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Song J, Campbell L, Vinqvist-Tymchuk M. Application of quantitative proteomics to investigate fruit ripening and eating quality. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153766. [PMID: 35921768 DOI: 10.1016/j.jplph.2022.153766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/30/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
The consumption of fruit and vegetables play an important role in human nutrition, dietary diversity and health. Fruit and vegetable industries impart significant impact on our society, economy, and environment, contributing towards sustainable development in both developing and developed countries. The eating quality of fruit is determined by its appearance, color, firmness, flavor, nutritional components, and the absence of defects from physiological disorders. However, all of these components are affected by many pre- and postharvest factors that influence fruit ripening and senescence. Significant efforts have been made to maintain and improve fruit eating quality by expanding our knowledge of fruit ripening and senescence, as well as by controlling and reducing losses. Innovative approaches are required to gain better understanding of the management of eating quality. With completion of the genome sequence for many horticultural products in recent years and development of the proteomic research technique, quantitative proteomic research on fruit is changing rapidly and represents a complementary research platform to address how genetics and environment influence the quality attributes of various produce. Quantiative proteomic research on fruit is advancing from protein abundance and protein quantitation to gene-protein interactions and post-translational modifications of proteins that occur during fruit development, ripening and in response to environmental influences. All of these techniques help to provide a comprehensive understanding of eating quality. This review focuses on current developments in the field as well as limitations and challenges, both in broad term and with specific examples. These examples include our own research experience in applying quantitative proteomic techniques to identify and quantify the protein changes in association with fruit ripening, quality and development of disorders, as well as possible control mechanisms.
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Affiliation(s)
- Jun Song
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada.
| | - Leslie Campbell
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada
| | - Melinda Vinqvist-Tymchuk
- Agriculture and Agri-Food Canada. KRDC, Kentville Research and Development Centre, Kentville, Nova Scotia, B4N 1J5, Canada
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2
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Thormann W, Mosher RA. Dynamic computer simulations of electrophoresis: 2010-2020. Electrophoresis 2021; 43:10-36. [PMID: 34287996 PMCID: PMC9292373 DOI: 10.1002/elps.202100191] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/12/2021] [Accepted: 07/15/2021] [Indexed: 02/05/2023]
Abstract
The transport of components in liquid media under the influence of an applied electric field can be described with the continuity equation. It represents a nonlinear conservation law that is based upon the balance laws of continuous transport processes and can be solved in time and space numerically. This procedure is referred to as dynamic computer simulation. Since its inception four decades ago, the state of dynamic computer simulation software and its use has progressed significantly. Dynamic models are the most versatile tools to explore the fundamentals of electrokinetic separations and provide insights into the behavior of buffer systems and sample components of all electrophoretic separation methods, including moving boundary electrophoresis, CZE, CGE, ITP, IEF, EKC, ACE, and CEC. This article is a continuation of previous reviews (Electrophoresis 2009, 30, S16–S26 and Electrophoresis 2010, 31, 726–754) and summarizes the progress and achievements made during the 2010 to 2020 time period in which some of the existing dynamic simulators were extended and new simulation packages were developed. This review presents the basics and extensions of the three most used one‐dimensional simulators, provides a survey of new one‐dimensional simulators, outlines an overview of multi‐dimensional models, and mentions models that were briefly reported in the literature. A comprehensive discussion of simulation applications and achievements of the 2010 to 2020 time period is also included.
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Affiliation(s)
- Wolfgang Thormann
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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3
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Lai A, Kinhal V, Nuzhat Z, Menon R, Rice GE, Salomon C. Proteomics Method to Identification of Protein Profiles in Exosomes. Methods Mol Biol 2018; 1710:139-153. [PMID: 29197000 DOI: 10.1007/978-1-4939-7498-6_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Exosomes are membrane-bound nanovesicles that transport molecular signals (e.g., proteins) between cells and are released from a wide range of cells, including the human placenta. Interestingly, the levels of exosomes present in maternal circulation are higher in preeclamptic pregnancies and their protein content profile change in response to the microenvironment milieu. Through the discovery of candidate biomarkers, mass spectrometry (MS)-based proteomics may provide a better understanding of the pathophysiology underlying pregnancy-associated disorders. With advances in sample preparation techniques, computational methodologies, and bioinformatics, MS-based proteomics have addressed the challenge of identifying and quantifying thousands of proteins and peptides from a variety of complex biological samples. Despite increasing interest in biomarker diagnostics, the complex nature of biological matrices (e.g., plasma) poses a challenge for candidate biomarker discovery. Here we describe a workflow to prepare exosomes for proteomic analysis.
