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Nickerson JL, Doucette AA. Maximizing Cumulative Trypsin Activity with Calcium at Elevated Temperature for Enhanced Bottom-Up Proteome Analysis. BIOLOGY 2022; 11:biology11101444. [PMID: 36290348 PMCID: PMC9598648 DOI: 10.3390/biology11101444] [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: 08/24/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Simple Summary Trypsin is frequently employed to cleave proteins ahead of mass spectrometry characterization. Traditionally, enzyme digestion involves overnight incubation of proteins at 37 °C, which is time consuming though still may yield poor digestion efficiency. While raising the temperature should theoretically accelerate the digestion, it also destabilizes the enzyme and promotes trypsin de-activation. We therefore questioned whether elevated temperature is beneficial for improving tryptic digestion. Here, we quantify protein digestion kinetics at elevated temperatures for calcium-stabilized trypsin and enforce the critical importance of calcium ions to preserve the enzyme. We quantitatively demonstrate that 1 h at 47 °C provides a superior digest when compared to conventional (overnight, 37 °C) processing of the proteome. The practical impact of our enhanced digestion protocol is shown through bottom-up mass spectrometry analysis of a complex proteome mixture. Abstract Bottom-up proteomics relies on efficient trypsin digestion ahead of MS analysis. Prior studies have suggested digestion at elevated temperature to accelerate proteolysis, showing an increase in the number of MS-identified peptides. However, improved sequence coverage may be a consequence of partial digestion, as higher temperatures destabilize and degrade the enzyme, causing enhanced activity to be short-lived. Here, we use a spectroscopic (BAEE) assay to quantify calcium-stabilized trypsin activity over the complete time course of a digestion. At 47 °C, the addition of calcium contributes a 25-fold enhancement in trypsin stability. Higher temperatures show a net decrease in cumulative trypsin activity. Through bottom-up MS analysis of a yeast proteome extract, we demonstrate that a 1 h digestion at 47 °C with 10 mM Ca2+ provides a 29% increase in the total number of peptide identifications. Simultaneously, the quantitative proportion of peptides with 1 or more missed cleavage sites was diminished in the 47 °C digestion, supporting enhanced digestion efficiency with the 1 h protocol. Trypsin specificity also improves, as seen by a drop in the quantitative abundance of semi-tryptic peptides. Our enhanced digestion protocol improves throughput for bottom-up sample preparation and validates the approach as a robust, low-cost alternative to maximized protein digestion efficiency.
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2
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Robinson MR, Vasicek LA, Hoppmann C, Li M, Jokhadze G, Spellman DS. Improving the throughput of immunoaffinity purification and enzymatic digestion of therapeutic proteins using membrane-immobilized reagent technology. Analyst 2020; 145:3148-3156. [PMID: 32191233 DOI: 10.1039/d0an00190b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Continued interest in protein therapeutics has motivated the development of improved bioanalytical tools to support development programs. LC-MS offers specificity, sensitivity, and multiplexing capabilities without the need for target-specific reagents, making it a valuable alternative to ligand binding assays. Immunoaffinity purification (IP) and enzymatic digestion are critical, yet extensive and time-consuming components of the "gold standard" bottom-up approach to LC-MS-based protein quantitation. In the present work, commercially available technology, based on membrane-immobilized reagents in spin column and plate format, is applied to reduce IP and digestion times from hours to minutes. For a standard monoclonal antibody, the lower limit of quantitation was 0.1 ng μL-1 compared to 0.05 ng μL-1 for the standard method. A pharmacokinetics (PK) study dosing Herceptin in rat was analyzed by both the membrane and the standard method with a total sample processing time of 4 h and 20 h, respectively. The calculated concentrations at each time point agreed within 8% between both methods, and PK values including area under the curve (AUC), half-life (T1/2), mean residence time (MRT), clearance (CL), and volume of distribution (Vdss) agreed within 6% underscoring the utility of the membrane methodology for quantitative bioanalysis workflows.
