1
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A simple and rapid pipeline for identification of receptor-binding sites on the surface proteins of pathogens. Sci Rep 2020; 10:1163. [PMID: 31980725 PMCID: PMC6981161 DOI: 10.1038/s41598-020-58305-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 01/14/2020] [Indexed: 12/02/2022] Open
Abstract
Ligand-receptor interactions play a crucial role in the plethora of biological processes. Several methods have been established to reveal ligand-receptor interface, however, the majority of methods are time-consuming, laborious and expensive. Here we present a straightforward and simple pipeline to identify putative receptor-binding sites on the pathogen ligands. Two model ligands (bait proteins), domain III of protein E of West Nile virus and NadA of Neisseria meningitidis, were incubated with the proteins of human brain microvascular endothelial cells immobilized on nitrocellulose or PVDF membrane, the complex was trypsinized on-membrane, bound peptides of the bait proteins were recovered and detected on MALDI-TOF. Two peptides of DIII (~916 Da and ~2003 Da) and four peptides of NadA (~1453 Da, ~1810 Da, ~2051 Da and ~2433 Da) were identified as plausible receptor-binders. Further, binding of the identified peptides to the proteins of endothelial cells was corroborated using biotinylated synthetic analogues in ELISA and immunocytochemistry. Experimental pipeline presented here can be upscaled easily to map receptor-binding sites on several ligands simultaneously. The approach is rapid, cost-effective and less laborious. The proposed experimental pipeline could be a simpler alternative or complementary method to the existing techniques used to reveal amino-acids involved in the ligand-receptor interface.
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2
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Armbruster KM, Meredith TC. Enrichment of Bacterial Lipoproteins and Preparation of N-terminal Lipopeptides for Structural Determination by Mass Spectrometry. J Vis Exp 2018. [PMID: 29863685 DOI: 10.3791/56842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Lipoproteins are important constituents of the bacterial cell envelope and potent activators of the mammalian innate immune response. Despite their significance to both cell physiology and immunology, much remains to be discovered about novel lipoprotein forms, how they are synthesized, and the effect of the various forms on host immunity. To enable thorough studies on lipoproteins, this protocol describes a method for bacterial lipoprotein enrichment and preparation of N-terminal tryptic lipopeptides for structural determination by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Expanding on an established Triton X-114 phase partitioning method for lipoprotein extraction and enrichment from the bacterial cell membrane, the protocol includes additional steps to remove non-lipoprotein contaminants, increasing lipoprotein yield and purity. Since lipoproteins are commonly used in Toll-like receptor (TLR) assays, it is critical to first characterize the N-terminal structure by MALDI-TOF MS. Herein, a method is presented to isolate concentrated hydrophobic peptides enriched in N-terminal lipopeptides suitable for direct analysis by MALDI-TOF MS/MS. Lipoproteins that have been separated by Sodium Dodecyl Sulfate Poly-Acrylamide Gel Electrophoresis (SDS-PAGE) are transferred to a nitrocellulose membrane, digested in situ with trypsin, sequentially washed to remove polar tryptic peptides, and finally eluted with chloroform-methanol. When coupled with MS of the more polar trypsinized peptides from wash solutions, this method provides the ability to both identify the lipoprotein and characterize its N-terminus in a single experiment. Intentional sodium adduct formation can also be employed as a tool to promote more structurally informative fragmentation spectra. Ultimately, enrichment of lipoproteins and determination of their N-terminal structures will permit more extensive studies on this ubiquitous class of bacterial proteins.
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Affiliation(s)
- Krista M Armbruster
- Department of Biochemistry and Molecular Biology, Pennsylvania State University
| | - Timothy C Meredith
- Department of Biochemistry and Molecular Biology, Pennsylvania State University;
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3
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O'Rourke MB, Djordjevic SP, Padula MP. The quest for improved reproducibility in MALDI mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:217-228. [PMID: 27420733 DOI: 10.1002/mas.21515] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/19/2016] [Accepted: 06/16/2016] [Indexed: 05/18/2023]
Abstract
Reproducibility has been one of the biggest hurdles faced when attempting to develop quantitative protocols for MALDI mass spectrometry. The heterogeneous nature of sample recrystallization has made automated sample acquisition somewhat "hit and miss" with manual intervention needed to ensure that all sample spots have been analyzed. In this review, we explore the last 30 years of literature and anecdotal evidence that has attempted to address and improve reproducibility in MALDI MS. Though many methods have been attempted, we have discovered a significant publication history surrounding the use of nitrocellulose as a substrate to improve homogeneity of crystal formation and therefore reproducibility. We therefore propose that this is the most promising avenue of research for developing a comprehensive and universal preparation protocol for quantitative MALDI MS analysis. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 37:217-228, 2018.
