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Said HH, Doucette AA. Enhanced Electrophoretic Depletion of Sodium Dodecyl Sulfate with Methanol for Membrane Proteome Analysis by Mass Spectrometry. Proteomes 2024; 12:5. [PMID: 38390965 PMCID: PMC10885059 DOI: 10.3390/proteomes12010005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/24/2024] Open
Abstract
Membrane proteins are underrepresented during proteome characterizations, primarily owing to their lower solubility. Sodium dodecyl sulfate (SDS) is favored to enhance protein solubility but interferes with downstream analysis by mass spectrometry. Here, we present an improved workflow for SDS depletion using transmembrane electrophoresis (TME) while retaining a higher recovery of membrane proteins. Though higher levels of organic solvent lower proteome solubility, we found that the inclusion of 40% methanol provided optimal solubility of membrane proteins, with 86% recovery relative to extraction with SDS. Incorporating 40% methanol during the electrophoretic depletion of SDS by TME also maximized membrane protein recovery. We further report that methanol accelerates the rate of detergent removal, allowing TME to deplete SDS below 100 ppm in under 3 min. This is attributed to a three-fold elevation in the critical micelle concentration (CMC) of SDS in the presence of methanol, combined with a reduction in the SDS to protein binding ratio in methanol (0.3 g SDS/g protein). MS analysis of membrane proteins isolated from the methanol-assisted workflow revealed enhanced proteome detection, particularly for proteins whose pI contributed a minimal net charge and therefore possessed reduced solubility in a purely aqueous solvent. This protocol presents a robust approach for the preparation of membrane proteins by maximizing their solubility in MS-compatible solvents, offering a tool to advance membrane proteome characterization.
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Affiliation(s)
- Hammam H Said
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS B3H 4R2, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS B3H 4R2, Canada
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2
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Goecker ZC, Salemi MR, Karim N, Phinney BS, Rice RH, Parker GJ. Optimal processing for proteomic genotyping of single human hairs. Forensic Sci Int Genet 2020; 47:102314. [DOI: 10.1016/j.fsigen.2020.102314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/25/2020] [Accepted: 05/15/2020] [Indexed: 01/08/2023]
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3
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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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4
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Plucinsky SM, Root KT, Glover KJ. Efficient solubilization and purification of highly insoluble membrane proteins expressed as inclusion bodies using perfluorooctanoic acid. Protein Expr Purif 2017; 143:34-37. [PMID: 29066155 DOI: 10.1016/j.pep.2017.10.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/14/2017] [Accepted: 10/19/2017] [Indexed: 02/06/2023]
Abstract
The purification of membrane proteins can be challenging due to their low solubility in conventional detergents and/or chaotropic solutions. The introduction of fusion systems that promote the formation of inclusion bodies has facilitated the over-expression of membrane proteins. In this protocol, we describe the use of perfluorooctanoic acid (PFOA) as an aid in the purification of highly hydrophobic membrane proteins expressed as inclusion bodies. The advantage of utilizing PFOA is threefold: first, PFOA is able to reliably solubilize inclusion bodies, second, PFOA is compatible with nickel affinity chromatography, and third, PFOA can be efficiently dialyzed away to produce a detergent free sample. To demonstrate the utility of employing PFOA, we expressed and purified a segment of the extremely hydrophobic membrane protein caveolin-1.
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Affiliation(s)
- Sarah M Plucinsky
- Department of Chemistry, Lehigh University, 6 E. Packer Ave, Bethlehem, PA 18015, USA
| | - Kyle T Root
- Department of Chemistry, Lock Haven University, 301 W. Church St, Lock Haven, PA 17745, USA
| | - Kerney Jebrell Glover
- Department of Chemistry, Lehigh University, 6 E. Packer Ave, Bethlehem, PA 18015, USA.
