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Zhou Z, Ren H, Zhou L, Wang P, Lou X, Zou H, Cao Y. Recent Development on Determination of Low-Level 90Sr in Environmental and Biological Samples: A Review. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010090. [PMID: 36615288 PMCID: PMC9821828 DOI: 10.3390/molecules28010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
In the context of the rapid development of the world's nuclear power industry, it is vital to establish reliable and efficient radioanalytical methods to support sound environment and food radioactivity monitoring programs and a cost-effective waste management strategy. As one of the most import fission products generated during human nuclear activities, 90Sr has been widely determined based on different analytical techniques for routine radioactivity monitoring, emergency preparedness and radioactive waste management. Herein, we summarize and critically review analytical methods developed over the last few decades for the determination of 90Sr in environmental and biological samples. Approaches applied in different steps of the analysis including sample preparation, chemical separation and detection are systematically discussed. The recent development of modern materials for 90Sr concentration and advanced instruments for rapid 90Sr measurement are also addressed.
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Affiliation(s)
| | | | | | | | | | | | - Yiyao Cao
- Correspondence: ; Tel.: +86-(0571)-87115089
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2
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Bottom-up sample preparation for the LC-MS/MS quantification of anti-cancer monoclonal antibodies in bio matrices. Bioanalysis 2020; 12:1405-1425. [PMID: 32975434 DOI: 10.4155/bio-2020-0204] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) are rapidly taking over the treatment of many malignancies, and an astonishing number of mAbs is in development. This causes a high demand for quantification of mAbs in biomatrices both for measuring therapeutic mAb concentrations and to support pharmacokinetics and pharmacodynamics studies. Conventionally, ligand-binding assays are used for these purposes, but LC-MS is gaining popularity. Although intact (top-down) and subunit (middle-down) mAb quantification is reported, signature peptide (bottom-up) quantification is currently most advantageous. This review provides an overview of the reported bottom-up mAb quantification methods in biomatrices as well as general recommendations regarding signature peptide and internal standard selection, reagent use and optimization of digestion in bottom-up quantification methods.
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Rivera-Albarran ME, Ray SJ. A Novel Combined Microstrip Resonator/Nanospray Ionization Source for Microwave-Assisted Trypsin Digestion of Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1684-1696. [PMID: 32573245 DOI: 10.1021/jasms.0c00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Enzymatic digestion of proteins is a critical step in bottom-up and middle-down proteomics. Here, we demonstrate a method for decreasing the time required for proteolytic digestion of proteins from multiple hours to minutes by using an in-line microstrip cavity for programmed microwave heating. When a nanospray emitter tip, containing a digestion sample, is exposed to a region of highly focused microwave field, the rate of proteolytic digestion is enhanced and the time required for digestion greatly decreased. The design is advantageous for mass spectrometry because the solution-based digestion can then be directly sprayed from a nanoelectrospray tip emitter, decreasing sample transfer loss and allowing the system to be used in a flow-through proteolytic workflow. Microwave-assisted digestion using this method is evaluated against standard overnight digestion protocols using a variety of proteins, evaluating sequence coverage and observed peptide location, digestion rate, and overall efficacy. The influence of applied microwave power is investigated, and enzymatic kinetic parameters are evaluated to estimate temperature within the microreactor. Finally, the modulation of the proteolytic digestion of proteins based upon the modulation of applied microwave power is demonstrated on a time scale of seconds in a flow-through system.