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Affiliation(s)
- Matthew B O'Rourke
- Proteomics Core Facility, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, New South Wales, 2007, Australia
| | - Steven P Djordjevic
- The iThree Institute, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, New South Wales, 2007, Australia
| | - Matthew P Padula
- Proteomics Core Facility, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, New South Wales, 2007, Australia
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4
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Kachuk C, Doucette AA. The benefits (and misfortunes) of SDS in top-down proteomics. J Proteomics 2018; 175:75-86. [DOI: 10.1016/j.jprot.2017.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/19/2017] [Accepted: 03/03/2017] [Indexed: 12/18/2022]
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5
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Nunes-Miranda JD, Bancel E, Viala D, Chambon C, Capelo JL, Branlard G, Ravel C, Igrejas G. Wheat glutenin: the “tail” of the 1By protein subunits. J Proteomics 2017; 169:136-142. [DOI: 10.1016/j.jprot.2017.05.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 04/03/2017] [Accepted: 05/18/2017] [Indexed: 10/19/2022]
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6
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Murphy S, Ohlendieck K. Mass spectrometric identification of dystrophin, the protein product of the Duchenne muscular dystrophy gene, in distinct muscle surface membranes. Int J Mol Med 2017; 40:1078-1088. [PMID: 28765879 PMCID: PMC5593493 DOI: 10.3892/ijmm.2017.3082] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/22/2017] [Indexed: 12/21/2022] Open
Abstract
Supramolecular membrane complexes of low abundance are difficult to study by routine bioanalytical techniques. The plasmalemmal complex consisting of sarcoglycans, dystroglycans, dystrobrevins and syntrophins, which is closely associated with the membrane cytoskeletal protein dystrophin, represents such a high‑molecular‑mass protein assembly in skeletal muscles. The almost complete loss of the dystrophin isoform Dp427‑M and concomitant reduction in the dystrophin‑associated glycoprotein complex is the underlying cause of the highly progressive neuromuscular disorder named Duchenne muscular dystrophy. This gives the detailed characterization of the dystrophin complex considerable pathophysiological importance. In order to carry out a comprehensive mass spectrometric identification of the dystrophin‑glycoprotein complex, in this study, we used extensive subcellular fractionation and enrichment procedures prior to subproteomic analysis. Mass spectrometry identified high levels of full‑length dystrophin isoform Dp427‑M, α/β‑dystroglycans, α/β/γ/δ‑sarcoglycans, α1/β1/β2‑syntrophins and α/β‑dystrobrevins in highly purified sarcolemma vesicles. By contrast, lower levels were detected in transverse tubules and no components of the dystrophin complex were identified in triads. For comparative purposes, the presence of organellar marker proteins was studied in crude surface membrane preparations vs. enriched fractions from the sarcolemma, transverse tubules and triad junctions using gradient gel electrophoresis and on‑membrane digestion. This involved the subproteomic assessment of various ion‑regulatory proteins and excitation‑contraction coupling components. The comparative profiling of skeletal muscle fractions established a relatively restricted subcellular localization of the dystrophin‑glycoprotein complex in the muscle fibre periphery by proteomic means and clearly demonstrated the absence of dystrophin from triad junctions by sensitive mass spectrometric analysis.
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Affiliation(s)
- Sandra Murphy
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co Kildare, Ireland
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co Kildare, Ireland
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7
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The comparison of CHCA solvent compositions for improving LC-MALDI performance and its application to study the impact of aflatoxin B1 on the liver proteome of diabetes mellitus type 1 mice. PLoS One 2017; 12:e0181423. [PMID: 28738076 PMCID: PMC5524319 DOI: 10.1371/journal.pone.0181423] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 06/19/2017] [Indexed: 01/16/2023] Open
Abstract
In nanoflow liquid chromatography-matrix-assisted laser desorption/ionization tandem time-of-flight (nanoLC-MALDI-TOF/TOF) approaches, it is critical to directly apply small amounts of the sample elutes on the sample target using a nanoLC system due to its low flow rate of 200 ~ 300 nl/min. It is recommended to apply a sheath liquid containing a matrix with a several μL/min flow rate at the end of the nanoLC column to ensure a larger co-eluted droplet for more reproducible sample spotting and avoid the laborious task of post-manual matrix spotting. In this study, to achieve a better nanoLC-MALDI performance on sample spotting, we first compared α-Cyano-4-hydroxycinnamic acid (CHCA) solvent composition for efficiently concentrating nanoLC elutes on an anchor chip. The solvent composition of isopropanol (IPA): acetonitrile (ACN):acetone:0.1% Trifluoroacetic acid (TFA) (2:7:7:2) provided strong and homogeneous signals with higher peptide ion yields than the other solvent compositions. Then, nanoLC-MALDI-TOF/TOF was applied to study the impact of aflatoxin B1 on the liver proteome from diabetes mellitus type 1 mice. Aflatoxin B1 (AFB1), produced by Aspergillus flavus and Aspergillus parasiticus is a carcinogen and a known causative agent of liver cancer. To evaluate the effects of long-term exposure to AFB1 on type 1 diabetes mellitus (TIDM), the livers of T1DM control mice and mice treated with AFB1 were analyzed using isotope-coded protein labeling (ICPL)-based quantitative proteomics. Our results showed that gluconeogenesis, lipid, and oxidative phosphorylation mechanisms, normally elevated in T1DM, were disordered following AFB1 treatment. In addition, major urinary protein 1 (MUP1), an indicator of increased insulin sensitivity, was significantly decreased in the T1DM/AFB1 group and may have resulted in higher blood glucose levels compared to the T1DM group. These results indicate that T1DM patients should avoid the AFB1 intake, as they could lead to increased blood glucose levels and disorders of energy-producing mechanisms.
