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Abstract
In-gel digestion of protein spots derived from two-dimensional gels and their subsequent identification by mass spectrometry is involved in a multitude of mass spectrometry-driven proteomic experiments, including fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). This type of proteomic methodology has been involved in the establishment of comparative proteome maps and in the identification of differentially expressed proteins and their isoforms in health and disease. Most in-gel digestion protocols follow a number of common steps including excision of the protein spots of interest, destaining, reduction and alkylation (for silver-stained gels), and dehydration and overnight digestion with the proteolytic enzyme of choice. While trypsin has been a mainstay of peptide digestion for many years, it does have its shortcomings, particularly related to incomplete peptide digestion, and this has led to a rise in popularity for other proteolytic enzymes either used alone or in combination. This chapter discusses the alternative enzymes available and describes the process of in-gel digestion using the enzyme trypsin.
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Affiliation(s)
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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2
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Recent advances in the fabrication and application of nanomaterial-based enzymatic microsystems in chemical and biological sciences. Anal Chim Acta 2019; 1067:31-47. [DOI: 10.1016/j.aca.2019.02.031] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 02/09/2019] [Accepted: 02/12/2019] [Indexed: 11/24/2022]
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3
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Naldi M, Tramarin A, Bartolini M. Immobilized enzyme-based analytical tools in the -omics era: Recent advances. J Pharm Biomed Anal 2018; 160:222-237. [DOI: 10.1016/j.jpba.2018.07.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 02/01/2023]
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4
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Abstract
In-gel digestion of protein spots derived from two-dimensional gels and their subsequent identification by mass spectrometry is involved in a multitude of mass spectrometry-driven proteomic experiments, including fluorescence difference gel electrophoresis (DIGE). This type of proteomic methodology has been involved in the establishment of comparative proteome maps and in the identification of differentially expressed proteins and protein isoforms in health and disease. Most in-gel digestion protocols follow a number of common steps including excision of the protein spots of interest, de-staining, reduction and alkylation (for silver-stained gels), dehydration and overnight digestion with the proteolytic enzyme of choice. While trypsin has been a mainstay of peptide digestion for many years, it does have its shortcomings, particularly related to incomplete peptide digestion, and this has led to a rise in popularity for other proteolytic enzymes either used alone or in combination. This chapter discusses the alternative enzymes available and describes the process of in-gel digestion using the enzyme trypsin.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
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5
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Towards automation in protein digestion: Development of a monolithic trypsin immobilized reactor for highly efficient on-line digestion and analysis. Talanta 2017; 167:143-157. [DOI: 10.1016/j.talanta.2017.02.016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/03/2017] [Accepted: 02/04/2017] [Indexed: 01/04/2023]
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6
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Wang B, Shangguan L, Wang S, Zhang L, Zhang W, Liu F. Preparation and application of immobilized enzymatic reactors for consecutive digestion with two enzymes. J Chromatogr A 2016; 1477:22-29. [DOI: 10.1016/j.chroma.2016.11.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 11/14/2016] [Accepted: 11/18/2016] [Indexed: 11/26/2022]
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7
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Preparation and evaluation of dual-enzyme microreactor with co-immobilized trypsin and chymotrypsin. J Chromatogr A 2016; 1440:45-54. [DOI: 10.1016/j.chroma.2016.02.070] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/22/2016] [Accepted: 02/23/2016] [Indexed: 11/22/2022]
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8
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Tian M, Mohamed AC, Wang S, Yang L. On-plate enzyme and inhibition assay of glucose-6-phosphate dehydrogenase using thin-layer chromatography. J Sep Sci 2015; 38:2907-14. [DOI: 10.1002/jssc.201500159] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Miaomiao Tian
- Faculty of Chemistry; Northeast Normal University; Changchun Jilin China
| | | | - Shengtian Wang
- Faculty of Chemistry; Northeast Normal University; Changchun Jilin China
| | - Li Yang
- Faculty of Chemistry; Northeast Normal University; Changchun Jilin China
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9
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Investigation of bi-enzymatic reactor based on hybrid monolith with nanoparticles embedded and its proteolytic characteristics. J Chromatogr A 2015; 1388:158-66. [DOI: 10.1016/j.chroma.2015.02.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 12/11/2022]
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10
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Yuan H, Zhang L, Zhang Y. Preparation of high efficiency and low carry-over immobilized enzymatic reactor with methacrylic acid-silica hybrid monolith as matrix for on-line protein digestion. J Chromatogr A 2014; 1371:48-57. [PMID: 25456586 DOI: 10.1016/j.chroma.2014.10.067] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 09/05/2014] [Accepted: 10/20/2014] [Indexed: 11/28/2022]
Abstract