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Affiliation(s)
- Andrew Lai
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Bldg. 71/918, Royal Brisbane Hospital, Brisbane, QLD, 4029, Australia
| | - Vyjayanthi Kinhal
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Bldg. 71/918, Royal Brisbane Hospital, Brisbane, QLD, 4029, Australia
| | - Zarin Nuzhat
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Bldg. 71/918, Royal Brisbane Hospital, Brisbane, QLD, 4029, Australia
| | - Ramkumar Menon
- Division of Maternal-Fetal Medicine & Perinatal Research, Department of Obstetrics & Gynecology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA.,Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Gregory E Rice
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Bldg. 71/918, Royal Brisbane Hospital, Brisbane, QLD, 4029, Australia.,Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Carlos Salomon
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, The University of Queensland, Bldg. 71/918, Royal Brisbane Hospital, Brisbane, QLD, 4029, Australia. .,Department of Biochemistry & Molecular Biology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA. .,Department of Clinical Biochemistry and Immunology, Faculty of Pharmacy, University of Concepción, Concepción, Chile.
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Ghanbari R, Ebrahimpour A. Separation and identification of bromelain-generated antibacterial peptides from Actinopyga lecanora. Food Sci Biotechnol 2017; 27:591-598. [PMID: 30263784 DOI: 10.1007/s10068-017-0267-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/16/2017] [Accepted: 11/15/2017] [Indexed: 11/24/2022] Open
Abstract
Actinopyga lecanora, as a rich protein source was hydrolysed to generate antibacterial bioactive peptides using different proteolytic enzymes. Bromelain hydrolysate, after 1 h hydrolysis, exhibited the highestantibacterial activities against Pseudomonas aeruginosa, Pseudomonas sp., Escherichia coli and Staphylococcus aureus. Two dimensional fractionation strategies, using a semi-preparative RP-HPLC and an isoelectric-focusing electrophoresis, were applied for peptide profiling. Furthermore, UPLC-QTOF-MS was used for peptides identification; 12 peptide sequences were successfully identified. The antibacterial activity of purified peptides from A. lecanora on P. aeruginosa, Pseudomonas sp., E. coli and S. aureus was investigated. These identified peptides exhibited growth inhibition against P. aeruginosa, Pseudomonas sp., E. coli and S. aureus with values ranging from 18.80 to 75.30%. These results revealed that the A. lecanora would be used as an economical protein source for the production of high value antibacterial bioactive peptides.
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Affiliation(s)
| | - Afshin Ebrahimpour
- 2Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Malaysia
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Kraiem H, Zouari F, Abderrazek RB, Manon Y, Ayeb ME, Fillaudeau L, Bedoui J, Bouhaouala-Zahar B. Two-Dimensional Isoelectric Focusing OFFGEL, Micro-Fluidic Lab-on-Chip Electrophoresis and FTIR for Assessment of Long-Term Stability of rhG-CSF Formulation. IEEE Trans Nanobioscience 2017; 16:694-702. [PMID: 29053450 DOI: 10.1109/tnb.2017.2763779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recombinant human granulocyte colony-stimulating factor (rhG-CSF) has been increasingly recognized from among one of the most abundant families of biosimilars. Upon long-term storage, the rhG-CSF is subject to subtle chemical modifications that rapidly occur and, in particular, produce deaminated variants with divergent charge. Indeed, changes in charge from glutamine deamination may alter the way rhG-SCF will refold and the structure of resulting molecule. To assess this charge heterogeneity, 2-D gel electrophoresis has limited application. Recent micro-fluidic- based technical advances offer a great alternative method to better control liquid volumes on a minute scale. Here, we used IEF OFFGEL-lab-on-chip electrophoresis for 2-D separation of the rhG-CSF peptides according to their isoelectric point (pI) and molecular weight (kDa). We used an rhG-CSF commercial therapeutic formulation, kept refrigerated 24 months after expiry. The samples were analyzed for particulate matter and charge variants. Subsequently, the secondary structure was assessed by FTIR spectroscopy and residual biological activity was recorded. Interestingly, we showed an additional band in the acidic gel area above and below the most intense protein band (fractions 10, 11, and 12 at 22.84s). This observation reveals the presence of the rhG-CSF variant charges without any additional high molecular weight impurity or biological activity decrease. We conclude that after two years of storage, the rhG-CSF solution maintained its native secondary structure with little -sheet deviation, as reflected in the 1622 cm-1 and 1695 cm-1. These data demonstrated that a combined strategy is a more suitable and accurate analytical assessment of the rhG-CSF and recombinant protein-based biosimilars.