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Affiliation(s)
- Michelle R Robinson
- Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA.
| | - Lisa A Vasicek
- Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA.
| | | | - Mandy Li
- Takara Bio USA, Inc., Mountain View, CA, USA
| | | | - Daniel S Spellman
- Department of Pharmacokinetics Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., West Point, PA, USA.
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3
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González-García E, Marina ML, García MC. Nanomaterials in Protein Sample Preparation. SEPARATION & PURIFICATION REVIEWS 2019. [DOI: 10.1080/15422119.2019.1581216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Estefanía González-García
- Departamento de Química Analítica, Química Física e Ingeniería Química, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| | - María Luisa Marina
- Departamento de Química Analítica, Química Física e Ingeniería Química, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
| | - María Concepción García
- Departamento de Química Analítica, Química Física e Ingeniería Química, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, Alcalá de Henares, Madrid, Spain
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4
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Liu W, Pang Y, Tan HY, Patel N, Jokhadze G, Guthals A, Bruening ML. Enzyme-containing spin membranes for rapid digestion and characterization of single proteins. Analyst 2018; 143:3907-3917. [PMID: 30039812 DOI: 10.1039/c8an00969d] [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
Proteolytic digestion is an important step in characterizing protein sequences and post-translational modifications (PTMs) using mass spectrometry (MS). This study uses pepsin- or trypsin-containing spin membranes for rapid digestion of single proteins or simple protein mixtures prior to ultrahigh-resolution Orbitrap MS analysis. Centrifugation of 100 μL of pretreated protein solutions through the functionalized membranes requires less than 1 min and conveniently digests proteins into large peptides that aid in confirming specific protein sequence variations and PTMs. Peptic and tryptic peptides from spin digestion of apomyoglobin and four commercial monoclonal antibodies (mAbs) typically cover 100% of the protein sequences in direct infusion MS analysis. Increasing the spin rate leads to a higher fraction of large peptic peptides for apomyoglobin, and MS analysis of peptic and tryptic peptides reveals mAb PTMs such as N-terminal pyroglutamate formation, C-terminal lysine clipping and glycosylation. Relative to overnight in-solution digestion of mAbs, spin digestion yields higher sequence coverages. Spin-membrane digestion followed by infusion MS readily differentiates a mAb to the Ebola virus from a related antibody that differs by addition of a single amino acid.
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Affiliation(s)
- Weijing Liu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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5
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Modh H, Scheper T, Walter JG. Aptamer-Modified Magnetic Beads in Biosensing. SENSORS 2018; 18:s18041041. [PMID: 29601533 PMCID: PMC5948603 DOI: 10.3390/s18041041] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/21/2018] [Accepted: 03/26/2018] [Indexed: 01/27/2023]
Abstract
Magnetic beads (MBs) are versatile tools for the purification, detection, and quantitative analysis of analytes from complex matrices. The superparamagnetic property of magnetic beads qualifies them for various analytical applications. To provide specificity, MBs can be decorated with ligands like aptamers, antibodies and peptides. In this context, aptamers are emerging as particular promising ligands due to a number of advantages. Most importantly, the chemical synthesis of aptamers enables straightforward and controlled chemical modification with linker molecules and dyes. Moreover, aptamers facilitate novel sensing strategies based on their oligonucleotide nature that cannot be realized with conventional peptide-based ligands. Due to these benefits, the combination of aptamers and MBs was already used in various analytical applications which are summarized in this article.
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Affiliation(s)
- Harshvardhan Modh
- Institute of Technical Chemistry, Leibniz University of Hannover, Hannover 30167, Germany.
| | - Thomas Scheper
- Institute of Technical Chemistry, Leibniz University of Hannover, Hannover 30167, Germany.