In this work, a novel kind of organic-silica hybrid monolith based immobilized enzymatic reactor (IMER) was developed. The monolithic support was prepared by a single step "one-pot" strategy via the polycondensation of tetramethoxysilane and vinyltrimethoxysilane and in situ copolymerization of methacrylic acid and vinyl group on the precondensed siloxanes with ammonium persulfate as the thermal initiator. Subsequently, the monolith was activated by N-(3-dimethylaminopropyl) - N'-ethylcarbodiimide (EDC) and N-hydroxysuccinimide (NHS), followed by the modification of branched polyethylenimine (PEI) to improve the hydrophilicity. Finally, after activated by EDC and NHS, trypsin was covalently immobilized onto the monolithic support. The performance of such a microreactor was evaluated by the in sequence digestion of bovine serum albumin (BSA) and myoglobin, followed by MALDI-TOF-MS analysis. Compared to those obtained by traditional in-solution digestion, not only higher sequence coverages for BSA (74±1.4% vs. 59.5±2.7%, n=6) and myoglobin (93±3% vs. 81±4.5%, n=6) were obtained, but also the digestion time was shortened from 24h to 2.5 min, demonstrating the high digestion efficiency of such an IMER. The carry-over of these two proteins on the IMER was investigated, and peptides from BSA could not be found in mass spectrum of myoglobin digests, attributed to the good hydrophilicity of our developed monolithic support. Moreover, the dynamic concentration range for protein digestion was proved to be four orders of magnitude, and the IMER could endure at least 7-day consecutive usage. Furthermore, such an IMER was coupled with nano-RPLC-ESI/MS/MS for the analysis of extracted proteins from Escherichia coli. Compared to formerly reported silica hybrid monolith based IMER and the traditional in-solution counterpart, by our developed IMER, although the identified protein number was similar, the identified distinct peptide number was improved by 7% and 25% respectively, beneficial to improve the reliability of protein identification. The IMER was further online integrated with two-dimensional nano-HPLC-MS/MS system for the analysis of protein extracts from hepatocellular carcinoma (HCC) cells with low metastasis rate, and more than 3000 protein groups were identified, with only 46 proteins identified from the residues of the IMER. All these results demonstrated that such a hybrid monolith based IMER would be of great promise in the high throughput and high confidence proteome analysis.
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Affiliation(s)
- Huiming Yuan
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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11
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Comparison of activity behaviors of particle based and monolithic immobilized enzyme reactors operated in semi-micro-liquid chromatography system. Sep Purif Technol 2013. [DOI: 10.1016/j.seppur.2013.07.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Vlakh EG, Tennikova TB. Flow-through immobilized enzyme reactors based on monoliths: II. Kinetics study and application. J Sep Sci 2013; 36:1149-67. [DOI: 10.1002/jssc.201201090] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 12/17/2012] [Accepted: 12/17/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Evgenia G. Vlakh
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
| | - Tatiana B. Tennikova
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
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Vlakh EG, Tennikova TB. Flow-through immobilized enzyme reactors based on monoliths: I. Preparation of heterogeneous biocatalysts. J Sep Sci 2013; 36:110-27. [DOI: 10.1002/jssc.201200594] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Revised: 08/13/2012] [Accepted: 08/13/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Evgenia G. Vlakh
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
| | - Tatiana B. Tennikova
- Institute of Macromolecular Compounds; Russian Academy of Sciences; St. Petersburg Russia
- Faculty of Chemistry; Saint-Petersburg State University; St. Petersburg Russia
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14
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Abstract
New analytical platforms have been developed in response to the need for attaining increased peak capacity for multicomponent complex analysis with higher sensitivity and characterization of the analytes, and high-throughput capabilities. This review outlines the fundamental principles of target and comprehensive 2D LC method development and encompasses applications of LC–LC and LC × LC coupled to MS in bioanalysis using a variety of online analytical procedures. It also provides a rationale for the usage of the most employed mass analyzers and ionization sources on these platforms.
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15
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Çelebi B, Bayraktar A, Tuncel A. Synthesis of a monolithic, micro-immobilised enzyme reactor via click-chemistry. Anal Bioanal Chem 2012; 403:2655-63. [DOI: 10.1007/s00216-012-6075-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 04/19/2012] [Accepted: 04/21/2012] [Indexed: 10/28/2022]
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16
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Stastna M, Van Eyk JE. Investigating the secretome: lessons about the cells that comprise the heart. CIRCULATION. CARDIOVASCULAR GENETICS 2012; 5:o8-o18. [PMID: 22337932 PMCID: PMC3282018 DOI: 10.1161/circgenetics.111.960187] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cell/environment interface is composed of the proteins of plasma membrane which face the extracellular space and by the proteins secreted directly by the cell of origin or by neighboring cells. The secreted proteins can act as extracellular matrix proteins and/or autocrine/paracrine proteins. This report discusses the technical aspects involved in the identification and characterization of the secreted proteins of specific cell types that comprise the heart. These aspects include the culturing of the cells, cell co-culturing and quantitative labeling, conditioned media collection and dealing with high abundant serum proteins, post-translational modification enrichment, the use of protein separation methods and mass spectrometry, protein identification and validation and the incorporation of pathway analysis to better understand the novel discovery on the background of already known experimental biological systems. The proteomic methods have the solid emplacement in cardiovascular research and the identification of proteins secreted by cardiac cells has been used in various applications such as determination the specificity between secretomes of different cell types, e.g. cardiac stem cells and cardiac myocytes, for the global secretome screening of e.g. human arterial smooth muscle cells, for the mapping of the beneficial effect of conditioned medium of one cell type on the other cell type, e.g. conditioned medium of human mesenchymal stem cells on cardiac myocytes, and for the searching the candidate paracrine factors and potential biomarkers.