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Affiliation(s)
- Maria E Rivera-Albarran
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
| | - Steven J Ray
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, United States
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4
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Lee JH, Kim HH, Ko JY, Jang JH, Kim GH, Lee JS, Nah JW, Jeon YJ. Rapid preparation of functional polysaccharides from Pyropia yezoensis by microwave-assistant rapid enzyme digest system. Carbohydr Polym 2016; 153:512-517. [PMID: 27561523 DOI: 10.1016/j.carbpol.2016.07.122] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 07/18/2016] [Accepted: 07/31/2016] [Indexed: 12/26/2022]
Abstract
This study describes a simple preparation of functional polysaccharides from Pyropia yezoensis using a microwave-assistant rapid enzyme digest system (MAREDS) with various carbohydrases, and evaluates their antioxidative effects. Polysaccharide hydrolysates were prepared using MAREDS under different hydrolytic conditions of the carbohydrases and microwave powers. Polysaccharides less than 10kDa (Low molecular weight polysaccharides, LMWP, ≤10kDa) were efficiently obtained using an ultrafiltration (molecular weight cut-off of 10kDa). MAREDS increases AMG activation via an increased degree of hydrolysis; the best AMG hydrolysate was prepared using a 10:1 ratio of substrate to enzyme for 2h in MAREDS with 400W. LMWP consisted of galactose (27.3%), glucose (64.5%), and mannose (8.3%) from the AMG hydrolysate had stronger antioxidant effects than the high molecular weight polysaccharides (>10kDa). We rapidly prepared functional LMWPs by using MAREDS with carbohydrases, and suggest that LMWP might be potentially a valuable algal polysaccharide antioxidant.
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Affiliation(s)
- Ji-Hyeok Lee
- Department of Marine Life Science, Jeju National University, Jeju 690-756, Republic of Korea
| | - Hyung-Ho Kim
- Department of Marine Life Science, Jeju National University, Jeju 690-756, Republic of Korea
| | - Ju-Young Ko
- Department of Marine Life Science, Jeju National University, Jeju 690-756, Republic of Korea
| | - Jun-Ho Jang
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of Pittsburgh and VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, USA
| | - Gwang-Hoon Kim
- Department of Biology, College of Natural Sciences, Kongju National University, Kongju 314-701, Republic of Korea
| | - Jung-Suck Lee
- Industry-Academic Cooperation Foundation, Jeju National University, Jeju 690-756, Republic of Korea
| | - Jae-Woon Nah
- Department of High Polymer Engineering, Sunchon National University, Jungang-ro, Suncheon, Jeollanam-do, Republic of Korea.
| | - You-Jin Jeon
- Department of Marine Life Science, Jeju National University, Jeju 690-756, Republic of Korea.
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5
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Bronsema KJ, Bischoff R, van de Merbel NC. High-Sensitivity LC-MS/MS Quantification of Peptides and Proteins in Complex Biological Samples: The Impact of Enzymatic Digestion and Internal Standard Selection on Method Performance. Anal Chem 2013; 85:9528-35. [DOI: 10.1021/ac4015116] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kees J. Bronsema
- Analytical Biochemistry, Department
of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Bioanalytical
Laboratory, PRA, Early Development Services, Westerbrink 3, 9405 BJ, Assen, The Netherlands
| | - Rainer Bischoff
- Analytical Biochemistry, Department
of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Nico C. van de Merbel
- Analytical Biochemistry, Department
of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- Bioanalytical
Laboratory, PRA, Early Development Services, Westerbrink 3, 9405 BJ, Assen, The Netherlands
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6
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Evaluating the potential nonthermal microwave effects of microwave-assisted proteolytic reactions. J Proteomics 2013; 80:160-70. [DOI: 10.1016/j.jprot.2013.01.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 01/09/2013] [Accepted: 01/09/2013] [Indexed: 11/18/2022]
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7
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Damm M, Nusshold C, Cantillo D, Rechberger GN, Gruber K, Sattler W, Kappe CO. Can electromagnetic fields influence the structure and enzymatic digest of proteins? A critical evaluation of microwave-assisted proteomics protocols. J Proteomics 2012; 75:5533-43. [PMID: 22889711 PMCID: PMC3484400 DOI: 10.1016/j.jprot.2012.07.043] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/27/2012] [Accepted: 07/27/2012] [Indexed: 10/31/2022]
Abstract
This study reevaluates the putative advantages of microwave-assisted tryptic digests compared to conventionally heated protocols performed at the same temperature. An initial investigation of enzyme stability in a temperature range of 37-80 °C demonstrated that trypsin activity declines sharply at temperatures above 60 °C, regardless if microwave dielectric heating or conventional heating is employed. Tryptic digests of three proteins of different size (bovine serum albumin, cytochrome c and β-casein) were thus performed at 37 °C and 50 °C using both microwave and conventional heating applying accurate internal fiber-optic probe reaction temperature measurements. The impact of the heating method on protein degradation and peptide fragment generation was analyzed by SDS-PAGE and MALDI-TOF-MS. Time-dependent tryptic digestion of the three proteins and subsequent analysis of the corresponding cleavage products by MALDI-TOF provided virtually identical results for both microwave and conventional heating. In addition, the impact of electromagnetic field strength on the tertiary structure of trypsin and BSA was evaluated by molecular mechanics calculations. These simulations revealed that the applied field in a typical laboratory microwave reactor is 3-4 orders of magnitude too low to induce conformational changes in proteins or enzymes.