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5
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In-depth analyses of native N-linked glycans facilitated by high-performance anion exchange chromatography-pulsed amperometric detection coupled to mass spectrometry. Anal Bioanal Chem 2017; 409:3089-3101. [DOI: 10.1007/s00216-017-0248-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/02/2017] [Accepted: 02/06/2017] [Indexed: 12/11/2022]
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Abstract
The static levels of proteins are the net results of their production and clearance regulated by the activities of proteins involved in their synthesis, degradation, and transportation. Therefore, the information on the rates of protein synthesis and clearance is needed to understand the underlying dynamic nature of a proteome. In this chapter, the experimental technique, we use in our laboratory for monitoring the synthesis of individual proteins in Caenorhabditis elegans (C. elegans) is described. The technique utilizes a preisotopically labeled amino acid (13C6-Lys) as a precursor for protein synthesis and monitors the kinetics of the precursor incorporation into the newly synthesized proteins. C. elegans is a powerful animal model in various fields of biomedical science such as aging, developmental biology, and neurobiology. The experimental technique would, therefore, be useful for research laboratories using C. elegans as an animal model.
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Affiliation(s)
- M Miyagi
- Center for Proteomics and Bioinformatics, Cleveland, OH, United States; Case Western Reserve University, Cleveland, OH, United States.
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7
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Zhao M, Wei W, Cheng L, Zhang Y, Wu F, He F, Xu P. Searching Missing Proteins Based on the Optimization of Membrane Protein Enrichment and Digestion Process. J Proteome Res 2016; 15:4020-4029. [PMID: 27485413 DOI: 10.1021/acs.jproteome.6b00389] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A membrane protein enrichment method composed of ultracentrifugation and detergent-based extraction was first developed based on MCF7 cell line. Then, in-solution digestion with detergents and eFASP (enhanced filter-aided sample preparation) with detergents were compared with the time-consuming in-gel digestion method. Among the in-solution digestion strategies, the eFASP combined with RapiGest identified 1125 membrane proteins. Similarly, the eFASP combined with sodium deoxycholate identified 1069 membrane proteins; however, the in-gel digestion characterized 1091 membrane proteins. Totally, with the five digestion methods, 1390 membrane proteins were identified with ≥1 unique peptides, among which 1345 membrane proteins contain unique peptides ≥2. This is the biggest membrane protein data set for MCF7 cell line and even breast cancer tissue samples. Interestingly, we identified 13 unique peptides belonging to 8 missing proteins (MPs). Finally, eight unique peptides were validated by synthesized peptides. Two proteins were confirmed as MPs, and another two proteins were candidate detections.
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Affiliation(s)
- Mingzhi Zhao
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine , Beijing 102206, P. R. China
| | - Wei Wei
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine , Beijing 102206, P. R. China
| | - Long Cheng
- Department of Medical Molecular Biology, Beijing Institute of Biotechnology , 27 Tai-Ping Lu Road, Beijing 100850, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine , Beijing 102206, P. R. China.,Institute of Microbiology, Chinese Academy of Science , Beijing 100101, China
| | - Feilin Wu
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine , Beijing 102206, P. R. China.,Life Science College, Southwest Forestry University , Kunming 650224, P. R. China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine , Beijing 102206, P. R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine , Beijing 102206, P. R. China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, and Wuhan University School of Pharmaceutical Sciences , Wuhan 430071, P. R. China.,Anhui Medical University , Hefei 230032, Anhui, P. R. China