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García-Otero N, Barciela-Alonso MC, Domínguez-González R, Herbello-Hermelo P, Moreda-Piñeiro A, Bermejo-Barrera P. Evaluation of offgel electrophoresis, electrothermal atomic absorption spectroscopy and inductively coupled plasma optical emission spectroscopy for trace metal analysis in marine plankton protein. Microchem J 2015. [DOI: 10.1016/j.microc.2014.11.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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7
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A shotgun approach for the identification of platinum–protein complexes. Anal Bioanal Chem 2015; 407:2393-403. [DOI: 10.1007/s00216-014-8452-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/17/2014] [Accepted: 12/23/2014] [Indexed: 12/11/2022]
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8
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Hsu WL, Inglis DW, Startsev MA, Goldys EM, Davidson MR, Harvie DJE. Isoelectric focusing in a silica nanofluidic channel: effects of electromigration and electroosmosis. Anal Chem 2014; 86:8711-8. [PMID: 25098739 DOI: 10.1021/ac501875u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Isoelectric focusing of proteins in a silica nanofluidic channel filled with citric acid and disodium phosphate buffers is investigated via numerical simulation. Ions in the channel migrate in response to (i) the electric field acting on their charge and (ii) the bulk electroosmotic flow (which is directed toward the cathode). Proteins are focused near the low pH (anode) end when the electromigration effect is more significant and closer to the high pH (cathode) end when the electroosmotic effect dominates. We simulate the focusing behavior of Dylight labeled streptavidin (Dyl-Strep) proteins in the channel, using a relationship between the protein's charge and pH measured in a previous experiment. Protein focusing results compare well to previous experimental measurements. The effect of some key parameters, such as applied voltage, isoelectric point (pI), bulk pH, and bulk conductivity, on the protein trapping behavior in a nanofluidic channel is examined.
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Affiliation(s)
- Wei-Lun Hsu
- Department of Chemical and Biomolecular Engineering, University of Melbourne , Parkville, Victoria 3010, Australia
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9
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OFFGEL fractionation of peptides: Where really is your sample? J Chromatogr A 2014; 1355:278-83. [DOI: 10.1016/j.chroma.2014.05.077] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/22/2014] [Accepted: 05/28/2014] [Indexed: 11/21/2022]
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10
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Moreda-Piñeiro A, García-Otero N, Bermejo-Barrera P. A review on preparative and semi-preparative offgel electrophoresis for multidimensional protein/peptide assessment. Anal Chim Acta 2014; 836:1-17. [PMID: 24974865 DOI: 10.1016/j.aca.2014.04.053] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 04/23/2014] [Accepted: 04/27/2014] [Indexed: 11/29/2022]
Abstract
Mass spectrometry (MS) techniques are commonly used for protein identification and further analysis of selected protein spots after high resolution 2-D electrophoresis. Complementary gel-free approaches have been developed during the last few years and have shown to be useful tools in modern proteomics. The development and application of various gel-free electrophoresis devices for performing protein fractionation according to the pI differences is therefore a topic of interest. This review describes the current state of isoelectric focusing (IEF) gel-free electrophoresis based on the Agilent offgel 3100 fractionator. The review includes, therefore, (i) an overview on IEF as well as other previous IEF gel-free electrophoresis developments; (ii) offgel fundamentals and future trends; (iii) advantages and disadvantages of current offgel procedures; (iv) requirements of isolated protein pellets for further offgel fractionation; (v) offgel fraction requirements to perform the second dimensional analysis by advance electrophoresis and chromatographic techniques; and (vi) effect of the offgel operating conditions on the stability of metal-protein complexes.
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Affiliation(s)
- Antonio Moreda-Piñeiro
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain.
| | - Natalia García-Otero
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain
| | - Pilar Bermejo-Barrera
- Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n. 15782 Santiago de Compostela, Spain
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11
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Rideau A, Besson D, Boissard A, Coqueret O, Guette C. Two-step OFFGEL approach for effective peptide separation compatible with iTRAQ labeling. Proteomics 2013; 13:3261-6. [DOI: 10.1002/pmic.201300161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 09/04/2013] [Accepted: 09/10/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Alexis Rideau
- Paul Papin Cancer Center; Institut de Cancérologie de l’Ouest; INSERM U892 Angers France
| | - Damien Besson
- Paul Papin Cancer Center; Institut de Cancérologie de l’Ouest; INSERM U892 Angers France
| | - Alice Boissard