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8
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Lin Y, Wang K, Liu Z, Lin H, Yu L. Enhanced SDC-assisted digestion coupled with lipid chromatography-tandem mass spectrometry for shotgun analysis of membrane proteome. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1002:144-51. [PMID: 26319803 DOI: 10.1016/j.jchromb.2015.08.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2015] [Revised: 07/07/2015] [Accepted: 08/14/2015] [Indexed: 01/09/2023]
Abstract
Despite the biological importance of membrane proteins, their analysis has lagged behind that of soluble proteins and still presents a great challenge mainly because of their highly hydrophobic nature and low abundance. Sodium deoxycholate (SDC)-assisted digestion strategy has been introduced in our previous papers, which cleverly circumvents many of the challenges in shotgun membrane proteomics. However, it is associated with significant sample loss due to the slightly weaker extraction/solubilization ability of 1% SDC. In this study, an enhanced SDC-assisted digestion method (ESDC method) was developed that incorporates the almost strongest ability of SDC with a high concentration (5%) to lyse membrane and extract/solubilize hydrophobic membrane proteins, and then dilution to 1% for more efficient digestion. The comparative study using rat liver membrane-enriched sample showed that, compared with previous SDC-assisted method and the "universal" filter-aided sample preparation (FASP) method, the ESDC method not only increased the identified number of total proteins, membrane proteins, hydrophobic proteins, integral membrane proteins (IMPs) and IMPs with more than 5 transmembrane domains (TMDs) by an average of 10.8%, 13.2%, 17.8%, 17.9% and 52.9%, respectively, but also enhanced the identified number of total peptides and hydrophobic peptides by averagely 12.5% and 14.2%. These results demonstrated that the ESDC method provides a substantial improvement in the recovery and identification of membrane proteins, especially those with high hydrophobicity and multiple TMDs, and thereby displaying more potential for shotgun membrane proteomics.
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Affiliation(s)
- Yong Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Hunan Collaborative Innovation Center for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha 410128, PR China.
| | - Kunbo Wang
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
| | - Zhonghua Liu
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China; Hunan Collaborative Innovation Center for Utilization of Functional Ingredients from Botanicals, Hunan Agricultural University, Changsha 410128, PR China.
| | - Haiyan Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
| | - Lijun Yu
- Key Laboratory of Tea Science of Ministry of Education, College of Horticulture and Landscape, Hunan Agricultural University, Changsha 410128, PR China
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9
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Harbers M. Shift-Western Blotting: Separate Analysis of Protein and DNA from Protein-DNA Complexes. Methods Mol Biol 2015; 1312:355-73. [PMID: 26044017 DOI: 10.1007/978-1-4939-2694-7_36] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The electrophoretic mobility shift assay (EMSA) is the most frequently used experiment for studying protein-DNA interactions and to identify DNA-binding proteins. Protein-DNA complexes formed during EMSA experiments can be further analyzed by shift-western blotting, where the protein and DNA components contained in a polyacrylamide gel are transferred to stacked membranes: First a nitrocellulose membrane retains the proteins while double-stranded DNA passes through the nitrocellulose membrane and binds only to a charged membrane placed below. Immobilized proteins can then be stained with specific antibodies while the DNA can be detected by a radioactive label or a nonradioactive detection system. Shift-western blotting can overcome many limitations of supershift experiments and allows for the analysis of complex protein-DNA complexes containing multiple protein factors. Moreover, proteins and/or DNA may be recovered from membranes after the blotting step for further analysis by other means.
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Affiliation(s)
- Matthias Harbers
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan,
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10
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Alfonso-Garrido J, Garcia-Calvo E, Luque-Garcia JL. Sample preparation strategies for improving the identification of membrane proteins by mass spectrometry. Anal Bioanal Chem 2015; 407:4893-905. [PMID: 25967148 DOI: 10.1007/s00216-015-8732-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 04/15/2015] [Accepted: 04/22/2015] [Indexed: 12/31/2022]
Abstract
Despite enormous advances in the mass spectrometry and proteomics fields during the last two decades, the analysis of membrane proteins still remains a challenge for the proteomic community. Membrane proteins play a wide number of key roles in several cellular events, making them relevant target molecules to study in a significant variety of investigations (e.g., cellular signaling, immune surveillance, drug targets, vaccine candidates, etc.). Here, we critically review the several attempts that have been carried out on the different steps of the sample preparation procedure to improve and modify existing conventional proteomic strategies in order to make them suitable for the study of membrane proteins. We also revise novel techniques that have been designed to tackle the difficult but relevant task of identifying and characterizing membrane proteins.
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Affiliation(s)
- Javier Alfonso-Garrido
- Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Av. Complutense s/n, 28004, Madrid, Spain
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11
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Abstract
Identification of proteins by mass spectrometry is crucial for better understanding of many biological, biochemical, and biomedical processes. Here we describe two methods for the identification of electroblotted proteins by on-membrane digestion prior to analysis by mass spectrometry. These on-membrane methods take approximately half the time of in-gel digestion and provide better digestion efficiency, due to the better accessibility of the protease to the proteins adsorbed onto the nitrocellulose, and better protein sequence coverage, especially for membrane proteins where large and hydrophobic peptides are commonly present.