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8
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Kachuk C, Faulkner M, Liu F, Doucette AA. Automated SDS Depletion for Mass Spectrometry of Intact Membrane Proteins though Transmembrane Electrophoresis. J Proteome Res 2016; 15:2634-42. [DOI: 10.1021/acs.jproteome.6b00199] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Carolyn Kachuk
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Melissa Faulkner
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Fang Liu
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alan A. Doucette
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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Vukoti K, Yu X, Sheng Q, Saha S, Feng Z, Hsu AL, Miyagi M. Monitoring newly synthesized proteins over the adult life span of Caenorhabditis elegans. J Proteome Res 2015; 14:1483-94. [PMID: 25686393 DOI: 10.1021/acs.jproteome.5b00021] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Little is known regarding how the synthesis and degradation of individual proteins change during the life of an organism. Such knowledge is vital to understanding the aging process. To fill this knowledge gap, we monitored newly synthesized proteins on a proteome scale in Caenorhabditis elegans over time during adulthood using a stable-isotope labeling by amino acids in cell culture (SILAC)-based label-chase approach. For most proteins, the rate of appearance of newly synthesized protein was high during the first 5 days of adulthood, slowed down between the fifth and the 11th days, and then increased again after the 11th day. However, the magnitude of appearance rate differed significantly from protein to protein. For example, the appearance of newly synthesized protein was fast for proteins involved in embryonic development, transcription regulation, and lipid binding/transport, with >70% of these proteins newly synthesized by day 5 of adulthood, whereas it was slow for proteins involved in cellular assembly and motility, such as actin and myosin, with <70% of these proteins newly synthesized even on day 16. The late-life increase of newly synthesized protein was especially high for ribosomal proteins and ATP synthases. We also investigated the effect of RNAi-mediated knockdown of the rpl-9 (ribosomal protein), atp-3 (ATP synthase), and ril-1 (RNAi-induced longevity-1) genes and found that inhibiting the expression of atp-3 and ril-1 beginning in late adulthood is still effective to extend the life span of C. elegans.
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Affiliation(s)
- Krishna Vukoti
- Center for Proteomics and Bioinformatics, ‡Department of Pharmacology, and §Department of Ophthalmology and Visual Sciences, Case Western Reserve University , Cleveland, Ohio, United States
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Doucette AA, Vieira DB, Orton DJ, Wall MJ. Resolubilization of precipitated intact membrane proteins with cold formic acid for analysis by mass spectrometry. J Proteome Res 2014; 13:6001-12. [PMID: 25384094 DOI: 10.1021/pr500864a] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein precipitation in organic solvent is an effective strategy to deplete sodium dodecyl sulfate (SDS) ahead of MS analysis. Here we evaluate the recovery of membrane and water-soluble proteins through precipitation with chloroform/methanol/water or with acetone (80%). With each solvent system, membrane protein recovery was greater than 90%, which was generally higher than that of cytosolic proteins. With few exceptions, residual supernatant proteins detected by MS were also detected in the precipitation pellet, having higher MS signal intensity in the pellet fraction. Following precipitation, we present a novel strategy for the quantitative resolubilization of proteins in an MS-compatible solvent system. The pellet is incubated at -20 °C in 80% formic acid/water and then diluted 10-fold with water. Membrane protein recovery matches that of sonication of the pellet in 1% SDS. The resolubilized proteins are stable at room temperature, with no observed formylation as is typical of proteins suspended in formic acid at room temperature. The protocol is applied to the molecular weight determination of membrane proteins from a GELFrEE-fractionated sample of Escherichia coli proteins.