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6
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Zhai R, Yuan Y, Jiao F, Hao F, Fang X, Zhang Y, Qian X. Facile synthesis of magnetic metal organic frameworks for highly efficient proteolytic digestion used in mass spectrometry-based proteomics. Anal Chim Acta 2017; 994:19-28. [DOI: 10.1016/j.aca.2017.08.048] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 08/23/2017] [Accepted: 08/26/2017] [Indexed: 12/12/2022]
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7
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Dulay MT, Eberlin LS, Zare RN. Protein Analysis by Ambient Ionization Mass Spectrometry Using Trypsin-Immobilized Organosiloxane Polymer Surfaces. Anal Chem 2015; 87:12324-30. [PMID: 26567450 DOI: 10.1021/acs.analchem.5b03669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In the growing field of proteomic research, rapid and simple protein analysis is a crucial component of protein identification. We report the use of immobilized trypsin on hybrid organic-inorganic organosiloxane (T-OSX) polymers for the on-surface, in situ digestion of four model proteins: melittin, cytochrome c, myoglobin, and bovine serum albumin. Tryptic digestion products were sampled, detected, and identified using desorption electrospray ionization mass spectrometry (DESI-MS) and nanoDESI-MS. These novel, reusable T-OSX arrays on glass slides allow for protein digestion in methanol:water solvents (1:1, v/v) and analysis directly from the same polymer surface without the need for sample preparation, high temperature, and pH conditions typically required for in-solution trypsin digestions. Digestion reactions were conducted with 2 μL protein sample droplets (0.35 mM) at incubation temperatures of 4, 25, 37, and 65 °C and digestion reaction times between 2 and 24 h. Sequence coverages were dependent on the hydrophobicity of the OSX polymer support and varied by temperature and digestion time. Under the best conditions, the sequence coverages, determined by DESI-MS, were 100% for melittin, 100% for cytochrome c, 90% for myoglobin, and 65% for bovine serum albumin.
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Affiliation(s)
- Maria T Dulay
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Livia S Eberlin
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Richard N Zare
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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8
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Derr L, Steckbeck S, Dringen R, Colombi Ciacchi L, Treccani L, Rezwan K. Assessment of the Proteolytic Activity of α-Chymotrypsin Immobilized on Colloidal Particles by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry. ANAL LETT 2014. [DOI: 10.1080/00032719.2014.951449] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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9
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Abstract
Sample preparation has lagged far behind the evolution of instrumentation used in mass-linked protein analysis. Trypsin digestion, for example, still takes a day, as it did 50 years ago, while mass spectral analyses are achieved in seconds. Higher order structure of proteins is frequently modified by varying digestion conditions: shifting the initial points of trypsin cleavage, changing digestion pathways, accelerating peptide bond demasking and altering the distribution of miscleaved products at the completion of proteolysis. Reduction and alkylation are even circumvented in many cases. This review focuses on immobilized enzyme reactor technology as a means to achieve accelerated trypsin digestion by exploiting these phenomena.
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10
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Cho YT, Chen CW, Chen MP, Hu JL, Su H, Shiea J, Wu WJ, Wu DC. Diagnosis of albuminuria by tryptic digestion and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry. Clin Chim Acta 2013; 420:76-81. [DOI: 10.1016/j.cca.2012.12.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2012] [Accepted: 12/17/2012] [Indexed: 11/25/2022]
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11
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Pečová M, Šebela M, Marková Z, Poláková K, Čuda J, Šafářová K, Zbořil R. Thermostable trypsin conjugates immobilized to biogenic magnetite show a high operational stability and remarkable reusability for protein digestion. NANOTECHNOLOGY 2013; 24:125102. [PMID: 23466477 DOI: 10.1088/0957-4484/24/12/125102] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this work, magnetosomes produced by microorganisms were chosen as a suitable magnetic carrier for covalent immobilization of thermostable trypsin conjugates with an expected applicability for efficient and rapid digestion of proteins at elevated temperatures. First, a biogenic magnetite was isolated from Magnetospirillum gryphiswaldense and its free surface was coated with the natural polysaccharide chitosan containing free amino and hydroxy groups. Prior to covalent immobilization, bovine trypsin was modified by conjugating with α-, β- and γ-cyclodextrin. Modified trypsin was bound to the magnetic carriers via amino groups using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydroxysulfosuccinimide as coupling reagents. The magnetic biomaterial was characterized by magnetometric analysis and electron microscopy. With regard to their biochemical properties, the immobilized trypsin conjugates showed an increased resistance to elevated temperatures, eliminated autolysis, had an unchanged pH optimum and a significant storage stability and reusability. Considering these parameters, the presented enzymatic system exhibits properties that are superior to those of trypsin forms obtained by other frequently used approaches. The proteolytic performance was demonstrated during in-solution digestion of model proteins (horseradish peroxidase, bovine serum albumin and hen egg white lysozyme) followed by mass spectrometry. It is shown that both magnetic immobilization and chemical modification enhance the characteristics of trypsin making it a promising tool for protein digestion.