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12
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Fournaise E, Chaurand P. Increasing specificity in imaging mass spectrometry: high spatial fidelity transfer of proteins from tissue sections to functionalized surfaces. Anal Bioanal Chem 2014; 407:2159-66. [DOI: 10.1007/s00216-014-8300-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/23/2014] [Accepted: 10/24/2014] [Indexed: 01/05/2023]
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13
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Lin Y, Lin H, Liu Z, Wang K, Yan Y. Improvement of a sample preparation method assisted by sodium deoxycholate for mass-spectrometry-based shotgun membrane proteomics†. J Sep Sci 2014; 37:3321-9. [DOI: 10.1002/jssc.201400569] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 08/18/2014] [Accepted: 08/24/2014] [Indexed: 11/10/2022]
Affiliation(s)
- Yong Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Haiyan Lin
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Zhonghua Liu
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Kunbo Wang
- National Research Center of Engineering & Technology for Utilization of Botanical Functional Ingredients; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
| | - Yujun Yan
- Key Laboratory of Tea Science of Ministry of Education; College of Horticulture and Landscape; Hunan Agricultural University; Changsha P.R. China
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14
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Sims KH, Tytler EM, Tipton J, Hill KL, Burgess SW, Shaw WA. Avanti lipid tools: connecting lipids, technology, and cell biology. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1038-48. [PMID: 24954118 DOI: 10.1016/j.bbalip.2014.05.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 05/21/2014] [Accepted: 05/23/2014] [Indexed: 11/15/2022]
Abstract
Lipid research is challenging owing to the complexity and diversity of the lipidome. Here we review a set of experimental tools developed for the seasoned lipid researcher, as well as, those who are new to the field of lipid research. Novel tools for probing protein-lipid interactions, applications for lipid binding antibodies, enhanced systems for the cellular delivery of lipids, improved visualization of lipid membranes using gold-labeled lipids, and advances in mass spectrometric analysis techniques will be discussed. Because lipid mediators are known to participate in a host of signal transduction and trafficking pathways within the cell, a comprehensive lipid toolbox that aids the science of lipidomics research is essential to better understand the molecular mechanisms of interactions between cellular components. This article is part of a Special Issue entitled Tools to study lipid functions.
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Affiliation(s)
- Kacee H Sims
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
| | - Ewan M Tytler
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
| | - John Tipton
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
| | - Kasey L Hill
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
| | - Stephen W Burgess
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
| | - Walter A Shaw
- Avanti Polar Lipids, Inc., 700 Industrial Park Drive, Alabaster, Al 35007, USA.
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15
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Papasotiriou DG, Markoutsa S, Gorka J, Schleiff E, Karas M, Meyer B. MALDI analysis of proteins after extraction from dissolvable ethylene glycol diacrylate cross-linked polyacrylamide gels. Electrophoresis 2013; 34:2484-94. [DOI: 10.1002/elps.201300132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 04/20/2013] [Accepted: 05/12/2013] [Indexed: 12/23/2022]
Affiliation(s)
- Dimitrios G. Papasotiriou
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Stavroula Markoutsa
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Jan Gorka
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Enrico Schleiff
- Molecular Cell Biology of Plants; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Michael Karas
- Institute of Pharmaceutical Chemistry; Cluster of Excellence “Macromolecular Complexes”, Goethe University; Frankfurt am Main Germany
| | - Bjoern Meyer
- Institute for Instrumental Analysis and Bioanalysis; Mannheim University of Applied Sciences; Mannheim Germany
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16
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Liu F, Ye M, Wang C, Hu Z, Zhang Y, Qin H, Cheng K, Zou H. Polyacrylamide Gel with Switchable Trypsin Activity for Analysis of Proteins. Anal Chem 2013; 85:7024-8. [DOI: 10.1021/ac4017693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Fangjie Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chunli Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhengyan Hu
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongqiang Qin
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cheng
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- Graduate School of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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17
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Saveliev SV, Woodroofe CC, Sabat G, Adams CM, Klaubert D, Wood K, Urh M. Mass Spectrometry Compatible Surfactant for Optimized In-Gel Protein Digestion. Anal Chem 2013; 85:907-14. [DOI: 10.1021/ac302423t] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sergei V. Saveliev
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Carolyn C. Woodroofe
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Grzegorz Sabat
- University of Wisconsin-Madison Biotechnology Center, 425 Henry Mall, Madison, Wisconsin
53706, United States
| | - Christopher M. Adams
- Stanford University Mass Spectrometry, 333 Campus Drive, Stanford, California
94305, United States
| | - Dieter Klaubert
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Keith Wood
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Marjeta Urh
- Promega Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
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18
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Lin Y, Liu H, Liu Z, Liu Y, He Q, Chen P, Wang X, Liang S. Development and evaluation of an entirely solution-based combinative sample preparation method for membrane proteomics. Anal Biochem 2013; 432:41-8. [DOI: 10.1016/j.ab.2012.09.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 08/31/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
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19
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Lin Y, Jiang H, Yan Y, Peng B, Chen J, Lin H, Liu Z. Shotgun analysis of membrane proteomes by an improved SDS-assisted sample preparation method coupled with liquid chromatography–tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 911:6-14. [DOI: 10.1016/j.jchromb.2012.10.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 10/14/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
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20
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Liu YC, Chang HT, Chiang CK, Huang CC. Pulsed-laser desorption/ionization of clusters from biofunctional gold nanoparticles: implications for protein detections. ACS APPLIED MATERIALS & INTERFACES 2012; 4:5241-5248. [PMID: 22998761 DOI: 10.1021/am3011934] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this paper, we describe a pulsed-laser desorption/ionization mass spectrometry (LDI-MS) approach for the detection of proteins with femtomolar sensitivity through the analysis of gold (Au) clusters desorbed from aptamer-modified gold nanoparticles (Apt-AuNPs) on a nitrocellulose membrane (NCM). After the target protein (thrombin) was selectively captured by the surface-bound 29-mer thrombin-binding aptamer (TBA(29)), the thrombin/TBA(29)-AuNP complexes were concentrated and deposited onto the NCM to form a highly efficient background-free surface-assisted LDI substrate. Under pulsed laser irradiation (355 nm), the binding of thrombin decreased the desorption and/or ionization efficiencies of the Au atoms from the AuNP surfaces. The resulting decreases in the intensities of the signals for Au clusters in the mass spectra provided a highly amplified target-labeling indicator for the targeted protein. Under optimized conditions, this probe was highly sensitive (limit of detection: ca. 50 fM) and selective (by at least 1000-fold over other proteins) toward thrombin; it also improved reproducibility (<5%) of ion production by presenting a more-homogeneous substrate surface, thereby enabling LDI-based measurements for the accurate and precise quantification of thrombin in human serum. This novel LDI-MS approach allows high-speed analyses of low-abundance thrombin with ultrahigh sensitivity; decorating the AuNP surfaces with other aptamers also allowed amplification of other biological signals.