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Affiliation(s)
- Alan A Doucette
- Department of Chemistry and ‡Department of Pathology, Dalhousie University , Halifax, Nova Scotia, Canada
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Crowell AMJ, MacLellan DL, Doucette AA. A two-stage spin cartridge for integrated protein precipitation, digestion and SDS removal in a comparative bottom-up proteomics workflow. J Proteomics 2014; 118:140-50. [PMID: 25316050 DOI: 10.1016/j.jprot.2014.09.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/23/2014] [Accepted: 09/28/2014] [Indexed: 12/17/2022]
Abstract
UNLABELLED Protein precipitation with organic solvent is an effective means of depleting contaminants such as sodium dodecyl sulfate (SDS), while maintaining high analyte recovery. Here, we report the use of a disposable two-stage spin cartridge to facilitate isolation of the precipitated protein, with subsequent enzyme digestion and peptide cleanup in the cartridge. An upper filtration cartridge retains over 95% of the protein (10 μg BSA), with 99.75% detergent depleted from a sample initially containing 2% SDS. Following precipitation, a plug attached to the base of the filtration cartridge retains the solution to enable tryptic digestion in the vial, while a solid phase extraction cartridge attached to the base of the filter facilitates peptide cleanup post-digestion. A GELFrEE fractionated Escherichia coli proteome extract processed with the spin cartridge yields similar protein identifications compared to controls (226 vs 216 for control), and with an increased number of unique peptides (1753 vs 1554 for control). The device is applied to proteome characterization of rat kidneys experiencing a surgically induced ureteral tract obstruction, revealing several statistically altered proteins, consistent with the morphology and expected pathophysiology of the disease. BIOLOGICAL SIGNIFICANCE Conventionally, protein precipitation involves extended centrifugation to pellet the sample, with careful pipetting to remove the supernatant without disturbing the pellet. The method is not only time consuming but is highly subject to the skill of the individual, particularly at lower protein concentrations where the pellet may not be visible. As such, protein precipitation is often overlooked in proteomics, favoring column-based approaches to concentrate or purify samples. Here, all aspects of sample manipulation are integrated into a simple disposable cartridge. The device enables SDS depletion, sample preconcentration, resolubilization, derivatization, digestion, and peptide cleanup in a highly repeatable and easily multiplexed format. The device is ideally suited for comparative proteome studies. Antenatal hydronephrosis is a congenital disorder affecting 1-5% of all pregnancies, and can require surgical intervention to avoid loss of renal function. Using our device, we investigated the impact of hydronephrosis on the kidneys in a surgically induced animal model of the disease. Proteome analysis points to decreased metabolic activity in the obstructed kidney, with upregulation of proteins involved in cytoskeletal organization. This article is part of a Special Issue entitled: Protein dynamics in health and disease. Guest Editors: Pierre Thibault and Anne-Claude Gingras.
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Affiliation(s)
| | - Dawn L MacLellan
- Department of Urology and Pathology, Dalhousie University, Canada
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12
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O18Quant: a semiautomatic strategy for quantitative analysis of high-resolution 16O/18O labeled data. BIOMED RESEARCH INTERNATIONAL 2014; 2014:971857. [PMID: 24901003 PMCID: PMC4037588 DOI: 10.1155/2014/971857] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/18/2014] [Indexed: 01/09/2023]
Abstract
Proteolytic 18O-labeling has been widely used in quantitative proteomics since it can uniformly label all peptides from different kinds of proteins. There have been multiple algorithms and tools developed over the last few years to analyze high-resolution proteolytic 16O/18O labeled mass spectra. We have developed a software package, O18Quant, which addresses two major issues in the previously developed algorithms. First, O18Quant uses a robust linear model (RLM) for peptide-to-protein ratio estimation. RLM can minimize the effect of outliers instead of iteratively removing them which is a common practice in other approaches. Second, the existing algorithms lack applicable implementation. We address this by implementing O18Quant using C# under Microsoft.net framework and R. O18Quant automatically calculates the peptide/protein relative ratio and provides a friendly graphical user interface (GUI) which allows the user to manually validate the quantification results at scan, peptide, and protein levels. The intuitive GUI of O18Quant can greatly enhance the user's visualization and understanding of the data analysis. O18Quant can be downloaded for free as part of the software suite ProteomicsTools.
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Zougman A, Selby PJ, Banks RE. Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis. Proteomics 2014; 14:1006-0. [PMID: 24678027 DOI: 10.1002/pmic.201300553] [Citation(s) in RCA: 254] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/16/2014] [Accepted: 02/11/2014] [Indexed: 01/28/2023]
Abstract
Despite recent developments in bottom-up proteomics, the need still exists in a fast, uncomplicated, and robust method for comprehensive sample processing especially when applied to low protein amounts. The suspension trapping method combines the advantage of efficient SDS-based protein extraction with rapid detergent removal, reactor-type protein digestion, and peptide cleanup. Proteins are solubilized in SDS. The sample is acidified and introduced into the suspension trapping tip incorporating the depth filter and hydrophobic compartments, filled with the neutral pH methanolic solution. The instantly formed fine protein suspension is trapped in the depth filter stack-this crucial step is aimed at separating the particulate matter in space. SDS and other contaminants are removed in the flow-through, and a protease is introduced. Following the digestion, the peptides are cleaned up using the tip's hydrophobic part. The methodology allows processing of protein loads down to the low microgram/submicrogram levels. The detergent removal takes about 5 min, whereas the tryptic proteolysis of a cellular lysate is complete in as little as 30 min. We have successfully utilized the method for analysis of cellular lysates, enriched membrane preparations, and immunoprecipitates. We expect that due to its robustness and simplicity, the method will become an essential proteomics tool.