- Paul Papin Cancer Center; Institut de Cancérologie de l’Ouest; INSERM U892 Angers France
| | - Olivier Coqueret
- Paul Papin Cancer Center; Institut de Cancérologie de l’Ouest; INSERM U892 Angers France
| | - Catherine Guette
- Paul Papin Cancer Center; Institut de Cancérologie de l’Ouest; INSERM U892 Angers France
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12
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García-Otero N, Barciela-Alonso MC, Moreda-Piñeiro A, Bermejo-Barrera P. Study of extraction procedures for protein analysis in plankton samples by OFFGEL electrophoresis hyphenated with Lab-on-a-chip technology. Talanta 2013; 115:631-41. [DOI: 10.1016/j.talanta.2013.05.066] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 05/24/2013] [Accepted: 05/30/2013] [Indexed: 11/29/2022]
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13
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Chiu CW, Chang CL, Chen SF. Evaluation of peptide fractionation strategies used in proteome analysis. J Sep Sci 2012; 35:3293-301. [DOI: 10.1002/jssc.201200631] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/13/2012] [Accepted: 08/13/2012] [Indexed: 12/12/2022]
Affiliation(s)
- Chih-Wei Chiu
- Department of Chemistry; National Taiwan Normal University; Taipei; Taiwan
| | - Chun-Lun Chang
- Department of Chemistry; National Taiwan Normal University; Taipei; Taiwan
| | - Sung-Fang Chen
- Department of Chemistry; National Taiwan Normal University; Taipei; Taiwan
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14
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Stoyanov A. IEF-based multidimensional applications in proteomics: Toward higher resolution. Electrophoresis 2012; 33:3281-90. [DOI: 10.1002/elps.201200221] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 08/20/2012] [Accepted: 08/21/2012] [Indexed: 01/08/2023]
Affiliation(s)
- Alexander Stoyanov
- Department of Pathology and Anatomical Sciences; University of Missouri; Columbia; MO; USA
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15
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Tobolkina E, Cortés-Salazar F, Momotenko D, Maillard J, Girault HH. Segmented field OFFGEL® electrophoresis. Electrophoresis 2012; 33:3331-8. [DOI: 10.1002/elps.201200180] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 06/11/2012] [Accepted: 06/11/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Elena Tobolkina
- Laboratoire d'Electrochimie Physique et Analytique; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne; Switzerland
| | - Fernando Cortés-Salazar
- Laboratoire d'Electrochimie Physique et Analytique; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne; Switzerland
| | - Dmitry Momotenko
- Laboratoire d'Electrochimie Physique et Analytique; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne; Switzerland
| | - Julien Maillard
- Laboratory for Environmental Biotechnology; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne; Switzerland
| | - Hubert H. Girault
- Laboratoire d'Electrochimie Physique et Analytique; Ecole Polytechnique Fédérale de Lausanne (EPFL); Lausanne; Switzerland
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Duša F, Křenková J, Moravcová D, Kahle V, Šlais K. Divergent-flow isoelectric focusing for separation and preparative analysis of peptides. Electrophoresis 2012; 33:1687-94. [DOI: 10.1002/elps.201100587] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Jana Křenková
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Dana Moravcová
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Vladislav Kahle
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
| | - Karel Šlais
- Institute of Analytical Chemistry of the Academy of Sciences of the Czech Republic; v. v. i.; Brno; Czech Republic
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Uquillas JA, Akkus O. Modeling the Electromobility of Type-I Collagen Molecules in the Electrochemical Fabrication of Dense and Aligned Tissue Constructs. Ann Biomed Eng 2012; 40:1641-53. [DOI: 10.1007/s10439-012-0528-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Accepted: 01/28/2012] [Indexed: 01/09/2023]
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18
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Marengo E, Robotti E. A new algorithm for the simulation of SDS 2D-PAGE datasets. Methods Mol Biol 2012; 869:407-425. [PMID: 22585505 DOI: 10.1007/978-1-61779-821-4_34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
This chapter describes a new software for the generation of simulated realistic sodium dodecyl sulfate two-dimensional polyacrylamide gel electrophoresis (SDS 2D-PAGE) images. In order to choose the simulation strategy to provide realistic 2D-PAGE maps the statistical characteristics of such images were taken into account, such as the distributions of sizes, intensities, and volumes of the spots. Also, the low reproducibility typical of replicated SDS 2D-PAGE maps of the same sample was simulated. This approach can be used to generate simulated datasets useful in the development and performance evaluation of new classification and/or image analysis algorithms applied to two-dimensional electrophoresis datasets, given the usually small number of experimental replications available.
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Affiliation(s)
- Emilio Marengo
- Department of Sciences and Technological Innovation, University of Eastern Piedmont, Alessandria, Italy.