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Affiliation(s)
- Yin-Chun Liu
- Institute of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
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21
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Wang X, Liang S. Sample preparation for the analysis of membrane proteomes by mass spectrometry. Protein Cell 2012; 3:661-8. [PMID: 22926766 DOI: 10.1007/s13238-012-2062-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 07/18/2012] [Indexed: 11/27/2022] Open
Abstract
The low abundance and highly hydrophobic nature of most membrane proteins make their analysis more difficult than that for common soluble proteins. Successful membrane protein identification is largely dependent on the sample preparation including the enrichment and dissolution of the membrane proteins. A series of conventional and newly developed methods has been applied to the enrichment of low-abundance membrane proteins at membrane and/or protein levels and to the dissolution of hydrophobic membrane proteins. However, all the existing methods have inherent advantages and limitations. Up to now, there has been no unique method that can universally be employed to solve all the problems and more efforts are needed in improving sample preparation for the analysis of membrane proteomes.
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Affiliation(s)
- Xianchun Wang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
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22
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Lin Y, Liu H, Liu Z, Wang X, Liang S. Shotgun analysis of membrane proteomes using a novel combinative strategy of solution-based sample preparation coupled with liquid chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 901:18-24. [PMID: 22721709 DOI: 10.1016/j.jchromb.2012.05.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 11/30/2022]
Abstract
Although much effort has been made in the field of membrane proteomics, the analysis of membrane proteins particularly integral membrane proteins with poor water solubility still presents a great challenge. In this paper, 2% SDS was used to extract membrane proteins and experimental conditions for the application of acetone precipitation method to the cleanup of SDS-solubilized membrane protein sample were optimized. For improving the re-dissolution and trypsinolysis of acetone-precipitated proteins, several commonly used additives, urea, methanol and sodium deoxycholate (SDC), were employed and compared. The results showed that, when the pre-cooled acetone-to-sample ratio was 6:1 (v/v) with one additional washing step, residual SDS in the protein sample could be lowered to below 0.01% and more than 90% of the proteins were precipitated and therefore recovered. 1% SDC-containing buffer could improve the re-dissolution and digestion of the acetone precipitated proteins more efficiently than the others. Using the combinative sample preparation strategy developed, 398 proteins were identified from the rat liver membrane-enriched fraction, including 188 membrane proteins. Compared with other three representative solution-based sample preparation methods commonly used in membrane proteomics, the newly developed combinative strategy increased the number of identified total proteins and membrane proteins on average by 29.2% and 28.5%, respectively. This combinative strategy was demonstrated to be easily operated at low cost and suitable for the analysis of membrane proteins varying in type and sample volume, etc.
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Affiliation(s)
- Yong Lin
- Key Laboratory of Protein Chemistry and Developmental Biology of National Education Committee, College of Life Sciences, Hunan Normal University, Changsha, Hunan 410081, PR China
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23
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Martos G, Pineda-Vadillo C, Miralles B, Alonso-Lebrero E, López-Fandiño R, Molina E, Belloque J. Identification of an IgE reactive peptide in hen egg riboflavin binding protein subjected to simulated gastrointestinal digestion. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:5215-5220. [PMID: 22583200 DOI: 10.1021/jf3001586] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Riboflavin binding protein (RfBP) is a minor protein in hen egg; its potential involvement in egg allergy has seldom been studied. The aim of this work was to investigate the IgE binding capacity of RfBP before and after simulated gastrointestinal digestion. It was shown that digestion of RfBP mainly occurred during the gastric phase. The protein fragments resulting from the subsequent duodenal phase remained linked through disulfide bonds. Both the intact protein and its digests were subjected to inhibition ELISA with sera obtained from patients allergic to egg. The results revealed significant IgE binding to intact RfBP, whereas the digests showed reduced but substantial IgE binding levels, with serum-to-serum variability. The RfBP digests were then subjected to immunoblot with allergic patients' sera, and the IgE-reactive peptides were further analyzed by MALDI-TOF/TOF mass spectrometry for sequence determination. The RfBP sequence 41-84 was identified as a novel IgE binding peptide in patients allergic to egg.