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Affiliation(s)
- Markus Damm
- Christian Doppler Laboratory for Microwave Chemistry (CDLMC) and Institute of Chemistry, Karl-Franzens-University Graz, Heinrichstrasse 28/I, A-8010 Graz, Austria
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Pellet digestion: a simple and efficient sample preparation technique for LC-MS/MS quantification of large therapeutic proteins in plasma. Bioanalysis 2012; 4:17-28. [PMID: 22191591 DOI: 10.4155/bio.11.286] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND There is a need for a simple and efficient sample preparation technique for LC-MS/MS quantification of large therapeutic proteins in plasma. RESULTS The sample preparation technique presented here is based upon trypsin digestion of the pellet obtained following precipitation of the protein analyte from plasma. The pellet digestion technique was shown to facilitate efficient digestion of large therapeutic proteins, with concomitant removal of a substantial amount of potentially problematic plasma phospholipids. The technique was successfully applied to a pharmacokinetic study of a large therapeutic protein. CONCLUSION This simple sample preparation approach will be beneficial to bioanalytical laboratories engaged in the LC-MS/MS quantification of large therapeutic proteins in biological matrices.
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Dycka F, Bobal P, Mazanec K, Bobalova J. Rapid and efficient protein enzymatic digestion: an experimental comparison. Electrophoresis 2011; 33:288-95. [PMID: 22170586 DOI: 10.1002/elps.201100123] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 08/02/2011] [Accepted: 08/10/2011] [Indexed: 11/08/2022]
Abstract
The major objective of proteomics is to identify and examine the large numbers of proteins extracted from complex biological systems. This is generally achieved by combining various techniques of protein separation with a mass spectrometric analysis of proteins that are digested enzymatically. Recently, several alternatives to this standard protocol have been developed for efficient and fast protein digestion. One option is the use of modified trypsin instead of native trypsin for the in-gel digestion of proteins. Microwave, ultrasonic-assisted protein enzymatic digestion and proteolysis accelerated by infrared radiation are other suitable alternatives. The application of the variable performance of the fast enzymatic digestion of proteins by using different techniques is reported here. The advantage of these methods is to have the ability to detect proteins in a shorter span of time. For example, using alternative protein digestion takes only minutes, in contrast to the several hours required by conventional methods. To demonstrate the suitability of this fast procedure, the digestion of carbonic anhydrase, bovine serum albumin, lysozyme and proteins extracted from plants (Hordeum vulgare, Arabidopsis thaliana) were used. Considering that the required reaction time for the conventional method is much longer, these applied methodic approaches tend to give in-gel digestion a much higher efficiency rating. This study examines the fast, efficient and low-cost proteolytic strategies for the digestion process, and for protein identification based on the use of ultrasound and infrared technology. In addition, comparisons of the applied techniques were studied. Several differences were found, suggesting the potential use of proteolysis accelerated by infrared radiation.