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Qiao L, Su F, Bi H, Girault HH, Liu B. Ga2O3 photocatalyzed on-line tagging of cysteine to facilitate peptide mass fingerprinting. Proteomics 2011; 11:3501-9. [DOI: 10.1002/pmic.201100208] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 04/20/2011] [Accepted: 06/08/2011] [Indexed: 11/06/2022]
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20
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Solis N, Cordwell SJ. Current methodologies for proteomics of bacterial surface-exposed and cell envelope proteins. Proteomics 2011; 11:3169-89. [DOI: 10.1002/pmic.201000808] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 03/16/2011] [Accepted: 04/05/2011] [Indexed: 12/18/2022]
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Seshi B, Raja K, Chandramouli K. Immobilized pH gradient-driven paper-based IEF: a new method for fractionating complex peptide mixtures before MS analysis. Clin Proteomics 2011; 8:10. [PMID: 21906381 PMCID: PMC3170271 DOI: 10.1186/1559-0275-8-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 02/11/2011] [Indexed: 11/30/2022] Open
Abstract
Introduction The vast difference in the abundance of different proteins in biological samples limits the determination of the complete proteome of a cell type, requiring fractionation of proteins and peptides before MS analysis. Methods We present a method consisting of electrophoresis of complex mixtures of peptides using a strip of filter paper cut into 20 sections laid end to end over a 24-cm-long IPG strip, the pH gradient of which would drive the electrophoresis. Peptides absorbed onto individual paper pads after electrophoresis are subsequently recovered into a buffer solution, thus dividing a complex peptide mixture according to pI into 20 liquid fractions. This paper-based IEF method (PIEF) was compared side-by-side with a similar but liquid-based Offgel electrophoresis (OGE) by analyzing iTRAQ-labeled peptide mixtures of membrane proteins from four different cell types. Results PIEF outperformed OGE in resolving acidic peptides, whereas OGE did a better job in recovering relatively basic peptides. OGE and PIEF were quite comparable in their coverage, identifying almost equal number of distinct proteins (PIEF =1174; OGE = 1080). Interestingly, however, only 675 were identified by both of them, each method identifying many unique proteins (PIEF = 499; OGE = 415). Thus, the two methods uncovered almost 40% more proteins compared to what is obtained by only one method. Conclusion: This initial investigation demonstrates the technical feasibility of PIEF for complementing OGE. PIEF uses standard IPG IEF equipment, requires no specialized apparatus (e.g., OGE fractionator) and may be integrated into peptide mapping strategies for clinical samples.
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Affiliation(s)
- Beerelli Seshi
- Department of Pathology and Laboratory Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, 1124 West Carson Street, Torrance, California 90502, USA.
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22
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Protéomique et médecine transfusionnelle. Transfus Clin Biol 2011; 18:79-96. [DOI: 10.1016/j.tracli.2011.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 02/17/2011] [Indexed: 01/02/2023]
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Schmid AW, Condemi E, Tuchscherer G, Chiappe D, Mutter M, Vogel H, Moniatte M, Tsybin YO. Tissue transglutaminase-mediated glutamine deamidation of beta-amyloid peptide increases peptide solubility, whereas enzymatic cross-linking and peptide fragmentation may serve as molecular triggers for rapid peptide aggregation. J Biol Chem 2011; 286:12172-88. [PMID: 21300794 DOI: 10.1074/jbc.m110.176149] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tissue transglutaminase (TGase) has been implicated in a number of cellular processes and disease states, where the enzymatic actions of TGase may serve in both, cell survival and apoptosis. To date, the precise functional properties of TGase in cell survival or cell death mechanisms still remain elusive. TGase-mediated cross-linking has been reported to account for the formation of insoluble lesions in conformational diseases. We report here that TGase induces intramolecular cross-linking of β-amyloid peptide (Aβ), resulting in structural changes of monomeric Aβ. Using high resolution mass spectrometry (MS) of cross-linked Aβ peptides, we observed a shift in mass, which is, presumably associated with the loss of NH3 due to enzymatic transamidation activity and hence intramolecular peptide cross-linking. We have observed that a large population of Aβ monomers contained an 0.984 Da increase in mass at a glutamine residue, indicating that glutamine 15 serves as an indispensable substrate in TGase-mediated deamidation to glutamate 15. We provide strong analytical evidence on TGase-mediated Aβ peptide dimerization, through covalent intermolecular cross-linking and hence the formation of Aβ1-40 dimers. Our in depth analyses indicate that TGase-induced post-translational modifications of Aβ peptide may serve as an important seed for aggregation.
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Affiliation(s)
- Adrien W Schmid
- Proteomics Core Facility, AI 0151, Station 15, Institute of Chemical Sciences and Engineering, Lausanne, Switzerland.
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Azulay DOD, Neubert H, Ocaña MF. Visualisation tool for peptide fractionation data in proteomics: application to OFFGEL isoelectric focussing. BMC Bioinformatics 2010; 11:371. [PMID: 20602788 PMCID: PMC2908104 DOI: 10.1186/1471-2105-11-371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Accepted: 07/05/2010] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND OFFGEL isoelectric focussing (IEF) has become a popular tool in proteomics to fractionate peptides or proteins. As a consequence there is a need for software solutions supporting data mining, interpretation and characterisation of experimental quality. RESULTS We can assess performance characteristics of OFFGEL IEF peptide fractionation in proteomics by generating plots of the overall fractionation patterns and the pairwise comparisons of adjacent fractions. CONCLUSIONS A visualisation tool for peptide fractionation has been developed to support the evaluation of IEF data quality and can be implemented in proteomics research.