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Affiliation(s)
- Gustavo Martos
- Institute of Food Science Research, CIAL (UAM-CSIC) , Nicolás Cabrera 9, 28049 Madrid, Spain
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24
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Ino Y, Hirano H. Mass spectrometric characterization of proteins transferred from polyacrylamide gels to membrane filters. FEBS J 2011; 278:3807-14. [DOI: 10.1111/j.1742-4658.2011.08303.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Dave KA, Headlam MJ, Wallis TP, Gorman JJ. Preparation and analysis of proteins and peptides using MALDI TOF/TOF mass spectrometry. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2011; Chapter 16:16.13.1-16.13.21. [PMID: 21400691 DOI: 10.1002/0471140864.ps1613s63] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight/time-of-flight mass spectrometry (MALDI-TOF/TOF-MS) is a valuable tool for the analysis of peptides and proteins. Particularly useful features include high sensitivity, fast data acquisition, ease of use, and robust instrumentation. Although MALDI is relatively tolerant to buffers and other impurities, substantial sensitivity enhancement can be achieved through removal of non-analyte components of samples. Therefore, sample processing to remove buffers and impurities can greatly improve the quality of results obtained by MALDI experiments. This unit describes optimized procedures for enzymatic digestion, preparation of MALDI target plates, thin layer matrix preparation, on-target sample cleanup, and capillary HPLC-MALDI co-spotting of analyte and matrix. Procedures are also described for analysis of on-membrane proteins by MALDI-TOF/TOF-MS before tryptic digestion. Some of these procedures are also applicable to protein spots from two-dimensional (2-D) gels. Guidance is also provided for acquisition and interpretation of MS and MS/MS spectra.
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Affiliation(s)
- Keyur A Dave
- PO Royal Brisbane Hospital, Herston, Queensland, Australia
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26
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Ohlendieck K. Skeletal muscle proteomics: current approaches, technical challenges and emerging techniques. Skelet Muscle 2011; 1:6. [PMID: 21798084 PMCID: PMC3143904 DOI: 10.1186/2044-5040-1-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Accepted: 02/01/2011] [Indexed: 01/08/2023] Open
Abstract
Background Skeletal muscle fibres represent one of the most abundant cell types in mammals. Their highly specialised contractile and metabolic functions depend on a large number of membrane-associated proteins with very high molecular masses, proteins with extensive posttranslational modifications and components that exist in highly complex supramolecular structures. This makes it extremely difficult to perform conventional biochemical studies of potential changes in protein clusters during physiological adaptations or pathological processes. Results Skeletal muscle proteomics attempts to establish the global identification and biochemical characterisation of all members of the muscle-associated protein complement. A considerable number of proteomic studies have employed large-scale separation techniques, such as high-resolution two-dimensional gel electrophoresis or liquid chromatography, and combined them with mass spectrometry as the method of choice for high-throughput protein identification. Muscle proteomics has been applied to the comprehensive biochemical profiling of developing, maturing and aging muscle, as well as the analysis of contractile tissues undergoing physiological adaptations seen in disuse atrophy, physical exercise and chronic muscle transformation. Biomedical investigations into proteome-wide alterations in skeletal muscle tissues were also used to establish novel biomarker signatures of neuromuscular disorders. Importantly, mass spectrometric studies have confirmed the enormous complexity of posttranslational modifications in skeletal muscle proteins. Conclusions This review critically examines the scientific impact of modern muscle proteomics and discusses its successful application for a better understanding of muscle biology, but also outlines its technical limitations and emerging techniques to establish new biomarker candidates.
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Affiliation(s)
- Kay Ohlendieck
- Muscle Biology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland.
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27
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Lewis C, Ohlendieck K. Mass spectrometric identification of dystrophin isoform Dp427 by on-membrane digestion of sarcolemma from skeletal muscle. Anal Biochem 2010; 404:197-203. [PMID: 20507823 DOI: 10.1016/j.ab.2010.05.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 05/06/2010] [Accepted: 05/20/2010] [Indexed: 01/18/2023]
Abstract
Although the membrane cytoskeletal protein dystrophin of 427kDa and its tightly associated glycoprotein complex are drastically affected in muscular dystrophy, recent large-scale proteomic investigations did not identify full-length dystrophin in muscle preparations and were unable to determine its molecular fate in dystrophinopathy. Because conventional two-dimensional gel electrophoresis underrepresents many low-abundance and membrane-associated protein species and in-gel trypsination is often hampered by an inefficient digestion of certain target proteins, here we have applied direct on-membrane digestion of one-dimensional blots of the sarcolemma-enriched fraction and the isolated dystrophin-glycoprotein complex. This method succeeded in the mass spectrometric identification of dystrophin isoform Dp427 and associated glycoproteins as well as sarcolemmal dysferlin. In addition, protein bands representing established signature molecules of cross-contaminating membrane systems, such as the voltage-sensing dihydropyridine receptor of transverse tubules, the ryanodine receptor Ca2+-release channel of triad junctions, and the Ca2+-ATPase of the sarcoplasmic reticulum, were identified by mass spectrometry. Thus, proteomic approaches using on-membrane digestion might be suitable for future studies of low-abundance proteins, integral proteins, peripheral membrane proteins, and high-molecular-mass proteins. On-membrane digestion has the potential to develop into the method of choice for studying these classes of proteins, whose presence is otherwise missed by conventional gel electrophoresis-based proteomics.