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Affiliation(s)
- Alexandre Zougman
- Cancer Research UK Centre, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
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Thomas JA, Chovanec P, Stolz JF, Basu P. Mapping the protein profile involved in the biotransformation of organoarsenicals using an arsenic metabolizing bacterium. Metallomics 2014; 6:1958-69. [DOI: 10.1039/c4mt00185k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Insight into the organoarsenic metabolism of Alkaliphilus oremlandii OhILAs by comprehensive proteomic analysis.
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Affiliation(s)
- John A. Thomas
- Department of Chemistry and Biochemistry
- Duquesne University
- Pittsburgh, USA
| | - Peter Chovanec
- Department of Chemistry and Biochemistry
- Duquesne University
- Pittsburgh, USA
- Biological Sciences
- Duquesne University
| | - John F. Stolz
- Biological Sciences
- Duquesne University
- Pittsburgh, USA
| | - Partha Basu
- Department of Chemistry and Biochemistry
- Duquesne University
- Pittsburgh, USA
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Yu XP, Guo RY, Su ML, Ming DS, Lin CZ, Deng Y, Lin ZZ, Su ZJ. Dynamic Changes of Treg and Th17 Cells and Related Cytokines Closely Correlate With the Virological and Biochemical Response in Chronic Hepatitis B Patients Undergoing Nucleos(t)ide Analogues Treatment. HEPATITIS MONTHLY 2013; 13:e15332. [PMID: 24403916 PMCID: PMC3877654 DOI: 10.5812/hepatmon.15332] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/07/2013] [Accepted: 11/17/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND The restoration of HBV-specific T-cell response during antiviral therapy is associated with CD4+T-cell activity. Treg cells and Th17 cells are subtypes of CD4+T cell. However, it has remained unknown how the Treg and Th17 cells and their associated cytokines affect nucleos(t)ide analogues (NA) antiviral efficacy. OBJECTIVES The aim of the present study was to provide a new insight to evaluate the NA antiviral therapy for patients with chronic hepatitis B (CHB). PATIENTS AND METHODS Forty-four CHB patients hospitalized between July 2010 and August 2011 were enrolled in this study. They were received NA (entecavir, lamivudine and adefovir) treatment for 14.42 ± 13.08 weeks, and the peripheral blood was collected. The frequencies of Treg and Th17 cells were detected by flow cytometric analysis, and the levels of IL-10, TGF-β1, IL-17 and IL-23 were measured by enzyme-linked immunosorbent assay (ELISA). RESULTS In complete and partial-responders, Treg cells frequencies and IL-10, TGF-β1, IL-23 levels were all decreased significantly after NA therapy, while Th17 cells and the IL-17 levels were increased slightly. Treg/Th17 ratio was only dramatically declined in complete-responders. But there was no significant difference in non-responders. Either HBV DNA decreased by at least 2 log copies /mL or ALT turned to normal level, Treg cells frequencies and IL-10, TGF-β1, IL-23 levels were significantly reduced. Meanwhile, Treg cells were positively correlated with HBV DNA and ALT. CONCLUSIONS The changes of Treg and Th17 cells and their associated cytokines were related to virological and biochemical responses.