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Affiliation(s)
- M Pečová
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 11, 783 71 Olomouc, Czech Republic
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12
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Switzar L, Giera M, Niessen WMA. Protein Digestion: An Overview of the Available Techniques and Recent Developments. J Proteome Res 2013; 12:1067-77. [DOI: 10.1021/pr301201x] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Switzar
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Martin Giera
- Division of Molecular Cell Physiology,
Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilfried M. A. Niessen
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
- hyphen MassSpec, de Wetstraat 8, 2332 XT Leiden, The Netherlands
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13
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Shen Y, Guo W, Qi L, Qiao J, Wang F, Mao L. Immobilization of trypsin via reactive polymer grafting from magnetic nanoparticles for microwave-assisted digestion. J Mater Chem B 2013; 1:2260-2267. [DOI: 10.1039/c3tb20116c] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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14
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Netto CG, Toma HE, Andrade LH. Superparamagnetic nanoparticles as versatile carriers and supporting materials for enzymes. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.08.010] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Li Y, Zhang X, Deng C. Functionalized magnetic nanoparticles for sample preparation in proteomics and peptidomics analysis. Chem Soc Rev 2013; 42:8517-39. [DOI: 10.1039/c3cs60156k] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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16
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Krenkova J, Foret F, Svec F. Less common applications of monoliths: V. Monolithic scaffolds modified with nanostructures for chromatographic separations and tissue engineering. J Sep Sci 2012; 35:1266-83. [DOI: 10.1002/jssc.201100956] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jana Krenkova
- Institute of Analytical Chemistry of the ASCR; Brno; Czech Republic
| | - Frantisek Foret
- Institute of Analytical Chemistry of the ASCR; Brno; Czech Republic
| | - Frantisek Svec
- The Molecular Foundry; E. O. Lawrence Berkeley National Laboratory; Berkeley; California; USA
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17
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Park EH, Song JS, Kim HJ. Sequence Coverage Enhancement Using Magnetic Nanoparticles in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometric Protein Analysis. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.3.987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Vale G, Santos HM, Carreira RJ, Fonseca L, Miró M, Cerdà V, Reboiro-Jato M, Capelo JL. An assessment of the ultrasonic probe-based enhancement of protein cleavage with immobilized trypsin. Proteomics 2011; 11:3866-76. [PMID: 21805637 DOI: 10.1002/pmic.201100200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 04/17/2011] [Accepted: 07/11/2011] [Indexed: 11/07/2022]
Abstract
The use of ultrasonic probe, in conjunction with immobilized trypsin, has been explored in this work for potential enhancement of protein digestion. Several solid supports commonly used to immobilize trypsin were subjected to different ultrasonication amplitudes and time in order to investigate their mechanical resistance to ultrasonic energy when provided by the ultrasonic probe. Glass beads and magnetic particles were found to remain intact in most conditions studied. It was found that immobilized trypsin cannot be reused after ultrasonication since the enzymatic activity was greatly diminished. For comparative purposes, vortex shaking was also explored for protein cleavage. Four standard proteins--bovine serum albumin, α-lactalbumin, carbonic anhydrase and ovalbumin--were successfully identified using peptide mass fingerprint, or peptide fragment fingerprint. In addition, the performance of the classical protein cleavage (overnight, 12 h) and the ultrasonic methods was found to be similar when the digestion of a complex proteome, human plasma, was assessed through 18-O quantification. The digestion yields found were 90-117% for the ultrasonic and 5-21% for the vortex when those methods were compared with the classical overnight digestion.