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Affiliation(s)
- Caroline Lewis
- Department of Biology, National University of Ireland, Maynooth, Co. Kildare, Ireland
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28
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Scott NE, Marzook NB, Deutscher A, Falconer L, Crossett B, Djordjevic SP, Cordwell SJ. Mass spectrometric characterization of the Campylobacter jejuni
adherence factor CadF reveals post-translational processing that removes immunogenicity while retaining fibronectin binding. Proteomics 2009; 10:277-88. [DOI: 10.1002/pmic.200900440] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Jiang D, Jarrett HW, Haskins WE. Methods for proteomic analysis of transcription factors. J Chromatogr A 2009; 1216:6881-9. [PMID: 19726046 PMCID: PMC2778203 DOI: 10.1016/j.chroma.2009.08.044] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 08/12/2009] [Accepted: 08/17/2009] [Indexed: 02/08/2023]
Abstract
Investigation of the transcription factor (TF) proteome presents challenges including the large number of low abundance and post-translationally modified proteins involved. Specialized purification and analysis methods have been developed over the last decades which facilitate the study of the TF proteome and these are reviewed here. Generally applicable proteomics methods that have been successfully applied are also discussed. TFs are selectively purified by affinity techniques using the DNA response element (RE) as the basis for highly specific binding, and several agents have been discovered that either enhance binding or diminish non-specific binding. One such affinity method called "trapping" enables purification of TFs bound to nM concentrations and recovery of TF complexes in a highly purified state. The electrophoretic mobility shift assay (EMSA) is the most important assay of TFs because it provides both measures of the affinity and amount of the TF present. Southwestern (SW) blotting and DNA-protein crosslinking (DPC) allow in vitro estimates of DNA-binding-protein mass, while chromatin immunoprecipitation (ChIP) allows confirmation of promoter binding in vivo. Two-dimensional gel electrophoresis methods (2-DE), and 3-DE methods which combines EMSA with 2-DE, allow further resolution of TFs. The synergy of highly selective purification and analytical strategies has led to an explosion of knowledge about the TF proteome and the proteomes of other DNA- and RNA-binding proteins.
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Affiliation(s)
- Daifeng Jiang
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249 USA
| | - Harry W. Jarrett
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249 USA
| | - William E. Haskins
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, 78249 USA
- RCMI Proteomics, University of Texas at San Antonio, San Antonio, TX, 78249 USA
- Protein Biomarkers Cores, University of Texas at San Antonio, San Antonio, TX, 78249 USA
- Department of Medicine, Division of Hematology & Medical Oncology, University of Texas Health Science Center at San Antonio, San Antonio, TX, 78229 USA
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30
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Lin Y, Li Y, Liu Y, Han W, He Q, Li J, Chen P, Wang X, Liang S. Improvement of gel-separated protein identification by DMF-assisted digestion and peptide recovery after electroblotting. Electrophoresis 2009; 30:3626-35. [DOI: 10.1002/elps.200900070] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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31
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Jiang D, Jia Y, Zhou Y, Jarrett HW. Two-dimensional southwestern blotting and characterization of transcription factors on-blot. J Proteome Res 2009; 8:3693-701. [PMID: 19388704 DOI: 10.1021/pr900214p] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two-dimensional Southwestern blotting (2D-SW) described here combines several steps. Proteins are separated by two-dimensional gel electrophoresis and transferred to nitrocellulose (NC) or polyvinylidene fluoride (PVDF) membrane. The blotted proteins are then partially renatured and probed with a specific radiolabeled oligonucleotide for Southwestern blotting (SW) analysis. The detected proteins are then processed by on-blot digestion and identified by LC-MS/MS analysis. A transcription factor, bound by a specific radiolabeled element, is thus characterized without aligning with protein spots on a gel. In this study, we systematically optimize conditions for 2D-SW and on-blot digestion. By quantifying the SW signal using a scintillation counter, the optimal conditions for SW were determined to be PVDF membrane, 0.5% PVP40 for membrane blocking, serial dilution of guanidine HCl for denaturing and renaturing proteins on the blot, and an SDS stripping buffer to remove radiation from the blot. By the quantification of the peptide yields using nano-ESI-MS analysis, the optimized conditions for on-blot digestions were found to be 0.5% Zwittergent 3-16 and 30% acetonitrile in trypsin digestion buffer. With the use of the optimized 2D-SW technique and on-blot digestion combined with HPLC-nano-ESI-MS/MS, a GFP-C/EBP model protein was successfully characterized from a bacterial extract, and native C/EBP beta was identified from 100 microg of HEK293 nuclear extract without any previous purification.
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Affiliation(s)
- Daifeng Jiang
- Department of Chemistry, University of Texas San Antonio, San Antonio, Texas 78249, USA
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32
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Rabilloud T, Vaezzadeh AR, Potier N, Lelong C, Leize-Wagner E, Chevallet M. Power and limitations of electrophoretic separations in proteomics strategies. MASS SPECTROMETRY REVIEWS 2009; 28:816-843. [PMID: 19072760 DOI: 10.1002/mas.20204] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed.