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Affiliation(s)
- Xue-Ping Yu
- Department of Infectious Diseases, the First Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Ru-Yi Guo
- Department of Infectious Diseases, the First Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Mi-Long Su
- Clinical Laboratory, the First Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - De-Song Ming
- Clinical Laboratory, the First Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Cheng-Zu Lin
- Clinical Laboratory, the First Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Yong Deng
- Department of Infectious Diseases, the Second People's Hospital of Pingxiang, Pingxiang, China
| | - Zhen-Zhong Lin
- Clinical Laboratory, the First Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
| | - Zhi-Jun Su
- Department of Infectious Diseases, the First Hospital of Quanzhou, Fujian Medical University, Quanzhou, China
- Corresponding Author: Zhi-Jun Su, Department of Infectious Diseases, the First Hospital of Quanzhou, Fujian Medical University, No. 250, East Street, Licheng District, 362000, Quanzhou, China. Tel/Fax: +86-595-22277281, E-mail:
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Wanner JP, Subbaiah R, Skomorovska-Prokvolit Y, Shishani Y, Boilard E, Mohan S, Gillespie R, Miyagi M, Gobezie R. Proteomic profiling and functional characterization of early and late shoulder osteoarthritis. Arthritis Res Ther 2013; 15:R180. [PMID: 24286485 PMCID: PMC3979061 DOI: 10.1186/ar4369] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 10/17/2013] [Indexed: 12/17/2022] Open
Abstract
INTRODUCTION The development of effective treatments for osteoarthritis (OA) has been hampered by a poor understanding of OA at the cellular and molecular levels. Emerging as a disease of the 'whole joint', the importance of the biochemical contribution of various tissues, including synovium, bone and articular cartilage, has become increasingly significant. Bathing the entire joint structure, the proteomic analysis of synovial fluid (SF) from osteoarthritic shoulders offers a valuable 'snapshot' of the biologic environment throughout disease progression. The purpose of this study was to identify differentially expressed proteins in early and late shoulder osteoarthritic SF in comparison to healthy SF. METHODS A quantitative 18O labeling proteomic approach was employed to identify the dysregulated SF proteins in early (n = 5) and late (n = 4) OA patients compared to control individuals (n = 5). In addition, ELISA was used to quantify six pro-inflammatory and two anti-inflammatory cytokines. RESULTS Key results include a greater relative abundance of proteins related to the complement system and the extracellular matrix in SF from both early and late OA. Pathway analyses suggests dysregulation of the acute phase response, liver x receptor/retinoid x receptor (LXR/RXR), complement system and coagulation pathways in both early and late OA. The network related to lipid metabolism was down-regulated in both early and late OA. Inflammatory cytokines including interleukin (IL) 6, IL 8 and IL 18 were up-regulated in early and late OA. CONCLUSIONS The results suggest a dysregulation of wound repair pathways in shoulder OA contributing to the presence of a 'chronic wound' that progresses irreversibly from early to later stages of OA. Protease inhibitors were downregulated in late OA suggesting uncontrolled proteolytic activity occurring in late OA. These results contribute to the theory that protease inhibitors represent promising therapeutic agents which could limit proteolytic activity that ultimately leads to cartilage destruction.