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25
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Marvin-Guy LF, Zinger T, Wagnière S, Parisod V, Affolter M, Kussmann M. Differential Human Plasma Proteomics Based on AniBal Quantification and Peptide-level Off-Gel Isoelectric Focussing. PROTEOMICS INSIGHTS 2010. [DOI: 10.4137/pri.s4851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Despite its enormous complexity, human plasma is still one of the most frequently used body fluids for identification and quantification of health and disease biomarkers. We have developed a new workflow for qualitative and quantitative analysis of human plasma proteins. The first step was to remove the seven most abundant plasma proteins (MARS). Moreover, in order to reduce the complexity of the sample and to increase protein and proteome coverage, Off-Gel fractionation was performed at peptide level. Our own stable isotope-based quantitative proteomics approach termed AniBAL was chosen for relative quantification of proteins between conditions. The method was developed with commercial human plasma and resulted in the identification of 85 proteins, of which 68 revealed quantitative information (Mascot database search combined with Peptide-/ProteinProphet validation). The combined methods consisting of MARS, AniBAL, Off-Gel and nano-LC-MS/MS on a Bruker HCT ion trap represent a new and efficient platform to quantify human plasma proteome differences between conditions. The method was also found technically compatible to a pair of human plasma pilot samples from the European FP6 project “DiOGenes”. Many of the identifiable/quantifiable proteins are relevant to obesity, diabetes and inflammation, which form the context of investigation within “DiOGenes”.
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Affiliation(s)
| | - Tatiana Zinger
- Functional Genomics Group, Department of Bioanalytical Sciences and
| | | | - Véronique Parisod
- Compound Identification Group, Department of Quality and Safety, Nestlέ Research Center, Vers-chez-les-Blanc, CH-1000 Lausanne 26, Switzerland and
| | - Michael Affolter
- Functional Genomics Group, Department of Bioanalytical Sciences and
| | - Martin Kussmann
- Functional Genomics Group, Department of Bioanalytical Sciences and
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26
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Thormann W, Breadmore MC, Caslavska J, Mosher RA. Dynamic computer simulations of electrophoresis: A versatile research and teaching tool. Electrophoresis 2010; 31:726-54. [DOI: 10.1002/elps.200900613] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Arrey TN, Rietschel B, Papasotiriou DG, Bornemann S, Baeumlisberger D, Karas M, Meyer B. Approaching the Complexity of Elastase-Digested Membrane Proteomes Using Off-Gel IEF/nLC-MALDI-MS/MS. Anal Chem 2010; 82:2145-9. [DOI: 10.1021/ac902776h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tabiwang N. Arrey
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Benjamin Rietschel
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Dimitrios G. Papasotiriou
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Sandra Bornemann
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Dominic Baeumlisberger
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Michael Karas
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Bjoern Meyer
- Cluster of Excellence, “Macromolecular Complexes”, Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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Elschenbroich S, Ignatchenko V, Sharma P, Schmitt-Ulms G, Gramolini AO, Kislinger T. Peptide separations by on-line MudPIT compared to isoelectric focusing in an off-gel format: application to a membrane-enriched fraction from C2C12 mouse skeletal muscle cells. J Proteome Res 2010; 8:4860-9. [PMID: 19670906 DOI: 10.1021/pr900318k] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
High-resolution peptide separation is pivotal for successful shotgun proteomics. The need for capable techniques propels invention and improvement of ever more sophisticated approaches. Recently, Agilent Technologies has introduced the OFFGEL fractionator, which conducts peptide separation by isoelectric focusing in an off-gel setup. This platform has been shown to accomplish high resolution of peptides for diverse sample types, yielding valuable advantages over comparable separation techniques. In this study, we deliver the first comparison of the newly emerging OFFGEL approach to the well-established on-line MudPIT platform. Samples from a membrane-enriched fraction isolated from murine C2C12 cells were subjected to replicate analysis by OFFGEL (12 fractions, pH 3-10) followed by RP-LC-MS/MS or 12-step on-line MudPIT. OFFGEL analyses yielded 1398 proteins (identified by 10,269 peptides), while 1428 proteins (11,078 peptides) were detected with the MudPIT approach. Thus, our data shows that both platforms produce highly comparable results in terms of protein/peptide identifications and reproducibility for the sample type analyzed. We achieve more accurate peptide focusing after OFFGEL fractionation with 88% of all peptides binned to a single fraction, as compared to 61% of peptides detected in only one step in MudPIT analyses. Our study suggests that both platforms are equally capable of high quality peptide separation of a sample with medium complexity, rendering them comparably valuable for comprehensive proteomic analyses.
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Rodthongkum N, Washington JD, Savariar EN, Thayumanavan S, Vachet RW. Generating peptide titration-type curves using polymeric reverse micelles as selective extraction agents along with matrix-assisted laser desorption ionization-mass spectrometry detection. Anal Chem 2009; 81:5046-53. [PMID: 19459656 DOI: 10.1021/ac900661e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amphiphilic homopolymers that self-assemble into reverse micelles in nonpolar solvents have been used by us in the context of a two-phase liquid-liquid extraction protocol to selectively extract peptides from aqueous solution for MALDI-MS detection. In this manuscript, we investigate the scope of these materials in terms of its extraction capabilities, using compounds with varying isoelectric points (pI) and pK(a) values over a range of aqueous solution pHs. We find that the aqueous solution pH and analyte pK(a) values are the major factors controlling extraction selectivity. We also find that the experimental extraction efficiencies correspond very well with the fractional compositions of species calculated using analyte pK(a) values, indicating that these extraction materials can be used to simultaneously generate titration-type curves for each individual peptide in a mixture. We predict that such titration curves, along with accurate mass measurements, could represent a new way of improving protein identification procedures.