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Affiliation(s)
- Filip Dycka
- Institute of Analytical Chemistry of the ASCR, Brno, Czech Republic
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10
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Zong W, Liu R, Guo C, Sun F. Novel biomarkers of protein oxidation sites and degrees using horse cytochrome c as the target by mass spectrometry. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 78:1581-1586. [PMID: 21377407 DOI: 10.1016/j.saa.2011.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 01/27/2011] [Accepted: 02/07/2011] [Indexed: 05/30/2023]
Abstract
Biomarkers held both incredible application and significant challenge in probing the oxidation mechanisms of proteins under oxidative stress. Here, mass spectrometry (MS) coupled with liquid chromatography (LC) was applied to establish a new pipeline to probe the oxidation sites and degrees of horse cytochrome c (HCC) with its oxidative products serving as the biomarkers. Samples of native and UV/H(2)O(2) oxidized HCCs were digested by trypsin and subjected to biomarker discovery using LC/MS and tandem mass spectrometry (MS/MS). Experiment results proved that the main oxidation sites were located at Cys(14), Cys(17), Met(65) and Met(80) residues in peptides C(14)AQC(heme)HTVEK(22), C(14)AQCHTVEK(22), E(60)ETLMEYLENPKK(73), M(80)IFAGIK(86) and M(80)IFAGIKK(87). Quantitative analysis on the oxidized peptides showed the oxidation degrees of target sites had positive correlations with extended oxidation dose and controlled by residues types and their accessibility to solvent molecules. Being able to provide plentiful information for the oxidation sites and oxidation degrees, the identified oxidized products were feasibility biomarkers for HCC oxidation, compared with the conventional protein carbonyl assay.
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Affiliation(s)
- Wansong Zong
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Shandong University, Jinan, PR China
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11
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Segu ZM, Hammad LA, Mechref Y. Rapid and efficient glycoprotein identification through microwave-assisted enzymatic digestion. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:3461-3468. [PMID: 21072803 DOI: 10.1002/rcm.4774] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Identification of protein glycosylation sites is analytically challenging due to the diverse glycan structures associated with a glycoprotein. Mass spectrometry (MS)-based identification and characterization of glycoproteins has been achieved predominantly with the bottom-up approach, which typically involves the enzymatic cleavage of proteins to peptides prior to LC/MS or LC/MS/MS analysis. However, the process can be challenging due to the structural variations and steric hindrance imposed by the attached glycans. Alternatives to conventional heating protocols, that increase the rate of enzymatic cleavage of glycoproteins, may aid in addressing these challenges. An enzymatic digestion of a glycoprotein can be accelerated and made more efficient through microwave-assisted digestion. In this paper, a systematic study was conducted to explore the efficiency of microwave-assisted enzymatic (trypsin) digestion (MAED) of glycoproteins as compared with the conventional method. In addition, the optimum experimental parameters for the digestion such as temperature, reaction time, and microwave radiation power were investigated. It was determined that efficient tryptic digestion of glycoproteins was attained in 15 min, allowing comparable if not better sequence coverage through LC/MS/MS analysis. Optimum tryptic cleavage was achieved at 45°C irrespective of the size and complexity of the glycoprotein. Moreover, MAED allowed the detection and identification of more peptides and subsequently higher sequence coverage for all model glycoprotein. MAED also did not appear to prompt a loss or partial cleavage of the glycan moieties attached to the peptide backbones.
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Affiliation(s)
- Zaneer M Segu
- METACyt Biochemical Analysis Center, Department of Chemistry, Indiana University, Bloomington, IN 47405, USA
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12
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Lin YJ, Le GW, Wang JY, Li YX, Shi YH, Sun J. Antioxidative peptides derived from enzyme hydrolysis of bone collagen after microwave assisted acid pre-treatment and nitrogen protection. Int J Mol Sci 2010; 11:4297-308. [PMID: 21151439 PMCID: PMC3000083 DOI: 10.3390/ijms11114297] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 10/21/2010] [Accepted: 10/21/2010] [Indexed: 11/16/2022] Open
Abstract
This study focused on the preparation method of antioxidant peptides by enzymatic hydrolysis of bone collagen after microwave assisted acid pre-treatment and nitrogen protection. Phosphoric acid showed the highest ability of hydrolysis among the four other acids tested (hydrochloric acid, sulfuric acid and/or citric acid). The highest degree of hydrolysis (DH) was 9.5% using 4 mol/L phosphoric acid with a ratio of 1:6 under a microwave intensity of 510 W for 240 s. Neutral proteinase gave higher DH among the four protease tested (Acid protease, neutral protease, Alcalase and papain), with an optimum condition of: (1) ratio of enzyme and substrate, 4760 U/g; (2) concentration of substrate, 4%; (3) reaction temperature, 55 °C and (4) pH 7.0. At 4 h, DH increased significantly (P < 0.01) under nitrogen protection compared with normal microwave assisted acid pre-treatment hydrolysis conditions. The antioxidant ability of the hydrolysate increased and reached its maximum value at 3 h; however DH decreased dramatically after 3 h. Microwave assisted acid pre-treatment and nitrogen protection could be a quick preparatory method for hydrolyzing bone collagen.