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Affiliation(s)
- Miroslava Stastna
- Johns Hopkins Bayview Proteomics Center, Department of Medicine, Division of Cardiology, School of Medicine, Johns Hopkins University, Baltimore, MD 21224, USA.
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17
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Vermachova M, Purkrtova Z, Santrucek J, Jolivet P, Chardot T, Kodicek M. New protein isoforms identified within Arabidopsis thaliana seed oil bodies combining chymotrypsin/trypsin digestion and peptide fragmentation analysis. Proteomics 2011; 11:3430-4. [PMID: 21751352 DOI: 10.1002/pmic.201000603] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Plant seed oil bodies, subcellular lipoprotein inclusions providing storage reserves, are composed of a neutral lipid core surrounded by a phospholipid monolayer with several integrated proteins that play a significant role in stabilization of the particles and probably also in lipid mobilization. Oil bodies' proteins are generally very hydrophobic, due to the long uncharged sequences anchoring them into the lipid core, which makes them extremely difficult to handle and to digest successfully. Although oil bodies have been intensively studied during last decades, not all their proteins have been identified yet. To overcome the problems connected with their identification, a method based on SDS-PAGE, in-gel digestion and LC-MS/MS analysis was used. Digestion was carried out with trypsin and chymotrypsin, single or in combination, which increased significantly the number of identified peptides, namely the hydrophobic ones. Thanks to this methodology it was possible to achieve an extensive coverage of proteins studied, to analyze their N-terminal modifications and moreover, to detect four new oil bodies' protein isoforms, which demonstrates the complexity of oil bodies' protein composition.
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Affiliation(s)
- Martina Vermachova
- Institute of Chemical Technology Prague, Department of Biochemistry and Microbiology, Prague, Czech Republic.
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18
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Kool J, Jonker N, Irth H, Niessen WMA. Studying protein-protein affinity and immobilized ligand-protein affinity interactions using MS-based methods. Anal Bioanal Chem 2011; 401:1109-25. [PMID: 21755271 PMCID: PMC3151372 DOI: 10.1007/s00216-011-5207-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 06/12/2011] [Accepted: 06/24/2011] [Indexed: 12/31/2022]
Abstract
This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein-protein and protein-immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of protein-protein and protein-immobilized ligand interactions are discussed. Presently, this field of research is often called interactomics or interaction proteomics. A slightly different approach that will be discussed, chemical proteomics, allows one to analyze selectivity profiles of ligands for multiple drug targets and off-targets. Additionally, of particular interest is the use of surface plasmon resonance technologies coupled with MS for the study of protein interactions. The review addresses the principle of each of the methods with a focus on recent developments and the applicability to lead compound generation in drug discovery as well as the elucidation of protein interactions involved in cellular processes. The review focuses on the analysis of bioaffinity interactions of proteins with other proteins and with ligands, where the proteins are considered as the bioactives analyzed by MS.
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Affiliation(s)
- Jeroen Kool
- BioMolecular Analysis, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands.
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19
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Tran BQ, Hernandez C, Waridel P, Potts A, Barblan J, Lisacek F, Quadroni M. Addressing Trypsin Bias in Large Scale (Phospho)proteome Analysis by Size Exclusion Chromatography and Secondary Digestion of Large Post-Trypsin Peptides. J Proteome Res 2010; 10:800-11. [DOI: 10.1021/pr100951t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bao Quoc Tran
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Celine Hernandez
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Patrice Waridel
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Alexandra Potts
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Jachen Barblan
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Frederique Lisacek
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
| | - Manfredo Quadroni
- Center for Integrative Genomics, University of Lausanne, Batiment Genopode, 1015 Lausanne, Switzerland, and Swiss Institute of Bioinformatics, CMU-Rue Michel-Servet 1, 1211 Geneva 4 Geneva, Switzerland
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Multidigestion in continuous flow tandem protease-immobilized microreactors for proteomic analysis. Anal Biochem 2010; 407:12-8. [DOI: 10.1016/j.ab.2010.07.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 06/09/2010] [Accepted: 07/23/2010] [Indexed: 11/17/2022]
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