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Affiliation(s)
- Gonçalo Vale
- REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa, Monte da Caparica, Portugal
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19
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Zhou J. Fast trypsin digestion of proteins on a cross-linked [Os(dmebpy)(2)Cl](+/2+)-derivatized copolymer of acrylamide and vinylimidazole column. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:2236-2244. [PMID: 20607841 DOI: 10.1002/rcm.4635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Fast digestion of proteins was observed when they were loaded together with trypsin onto the cross-linked [Os(dmebpy)(2)Cl](+/2+)-derivatized copolymer of acrylamide and vinylimidazole column. The insoluble Os-complexed polymer particles were packed into an electrospray tip to monitor peptides eluted during loading, washing and elution periods with a mass spectrometer. The proteolytic cleavage of proteins was observed immediately when the mixture of trypsin and substrates in 0.2 mM ammonium bicarbonate 50:50 H(2)O/acetonitrile reached the column tip, and continued through the loading period. Some tryptic peptides were released from the column during the loading and following washing periods. The others still stayed on the column until the low pH elution buffer reached the column. If a protein was first loaded onto the column, no tryptic peptides of the protein were observed when trypsin was loaded later for the on-column digestion. Only the autolysis peptides of trypsin were observed. On-column digestion of 100 fmol myoglobin was successfully detected with a low sensitivity quadrupole mass spectrometer. A hybrid Os-polymer/C(18) column tip was constructed for the online trypsin digestion of proteins in the aqueous buffers and the following trapping and elution of peptides from the C(18) column. The digestion of reduced and alkylated bovine serum albumin and human transferrin in 2.5 mM ammonium bicarbonate and 0.2 M urea buffer was observed on the column, with more peptide coverage than conventional 4 h in-solution digestion at 37 degrees C. Control experiments without the Os-polymer in the column tip excluded the spontaneous in-solution digestion of proteins in the short time window of buffer delivery onto the column, indirectly confirming the contribution of Os-polymer on the fast trypsin digestion.
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Affiliation(s)
- Jie Zhou
- The Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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20
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Kim J, Kim BC, Lopez-Ferrer D, Petritis K, Smith RD. Nanobiocatalysis for protein digestion in proteomic analysis. Proteomics 2010; 10:687-99. [PMID: 19953546 DOI: 10.1002/pmic.200900519] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The process of protein digestion is a critical step for successful protein identification in bottom-up proteomic analyses. To substitute the present practice of in-solution protein digestion, which is long, tedious, and difficult to automate, many efforts have been dedicated for the development of a rapid, recyclable and automated digestion system. Recent advances of nanobiocatalytic approaches have improved the performance of protein digestion by using various nanomaterials such as nanoporous materials, magnetic nanoparticles, and polymer nanofibers. Especially, the unprecedented success of trypsin stabilization in the form of trypsin-coated nanofibers, showing no activity decrease under repeated uses for 1 year and retaining good resistance to proteolysis, has demonstrated its great potential to be employed in the development of automated, high-throughput, and on-line digestion systems. This review discusses recent developments of nanobiocatalytic approaches for the improved performance of protein digestion in speed, detection sensitivity, recyclability, and trypsin stability. In addition, we also introduce approaches for protein digestion under unconventional energy input for protein denaturation and the development of microfluidic enzyme reactors that can benefit from recent successes of these nanobiocatalytic approaches.
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Affiliation(s)
- Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Anam-dong, Seongbuk-gu, Seoul, Republic of Korea.
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21
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Superparamagnetic maghemite nanoparticles from solid-state synthesis – Their functionalization towards peroral MRI contrast agent and magnetic carrier for trypsin immobilization. Biomaterials 2009; 30:2855-63. [DOI: 10.1016/j.biomaterials.2009.02.023] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Accepted: 02/12/2009] [Indexed: 11/24/2022]
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22
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Magnetic particle-based hybrid platforms for bioanalytical sensors. SENSORS 2009; 9:2976-99. [PMID: 22574058 PMCID: PMC3348820 DOI: 10.3390/s90402976] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 04/13/2009] [Accepted: 04/23/2009] [Indexed: 11/17/2022]
Abstract
Biomagnetic nano and microparticles platforms have attracted considerable interest in the field of biological sensors due to their interesting physico-chemical properties, high specific surface area, good mechanical stability and opportunities for generating magneto-switchable devices. This review discusses recent advances in the development and characterization of active biomagnetic nanoassemblies, their interaction with biological molecules and their use in bioanalytical sensors.