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Affiliation(s)
- Yun-Jian Lin
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; E-Mails: (Y.-J.L.); (J.-Y.W.); (Y.-X.L.)
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; E-Mails: (Y.-H.S.); (J.S.)
| | - Guo-Wei Le
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; E-Mails: (Y.-J.L.); (J.-Y.W.); (Y.-X.L.)
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; E-Mails: (Y.-H.S.); (J.S.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-510-85917789; Fax: +86-510-85917789
| | - Jie-Yun Wang
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; E-Mails: (Y.-J.L.); (J.-Y.W.); (Y.-X.L.)
| | - Ya-Xin Li
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; E-Mails: (Y.-J.L.); (J.-Y.W.); (Y.-X.L.)
| | - Yong-Hui Shi
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; E-Mails: (Y.-J.L.); (J.-Y.W.); (Y.-X.L.)
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; E-Mails: (Y.-H.S.); (J.S.)
| | - Jin Sun
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China; E-Mails: (Y.-J.L.); (J.-Y.W.); (Y.-X.L.)
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; E-Mails: (Y.-H.S.); (J.S.)
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Alam A, Mataj A, Yang Y, Boysen RI, Bowden DK, Hearn MTW. Rapid Microwave-Assisted Chemical Cleavage - Mass Spectrometric Method for the Identification of Hemoglobin Variants in Blood. Anal Chem 2010; 82:8922-30. [DOI: 10.1021/ac1017106] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Asif Alam
- ARC Special Research Centre for Green Chemistry, Monash University, Clayton, Victoria, Australia 3800, and Thalassaemia Service, Monash Medical Centre, Melbourne, Australia
| | - Agron Mataj
- ARC Special Research Centre for Green Chemistry, Monash University, Clayton, Victoria, Australia 3800, and Thalassaemia Service, Monash Medical Centre, Melbourne, Australia
| | - Yuanzhong Yang
- ARC Special Research Centre for Green Chemistry, Monash University, Clayton, Victoria, Australia 3800, and Thalassaemia Service, Monash Medical Centre, Melbourne, Australia
| | - Reinhard I. Boysen
- ARC Special Research Centre for Green Chemistry, Monash University, Clayton, Victoria, Australia 3800, and Thalassaemia Service, Monash Medical Centre, Melbourne, Australia
| | - Donald K. Bowden
- ARC Special Research Centre for Green Chemistry, Monash University, Clayton, Victoria, Australia 3800, and Thalassaemia Service, Monash Medical Centre, Melbourne, Australia
| | - Milton T. W. Hearn
- ARC Special Research Centre for Green Chemistry, Monash University, Clayton, Victoria, Australia 3800, and Thalassaemia Service, Monash Medical Centre, Melbourne, Australia
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14
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Kulkarni KP, Ramarathinam SH, Friend J, Yeo L, Purcell AW, Perlmutter P. Rapid microscale in-gel processing and digestion of proteins using surface acoustic waves. LAB ON A CHIP 2010; 10:1518-20. [PMID: 20517556 DOI: 10.1039/c001501f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A new method for in-gel sample processing and tryptic digestion of proteins is described. Sample preparation, rehydration, in situ digestion and peptide extraction from gel slices are dramatically accelerated by treating the gel slice with surface acoustic waves (SAWs). Only 30 minutes total workflow time is required for this new method to produce base peak chromatograms (BPCs) of similar coverage and intensity to those observed for traditional processing and overnight digestion. Simple set up, good reproducibility, excellent peptide recoveries, rapid turnover of samples and high confidence protein identifications put this technology at the fore-front of the next generation of proteomics sample processing tools.
