for the gas chromatography/mass spectrometry (GC/MS) determination of anabolic steroids in human urine has been developed. The new procedure makes use of ultrasonic energy to reduce reaction times and increase the overall sensitivity. The following variables affecting the performance of the ultrasonic treatment were optimised: (i) time, (ii) device, (iii) frequency, and (iv) temperature. It was found that, under an ultrasonic field, the hydrolysis of conjugated steroids with beta-glucuronidase from Escherichia coli K12 was possible with a treatment time of 10 min. The accuracy and precision of the ultrasonic method were found to be in agreement with those achieved with the conventional thermal conductivity procedure (Student's t-test; p = 0.05, n = 10). After the enzymatic hydrolysis, the derivatisation of the target compounds with trimethylsilyl (TMS) reagent, methyl-N-trimethylsilyltrifluoroacetamide (MSTFA)/NH(4)I/dithioerythritol (DTE) (1000:2:4, v/w/w), was also accelerated using ultrasonic energy. In order to test the applicability of the use of ultrasonic energy in the acceleration of the derivatisation reaction with TMS, the classic method of thermal conductivity was applied for comparative purposes to a pool of 35 androgenic anabolic steroids (AAS) and/or their metabolites. The results demonstrated that after 3 min of sonication in a Sonoreactor device (50% amplitude), 19 of the 35 compounds studied showed similar reaction yield to those obtained with the classic procedure requiring 30 min (Student's t-test; p = 0.05, n = 5); 13 increased to higher silylation yields; and for the steroids 1-testosterone, danazol and etiocholanolone-D5, the same results were obtained using a sonication time of 5 min.The overall applicability of the ultrasonic-based sample treatment method is shown by the analysis of five urine samples. The results are similar to those achieved by the routine procedure. The new method is fast, robust, and allows high sample throughput.
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Affiliation(s)
- M Galesio
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnología, Universidade Nova de Lisboa, 2829-516 Monte de Caparica, Portugal
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Overview on modern approaches to speed up protein identification workflows relying on enzymatic cleavage and mass spectrometry-based techniques. Anal Chim Acta 2009; 650:151-9. [DOI: 10.1016/j.aca.2009.07.034] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 07/14/2009] [Accepted: 07/15/2009] [Indexed: 11/19/2022]
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21
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López-Ferrer D, Heibeck TH, Petritis K, Hixson KK, Qian W, Monroe ME, Mayampurath A, Moore RJ, Belov ME, Camp DG, Smith RD. Rapid sample processing for LC-MS-based quantitative proteomics using high intensity focused ultrasound. J Proteome Res 2008; 7:3860-7. [PMID: 18686986 DOI: 10.1021/pr800161x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new sample processing workflow that uses high intensity focused ultrasound to rapidly reduce and alkylate cysteines, digest proteins and then label peptides with (18)O was developed for quantitative proteomics applications. Each step was individually refined to minimize reaction times, peptide loses and undesired byproducts or modifications. When this novel workflow was used, mouse plasma proteins were successfully denatured, alkylated, in-solution digested, and (18)O-labeled in <10 min for subsequent analysis by liquid chromatography-electrospray ionization high resolution mass spectrometry. Performance was evaluated in terms of the number of mouse plasma peptides and proteins identified in a shotgun approach and the quantitative dynamic range. The results were compared with previously published results obtained using conventional sample preparation methods and were found to be similar. Advantages of the new method include greatly simplified and accelerated sample processing, as well as being readily amenable to automation.
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Affiliation(s)
- Daniel López-Ferrer
- Biological Science Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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