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Affiliation(s)
- Nadnudda Rodthongkum
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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30
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Hohmann L, Sherwood C, Eastham A, Peterson A, Eng JK, Eddes JS, Shteynberg D, Martin DB. Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N. J Proteome Res 2009; 8:1415-22. [PMID: 19195997 PMCID: PMC2798736 DOI: 10.1021/pr800774h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteomic analysis typically has been performed using proteins digested with trypsin because of the excellent fragmentation patterns they produce in collision induced dissociation (CID). For analyses in which high protein coverage is desirable, such as global monitoring of post-translational modifications, additional sequences can be seen using parallel digestion with a second enzyme. We have benchmarked a relatively obscure basidomycete-derived zinc metalloendopeptidase, Lys-N, that selectively cleaves the amide bond N-terminal of lysine residues. We have found that Lys-N digestion yields peptides with easily assigned CID spectra. Using a mixture of purified proteins as well as a complex yeast lysate, we have shown that Lys-N efficiently digests all proteins at the predicted sites of cleavage. Shotgun proteomics analyses of Lys-N digests of both the standard mixture and yeast lysate yielded peptide and protein identification numbers that were generally comparable to trypsin digestion, whereas the combination data from Lys-N and trypsin digestion substantially enhanced protein coverage. During CID fragmentation, the additional amino terminal basicity enhanced b-ion intensity which was reflected in long b-ion tags that were particularly pronounced during CID in a quadrupole. Finally, immonium ion peaks produced from Lys-N digested peptides originate from the carboxy terminus in contrast to tryptic peptides where immonium ions originate from the amino terminus.
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Affiliation(s)
- Laura Hohmann
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
| | - Carly Sherwood
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
| | - Ashley Eastham
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
| | - Amelia Peterson
- University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706
| | - Jimmy K. Eng
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
- UW Medicine at South Lake Union, 815 Mercer Street, Seattle, Washington 98109
| | - James S. Eddes
- Institute of Molecular Systems Biology, ETH Zurich and Faculty of Science, University of Zurich, Switzerland
| | - David Shteynberg
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
| | - Daniel B. Martin
- Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103
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Hubner NC, Ren S, Mann M. Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis. Proteomics 2009; 8:4862-72. [PMID: 19003865 DOI: 10.1002/pmic.200800351] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Complex protein mixtures have traditionally been separated by 2-DE. Görg introduced IPGs as the first dimension of protein separation. In recent years, MS-based proteomics has increasingly become the method of choice for identifying and quantifying large number of proteins. In that technology, to decrease analyte complexity, proteins are often separated by 1-D SDS-gel electrophoresis before online MS analysis. Here, we investigate a recently introduced device for peptide separation with IPGs (Agilent OFFGEL). Loading capacity for optimal peptide focusing is below 100 microg and--similar to 2-D gels--IEF is more efficient in the acidic than the basic pH region. The 24-well fractionation format resulted in about 40% additional peptide identifications but less than 20% additional protein identifications than the 12-well format. Compared to in-gel digestion, peptide IEF consistently identified a third more proteins with equal number of fractions. Low protein starting amounts (10 microg) still resulted in deep proteome coverage. Advantages of the in-gel format include better reliability and robustness. Considering its superior performance, diminished sample and work-up requirements, peptide IEF will become a method of choice for sample preparation in proteomics.
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Affiliation(s)
- Nina C Hubner
- Department of Proteomics and Signal Transduction, Max-Planck-Institute for Biochemistry, Martinsried, Germany
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32
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Waller LN, Shores K, Knapp DR. Shotgun proteomic analysis of cerebrospinal fluid using off-gel electrophoresis as the first-dimension separation. J Proteome Res 2008; 7:4577-84. [PMID: 18778093 PMCID: PMC4582942 DOI: 10.1021/pr8001518] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Shotgun proteomic analysis usually employs multidimensional separations with the first dimension most commonly being strong cation exchange (SCX) liquid chromatography (LC). SCX-LC is necessarily a serial process for preparation of multiple samples. Here, we apply a newly available tool, off-gel electrophoresis (OGE), for first-dimension separation of peptide mixtures from digests of cerebrospinal fluid (CSF), a complex and low total protein-containing sample. OGE first-dimension fractionation enabled identification of a total of 156 unique proteins compared to 115 identified in previous work using first-dimension SCX fractionation. OGE can be used to process multiple samples unattended with easy retrieval of the separated fractions. Thus, shotgun analysis using OGE as the first-dimension separation offers a significant advantage both in terms of sample throughput as well as increased numbers of identified proteins.