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Affiliation(s)
- Ketav P Kulkarni
- School of Chemistry, Monash University, PO Box 23, Melbourne, 3800, Australia
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15
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Accelerated digestion for high-throughput proteomics analysis of whole bacterial proteomes. J Microbiol Methods 2010; 80:56-62. [DOI: 10.1016/j.mimet.2009.10.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2009] [Revised: 10/27/2009] [Accepted: 10/29/2009] [Indexed: 11/21/2022]
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16
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Lesur A, Varesio E, Hopfgartner G. Accelerated tryptic digestion for the analysis of biopharmaceutical monoclonal antibodies in plasma by liquid chromatography with tandem mass spectrometric detection. J Chromatogr A 2009; 1217:57-64. [PMID: 19939394 DOI: 10.1016/j.chroma.2009.11.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 10/29/2009] [Accepted: 11/02/2009] [Indexed: 11/27/2022]
Abstract
Accelerated tryptic digestion of a therapeutic protein including microwave irradiation and thermal transfer by convection at 60 degrees C and 37 degrees C was investigated. An analytical setup was devised to follow the protein digestion rate using 1D gel electrophoresis and liquid chromatography coupled a triple quadrupole linear ion trap mass spectrometer. The formation kinetic of its tryptic peptides was monitored in the selected monitoring mode (LC-SRM/MS). Different digestion end points (e.g. 2, 5, 10, 15, 30 and 60min) as well as an overnight digestion were tested using a therapeutic human monoclonal antibody (mAb) with the goal of its LC-SRM/MS quantification in human plasma. The peptides from the human mAb were generated at different rates and were classified into three categories: (1) the fast forming peptides, (2) the slow forming peptides and (3) the peptides degrading over time. For many monitored peptides, a heating temperature of 37 degrees C with a 750rpm mixing applied for at least 30min provided equivalent results to microwave-assisted digestion and generally allowed the achievement of an equivalent peptide concentration as an overnight digestion carried out at 37 degrees C. The disappearance of the protein of the heavy and light chains can be monitored by 1D gel electrophoresis but was found not to be representative of the final tryptic peptide concentrations. For quantitative purposes a stable isotope labeled version ((13)C(4), (15)N(1)) of the therapeutic protein was used. The labeled protein as internal standard was found to be very efficient to compensate for incomplete digestion or losses during sample preparation.
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Affiliation(s)
- Antoine Lesur
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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17
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Berna M, Ackermann B. Increased Throughput for Low-Abundance Protein Biomarker Verification by Liquid Chromatography/Tandem Mass Spectrometry. Anal Chem 2009; 81:3950-6. [DOI: 10.1021/ac9002744] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael Berna
- Eli Lilly and Company, Drug Disposition Biomarker Group, Lilly Corporate Center, Indianapolis, Indiana, 46285
| | - Bradley Ackermann
- Eli Lilly and Company, Drug Disposition Biomarker Group, Lilly Corporate Center, Indianapolis, Indiana, 46285
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18
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Stencel LM, Kormos CM, Avery KB, Leadbeater NE. Assessment and use of two silicon carbide multi-well plates for library synthesis and proteolytic digests using microwave heating. Org Biomol Chem 2009; 7:2452-7. [DOI: 10.1039/b902112d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Rapid method for sensitive screening of oligosaccharide epitopes in the lipooligosaccharide from Campylobacter jejuni strains isolated from Guillain-Barré syndrome and Miller Fisher syndrome patients. J Clin Microbiol 2008; 46:3429-36. [PMID: 18753342 DOI: 10.1128/jcm.00681-08] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter jejuni lipooligosaccharide (LOS) can trigger Guillain-Barré syndrome (GBS) due to its similarity to human gangliosides. Rapid and accurate structural elucidation of the LOS glycan of a strain isolated from a GBS patient could help physicians determine the spectrum of anti-ganglioside antibodies likely to be found and therefore provide valuable assistance in establishing an appropriate course of treatment. The ability of implemented mass spectrometry-based approaches in a clinical setting has been limited by the laborious and time-consuming nature of the protocols, typically 3 to 4 days, used to prepare LOS. In order to improve the analytical throughput, microwave-assisted enzymatic digestion was investigated. In this study, the bacterial cells were suspended in 50 microl of 20 mM ammonium acetate buffer containing DNase and RNase and treated by direct microwave irradiation for 3 min. Then, proteinase K was added and the samples were again microwaved. The intact LOS samples were analyzed using electrophoresis-assisted open-tubular liquid chromatography-mass spectrometry. The reliability of the rapid, high-throughput technique was demonstrated through analysis of LOS glycans from 73 C. jejuni strains. The structure was elucidated using material from a single colony. The total time for sample preparation and MS analysis is less than 60 min.