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33
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Lee J, Soper SA, Murray KK. Microfluidics with MALDI analysis for proteomics--a review. Anal Chim Acta 2009; 649:180-90. [PMID: 19699392 DOI: 10.1016/j.aca.2009.07.037] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 07/13/2009] [Accepted: 07/15/2009] [Indexed: 01/01/2023]
Abstract
Various microfluidic devices have been developed for proteomic analyses and many of these have been designed specifically for mass spectrometry detection. In this review, we present an overview of chip fabrication, microfluidic components, and the interfacing of these devices to matrix-assisted laser desorption ionization (MALDI) mass spectrometry. These devices can be directly coupled to the mass spectrometer for on-line analysis in real-time, or samples can be analyzed on-chip or deposited onto targets for off-line readout. Several approaches for combining microfluidic devices with analytical functions such as sample cleanup, digestion, and separations with MALDI mass spectrometry are discussed.
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Affiliation(s)
- Jeonghoon Lee
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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34
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Kouvonen P, McDonnell LA, Heeren RMA, Corthals GL. Nitromatrix provides improved LC-MALDI signals and more protein identifications. Proteomics 2009; 9:1662-71. [DOI: 10.1002/pmic.200800302] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Abstract
Identification of proteins and characterization of posttranslational modifications are crucial steps for many biological, biochemical, and biomedical studies, and mass spectrometry has become the method of choice for these analyses. Here we describe two methods for the on-membrane digestion of proteins electroblotted onto nitrocellulose membranes prior to analysis by mass spectrometry. These on-membrane methods take approximately half the time of in-gel digestion and provide better digestion efficiency, due to the better accessibility of the protease to the proteins adsorbed onto the nitrocellulose, and better protein sequence coverage, especially for membrane proteins where large and hydrophobic peptides are commonly present.
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36
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Enabling technologies in the life sciences. Abstracts of an international symposium by the Association of Biomolecular Resource Facilities. February 9-12, 2008. Salt Lake City, Utah, USA. J Biomol Tech 2008; 19:1-93. [PMID: 18300397 PMCID: PMC2359594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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37
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Selective immobilization of biomolecules onto an activated polymeric adlayer. Biointerphases 2007; 2:136-42. [DOI: 10.1116/1.2801974] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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38
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Chen Y, Guo Z, Wang X, Qiu C. Sample preparation. J Chromatogr A 2007; 1184:191-219. [PMID: 17991475 DOI: 10.1016/j.chroma.2007.10.026] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 10/08/2007] [Accepted: 10/10/2007] [Indexed: 11/17/2022]
Abstract
A panorama of sample preparation methods has been composed from 481 references, with a highlight of some promising methods fast developed during recent years and a somewhat brief introduction on most of the well-developed methods. All the samples were commonly referred to molecular composition, being extendable to particles including cells but not to organs, tissues and larger bodies. Some criteria to evaluate or validate a sample preparation method were proposed for reference. Strategy for integration of several methods to prepare complicated protein samples for proteomic studies was illustrated and discussed.
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Affiliation(s)
- Yi Chen
- Beijing National Laboratory of Molecular Science, Laboratory of Analytical Chemistry for Life Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China.
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39
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Luque-Garcia JL, Zhou G, Spellman DS, Sun TT, Neubert TA. Analysis of electroblotted proteins by mass spectrometry: protein identification after Western blotting. Mol Cell Proteomics 2007; 7:308-14. [PMID: 17938404 DOI: 10.1074/mcp.m700415-mcp200] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We describe a new approach for the identification and characterization by mass spectrometry of proteins that have been electroblotted onto nitrocellulose. Using this method (Blotting and Removal of Nitrocellulose (BARN)), proteins can be analyzed either as intact proteins for molecular weight determination or as peptides generated by on-membrane proteolysis. Acetone is used to dissolve the nitrocellulose and to precipitate the adsorbed proteins/peptides, thus removing the nitrocellulose which can interfere with MS analysis. This method offers improved protein coverage, especially for membrane proteins, such as uroplakins, because the extraction step after in-gel digestion is avoided. Moreover, removal of nitrocellulose from the sample solution allows sample analysis by both MALDI- and (LC) ESI-based mass spectrometers. Finally, we demonstrate the utility of BARN for the direct identification of soluble and membrane proteins after Western blotting, obtaining comparable or better results than with in-gel digestion.
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Affiliation(s)
- Jose L Luque-Garcia
- Kimmel Center for Biology and Medicine, Skirball Institute and Department of Pharmacology
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40
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Cañas B, Piñeiro C, Calvo E, López-Ferrer D, Gallardo JM. Trends in sample preparation for classical and second generation proteomics. J Chromatogr A 2007; 1153:235-58. [PMID: 17276441 DOI: 10.1016/j.chroma.2007.01.045] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 12/18/2006] [Accepted: 01/12/2007] [Indexed: 11/16/2022]
Abstract
Sample preparation is a fundamental step in the proteomics workflow. However, it is not easy to find compiled information updating this subject. In this paper, the strategies and protocols for protein extraction and identification, following either classical or second generation proteomics methodologies, are reviewed. Procedures for: tissue disruption, cell lysis, sample pre-fractionation, protein separation by 2-DE, protein digestion, mass spectrometry analysis, multidimensional peptide separations and quantification of protein expression level are described.
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Affiliation(s)
- Benito Cañas
- Dept. Química Analítica, Facultad de CC, Químicas, UCM, Av.Complutense s/n, Madrid 28040, Spain.
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41
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2007; 42:407-418. [PMID: 17326037 DOI: 10.1002/jms.1072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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