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Affiliation(s)
- Lashanda N. Waller
- Department of Pharmacology and MUSC Proteomics Center, Medical University of South Carolina, Charleston, South Carolina, 29425
| | | | - Daniel R. Knapp
- Department of Pharmacology and MUSC Proteomics Center, Medical University of South Carolina, Charleston, South Carolina, 29425
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Mulvenna J, Hamilton B, Nagaraj SH, Smyth D, Loukas A, Gorman JJ. Proteomics analysis of the excretory/secretory component of the blood-feeding stage of the hookworm, Ancylostoma caninum. Mol Cell Proteomics 2008; 8:109-21. [PMID: 18753127 DOI: 10.1074/mcp.m800206-mcp200] [Citation(s) in RCA: 146] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Hookworms are blood-feeding intestinal parasites of mammalian hosts and are one of the major human ailments affecting approximately 600 million people worldwide. These parasites form an intimate association with the host and are able to avoid vigorous immune responses in many ways including skewing of the response phenotype to promote parasite survival and longevity. The primary interface between the parasite and the host is the excretory/secretory component, a complex mixture of proteins, carbohydrates, and lipids secreted from the surface or oral openings of the parasite. The composition of this complex mixture is for the most part unknown but is likely to contain proteins important for the parasitic lifestyle and hence suitable as drug or vaccine targets. Using a strategy combining the traditional technology of one-dimensional SDS-PAGE and the newer fractionation technology of OFFGEL electrophoresis we identified 105 proteins from the excretory/secretory products of the blood-feeding stage of the dog hookworm, Ancylostoma caninum. Highly represented among the identified proteins were lectins, including three C-type lectins and three beta-galactoside-specific S-type galectins, as well as a number of proteases belonging to the three major classes found in nematodes, aspartic, cysteine, and metalloproteases. Interestingly 28% of the identified proteins were homologous to activation-associated secreted proteins, a family of cysteine-rich secreted proteins belonging to the sterol carrier protein/Tpx-1/Ag5/PR-1/Sc-7 (TAPS) superfamily. Thirty-four of these proteins were identified suggesting an important role in host-parasite interactions. Other protein families identified included hyaluronidases, lysozyme-like proteins, and transthyretin-like proteins. This work identified a suite of proteins important for the parasitic lifestyle and provides new insight into the biology of hookworm infection.
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Affiliation(s)
- Jason Mulvenna
- Helminth Biology Laboratory, Division of Infectious Diseases, Queensland Institute of Medical Research, Brisbane, Queensland 4006, Australia.
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Balgley BM, Wang W, Song T, Fang X, Yang L, Lee CS. Evaluation of confidence and reproducibility in quantitative proteomics performed by a capillary isoelectric focusing-based proteomic platform coupled with a spectral counting approach. Electrophoresis 2008; 29:3047-54. [DOI: 10.1002/elps.200800050] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Chenau J, Michelland S, Sidibe J, Seve M. Peptides OFFGEL electrophoresis: a suitable pre-analytical step for complex eukaryotic samples fractionation compatible with quantitative iTRAQ labeling. Proteome Sci 2008; 6:9. [PMID: 18302743 PMCID: PMC2277393 DOI: 10.1186/1477-5956-6-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2007] [Accepted: 02/26/2008] [Indexed: 11/21/2022] Open
Abstract
Background The proteomes of mammalian biological fluids, cells and tissues are complex and composed of proteins with a wide dynamic range. The effective way to overcome the complexity of these proteomes is to combine several fractionation steps. OFFGEL fractionation, recently developed by Agilent Technologies, provides the ability to pre-fractionate peptides into discrete liquid fractions and demonstrated high efficiency and repeatability necessary for the analysis of such complex proteomes. Results We evaluated OFFGEL fractionator technology to separate peptides from two complex proteomes, human secretome and human plasma, using a 24-wells device encompassing the pH range 3–10. In combination with reverse phase liquid chromatography, peptides from these two samples were separated and identified by MALDI TOF-TOF. The repartition profiles of the peptides in the different fractions were analyzed and explained by their content in charged amino acids using an algorithmic model based on the possible combinations of amino acids. We also demonstrated for the first time the compatibility of OFFGEL separation technology with the quantitative proteomic labeling technique iTRAQ allowing inclusion of this technique in complex samples comparative proteomic workflow. Conclusion The reported data showed that OFFGEL system provides a highly valuable tool to fractionate peptides from complex eukaryotic proteomes (plasma and secretome) and is compatible with iTRAQ labeling quantitative studies. We therefore consider peptides OFFGEL fractionation as an effective addition to our strategy and an important system for quantitative proteomics studies.
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Affiliation(s)
- Jérôme Chenau
- Centre de Recherche INSERM/UJF U, Cibles Diagnostiques ou Thérapeutiques et Vectorisation des Drogues dans le Cancer du Poumon Institut Albert Bonniot, La Tronche, France.
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