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Turapov OA, Mukamolova GV, Bottrill AR, Pangburn MK. Digestion of native proteins for proteomics using a thermocycler. Anal Chem 2008; 80:6093-9. [PMID: 18578500 DOI: 10.1021/ac702527b] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient protein digestion is a critical step for successful mass spectrometry analysis. Here we describe simultaneous tryptic digestion and gradual unfolding of native proteins by application of a temperature gradient using a single cycle of 5 min or less in a PCR thermocycler. Chemicals typically used for chromatographic techniques did not affect the digestion efficiency. Tryptic digestion was performed in a small volume (3 microL) with 1.5 microg of trypsin without denaturing agents. This rapid procedure yielded more peptides than conventional methods utilizing chemical denaturation for 18 proteins out of 20. Samples were directly spotted on the MALDI-TOF target plate, without additional purification, thus reducing losses on reversed-phase resins.
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Affiliation(s)
- Obolbek A Turapov
- Department of Biochemistry, Center for Biomedical Research, University of Texas Health Science Center, Tyler, Texas 75708, USA.
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21
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Mirzaei H, McBee JK, Watts J, Aebersold R. Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol Cell Proteomics 2008; 7:813-23. [PMID: 18089551 PMCID: PMC2401334 DOI: 10.1074/mcp.m700495-mcp200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 12/13/2007] [Indexed: 11/06/2022] Open
Abstract
Absolute quantification of peptides by mass spectrometry requires a reference, frequently using heavy isotope-coded peptides as internal standards. These peptides have traditionally been generated by chemical stepwise synthesis. Recently a new way to supply such peptides was described in which nucleotide sequences coding for the respective peptides are concatenated into a synthetic gene (QconCAT). These QconCATs are then expressed to produce a polypeptide consisting of concatenated peptides, purified, quantified by various methods, and then digested to yield the final internal standard peptides. Although both of these methods for peptide production are routinely used for absolute quantifications, there is currently no information regarding the accuracy of the quantifications made in each case. In this study, we used sets of synthetic and biological peptides in parallel to evaluate the accuracy of either method. We also addressed some technical issues regarding the preparation and proper utilization of such standard peptides. Twenty-five peptides derived from the Caenorhabditis elegans proteome were selected for this study. Twenty-four were successfully chemically synthesized. Five QconCAT genes were designed, each a concatenation of the same 25 peptides but each in separate, different randomized order, and expressed via in vitro translation reactions that contained heavy isotope-labeled lysine and arginine. Three of the five QconCATs were successfully produced. Different digestion conditions, including various detergents and incubation conditions, were tested to find those optimal for the generation of a reproducible and accurate reference sample mixture. All three QconCAT polypeptides were then digested using the optimized conditions and then mixed in a 1:1 ratio with their synthetic counterparts. Multireaction monitoring mass spectrometry was then used for quantification. Results showed that the digestion protocol had a significant impact on equimolarity of final peptides, confirming the need for optimization. Under optimal conditions, however, most QconCAT peptides were produced at an equimolar ratio. A few QconCAT-derived peptides were largely overestimated due to problems with solubilization or stability of the synthetic peptides. Although the order in which the peptide sequences appeared in the QconCAT sequence proved to affect the success rate of in vitro translation, it did not significantly affect the final peptide yields. Overall neither the chemical synthesis nor the recombinant genetic approach proved to be superior as a method for the production of reference peptides for absolute quantification.
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Affiliation(s)
- Hamid Mirzaei
- Institute for Systems Biology, Seattle, Washington 98103, USA
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22
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Lill JR, Ingle ES, Liu PS, Pham V, Sandoval WN. Microwave-assisted proteomics. MASS SPECTROMETRY REVIEWS 2007; 26:657-71. [PMID: 17474122 DOI: 10.1002/mas.20140] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
State-of-the-art proteomic analysis has recently undergone a rapid evolution; with more high-throughput analytical instrumentation and informatic tools available, sample preparation is becoming one of the rate-limiting steps in protein characterization workflows. Recently several protocols have appeared in the literature that employ microwave irradiation as a tool for the preparation of biological samples for subsequent mass spectrometric characterization. Techniques for microwave-assisted bio-catalyzed reactions (including sample reduction and alkylation, enzymatic and chemical digestion, removal and analysis of post-translational modifications and characterization of enzymes and protein-interaction sites) are described. This review summarizes the various approaches undertaken, instrumentation employed, and reduction in overall experimental time observed when microwave assistance is applied.