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23
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Cheng CY, Yuan CH, Cheng SC, Huang MZ, Chang HC, Cheng TL, Yeh CS, Shiea J. Electrospray-Assisted Laser Desorption/Ionization Mass Spectrometry for Continuously Monitoring the States of Ongoing Chemical Reactions in Organic or Aqueous Solution under Ambient Conditions. Anal Chem 2008; 80:7699-705. [DOI: 10.1021/ac800952e] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chi-Yuan Cheng
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan, National Sun Yat-Sen University—Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan, Graduate Institute of Medicine, and Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, and Department of Chemistry, National Cheng-Kung University, Tainan, Taiwan
| | - Cheng-Hui Yuan
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan, National Sun Yat-Sen University—Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan, Graduate Institute of Medicine, and Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, and Department of Chemistry, National Cheng-Kung University, Tainan, Taiwan
| | - Sy-Chyi Cheng
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan, National Sun Yat-Sen University—Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan, Graduate Institute of Medicine, and Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, and Department of Chemistry, National Cheng-Kung University, Tainan, Taiwan
| | - Min-Zong Huang
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan, National Sun Yat-Sen University—Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan, Graduate Institute of Medicine, and Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, and Department of Chemistry, National Cheng-Kung University, Tainan, Taiwan
| | - Hui-Chiu Chang
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan, National Sun Yat-Sen University—Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan, Graduate Institute of Medicine, and Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, and Department of Chemistry, National Cheng-Kung University, Tainan, Taiwan
| | - Tien-Lu Cheng
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan, National Sun Yat-Sen University—Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan, Graduate Institute of Medicine, and Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, and Department of Chemistry, National Cheng-Kung University, Tainan, Taiwan
| | - Chen-Sheng Yeh
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan, National Sun Yat-Sen University—Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan, Graduate Institute of Medicine, and Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, and Department of Chemistry, National Cheng-Kung University, Tainan, Taiwan
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung, Taiwan, National Sun Yat-Sen University—Kaohsiung Medical University Joint Research Center, Kaohsiung, Taiwan, Graduate Institute of Medicine, and Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan, and Department of Chemistry, National Cheng-Kung University, Tainan, Taiwan
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24
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Pershina AG, Sazonov AE, Milto IV. Application of magnetic nanoparticles in biomedicine. BULLETIN OF SIBERIAN MEDICINE 2008. [DOI: 10.20538/1682-0363-2008-2-70-78] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The use of nanomaterials offers many advantages due to their unique properties. They can be used as building blocks for the fabrication of various functional diagnostic systems and agents of therapy. This article focuses on the application of magnetic nanoparticles in biomedicine such as magnetic separation, biosensor, contrast agents for MRI (magnetic resonance imaging), local operated hyperthermic treatment of tumors, drug delivery, gene therapy, tissue engineering.
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25
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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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26
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Tran BQ, Pepaj M, Lundanes E, Greibrokk T. On‐line Method for Identification of Native Proteins using pH‐Gradient SAX Chromatography and Reversed Phase Chromatography‐Mass Spectrometry of Tryptic Peptides. J LIQ CHROMATOGR R T 2008. [DOI: 10.1080/10826070802039291] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bao Quoc Tran
- a Department of Chemistry , University of Oslo , Oslo, Norway
| | - Miliam Pepaj
- a Department of Chemistry , University of Oslo , Oslo, Norway
| | - Elsa Lundanes
- a Department of Chemistry , University of Oslo , Oslo, Norway
| | - Tyge Greibrokk
- a Department of Chemistry , University of Oslo , Oslo, Norway
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