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Affiliation(s)
- Jennie R Lill
- Protein Chemistry Department, Genentech Inc, South San Francisco, CA 94080, USA.
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23
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Granvogl B, Plöscher M, Eichacker LA. Sample preparation by in-gel digestion for mass spectrometry-based proteomics. Anal Bioanal Chem 2007; 389:991-1002. [PMID: 17639354 DOI: 10.1007/s00216-007-1451-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Revised: 06/14/2007] [Accepted: 06/20/2007] [Indexed: 10/23/2022]
Abstract
The proteomic characterization of proteins and protein complexes from cells and cell organelles is the next challenge for investigation of the cell. After isolation of the cell compartment, three steps have to be performed in the laboratory to yield information about the proteins present. The protein mixtures must be separated into single species, broken down into peptides, and, finally, identified by mass spectrometry. Most scientists engaged in proteomics separate proteins by electrophoresis. For characterization and identification of proteomes, mass spectrometry of peptides is the method of choice. To combine electrophoresis and mass spectrometry, sample preparation by "in-gel digestion" has been developed. Many procedures are available for in-gel digestion, which inspired us to review in-gel digestion approaches.
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Affiliation(s)
- Bernhard Granvogl
- Department für Biologie I, Ludwig-Maximilians-Universität, Menzinger Strasse 67, 80638, München, Germany
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24
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Slysz GW, Lewis DF, Schriemer DC. Detection and identification of sub-nanogram levels of protein in a nanoLC-trypsin-MS system. J Proteome Res 2007; 5:1959-66. [PMID: 16889418 DOI: 10.1021/pr060142d] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proteomic workflows involving liquid-based protein separations are an alternative to gel-based protein analysis, however the trypsin digestion procedure is usually difficult to implement, particularly when processing low abundance proteins from capillary column effluent. To convert the protein to peptides for the purpose of identification, current protocols require several sample handling steps, and sample losses become an issue. In this study, we present an improved system that conducts reversed-phase protein chromatography and rapid on-line tryptic digestion requiring sub-nanogram quantities of protein. This system employs a novel mirror-gradient concept that allows for dynamic titration of the column effluent to create optimal conditions for real-time tryptic digestion. The purpose behind this development was to improve the limits of detection of the online concept, to support flow-based alternatives to gel-based proteomics and to simplify the characterization of low abundance proteins. Using test mixtures of proteins, we show that peptide mass fingerprinting with high sequence representation can be easily achieved at the 20 fmol level, with detection limits down to 5 fmol (85 pg myoglobin). Limits of identification using standard data-dependent MS/MS experiments are as low as 10 fmol. These results suggest that the nanoLC-trypsin-MS/MS system could represent an alternative to the conventional "1D-gel to MS" proteomic strategy.
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Affiliation(s)
- Gordon W Slysz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada, T2N 4N1
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25
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Leadbeater NE, Stencel LM, Wood EC. Probing the effects of microwave irradiation on enzyme-catalysed organic transformations: the case of lipase-catalysed transesterification reactions. Org Biomol Chem 2007; 5:1052-5. [PMID: 17377658 DOI: 10.1039/b617544a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The lipase-catalysed transesterification reaction of methyl acetoacetate in toluene as a solvent has been studied using carefully controlled conditions. Results suggest that microwave heating does not have a noticeable effect on reaction rate or product conversion.
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Affiliation(s)
- Nicholas E Leadbeater
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT 06269-3060, USA.
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Abstract
As the range of techniques for microwave heating has expanded, so have the areas in which it can have a profound impact. Two emerging areas are the application of microwave heating for the synthesis of peptides, peptoids, oligopeptides and carbohydrates and in the field of proteomics.
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