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Affiliation(s)
- John Paul Wanner
- Department of Orthopaedics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - Roopashree Subbaiah
- Department of Orthopaedics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - Yelenna Skomorovska-Prokvolit
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - Yousef Shishani
- Department of Orthopaedics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - Eric Boilard
- Centre de Recherche en Rhumatologie et Immunologie, Centre de Recherche du Centre Hospitalier Universitaire de Québec, Faculté de Médecine de l’Université Laval, Québec, QC G1V 4G2, Canada
| | - Sujatha Mohan
- Laboratory for Integrated Bioinformatics, RIKEN Center for Integrative Medical Sciences (IMS-RCAI), RIKEN Yokohama Institute, Kanagawa, 230 0045, Japan
| | - Robert Gillespie
- Department of Orthopaedics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - Masaru Miyagi
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
| | - Reuben Gobezie
- Department of Orthopaedics, Case Western Reserve University, School of Medicine, Cleveland, OH, USA
- Cleveland Shoulder Institute, University Hospitals of Cleveland, 5885 Landerbrook Drive, Monarch Center, Mayfield Heights, OH, 44121, USA
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Shan G, Ye M, Zhu B, Zhu L. Enhanced cytotoxicity of pentachlorophenol by perfluorooctane sulfonate or perfluorooctanoic acid in HepG2 cells. CHEMOSPHERE 2013; 93:2101-2107. [PMID: 23972907 DOI: 10.1016/j.chemosphere.2013.07.054] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 07/25/2013] [Accepted: 07/29/2013] [Indexed: 06/02/2023]
Abstract
Chlorinated phenols and perfluoroalkyl acids (PFAAs) are two kinds of pollutants which are widely present in the environment. Considering liver is the primary toxic target organ for these two groups of chemicals, it is interesting to evaluate the possible joint effects of them on liver. In this work, the combined toxicity of pentachlorophenol (PCP) and perfluorooctane sulfonate (PFOS) or perfluorooctanoic acid (PFOA) were investigated using HepG2 cells. The results indicated that PFOS and PFOA could strengthen PCP's hepatotoxicity. Further studies showed that rather than intensify the oxidative stress or promote the biotransformation of PCP, PFOS (or PFOA) might lead to strengthening of the oxidative phosphorylation uncoupling of PCP. By measuring the intracellular PCP concentration and the cell membrane properties, it was suggested that PFOS and PFOA could disrupt the plasma membrane and increase the membrane permeability. Thus, more cellular accessibility of PCP was induced when they were co-exposed to PCP and PFOS (or PFOA), leading to increased cytotoxicity. Further research is warranted to better understand the combined toxicity of PFAAs and other environmental pollutants.
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Affiliation(s)
- Guoqiang Shan
- College of Environmental Science and Engineering, Tianjin Key Laboratory of Urban Ecology Environmental Remediation and Pollution Control, Nankai University, Tianjin 300071, PR China
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18
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 970] [Impact Index Per Article: 88.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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19
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Kohno H, Chen Y, Kevany BM, Pearlman E, Miyagi M, Maeda T, Palczewski K, Maeda A. Photoreceptor proteins initiate microglial activation via Toll-like receptor 4 in retinal degeneration mediated by all-trans-retinal. J Biol Chem 2013; 288:15326-41. [PMID: 23572532 DOI: 10.1074/jbc.m112.448712] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although several genetic and biochemical factors are associated with the pathogenesis of retinal degeneration, it has yet to be determined how these different impairments can cause similar degenerative phenotypes. Here, we report microglial/macrophage activation in both a Stargardt disease and age-related macular degeneration mouse model caused by delayed clearance of all-trans-retinal from the retina, and in a retinitis pigmentosa mouse model with impaired retinal pigment epithelium (RPE) phagocytosis. Mouse microglia displayed RPE cytotoxicity and increased production of inflammatory chemokines/cytokines, Ccl2, Il1b, and Tnf, after coincubation with ligands that activate innate immunity. Notably, phagocytosis of photoreceptor proteins increased the activation of microglia/macrophages and RPE cells isolated from model mice as well as wild-type mice. The mRNA levels of Tlr2 and Tlr4, which can recognize proteins as their ligands, were elevated in mice with retinal degeneration. Bone marrow-derived macrophages from Tlr4-deficient mice did not increase Ccl2 after coincubation with photoreceptor proteins. Tlr4(-/-)Abca4(-/-)Rdh8(-/-) mice displayed milder retinal degenerative phenotypes than Abca4(-/-)Rdh8(-/-) mice. Additionally, inactivation of microglia/macrophages by pharmacological approaches attenuated mouse retinal degeneration. This study demonstrates an important contribution of TLR4-mediated microglial activation by endogenous photoreceptor proteins in retinal inflammation that aggravates retinal cell death. This pathway is likely to represent an underlying common pathology in degenerative retinal disorders.
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Affiliation(s)
- Hideo Kohno
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106-7286, USA
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Abstract
Integral membrane proteins reside within the bilayer membranes that surround cells and organelles, playing critical roles in movement of molecules across them and the transduction of energy and signals. While their extreme amphipathicity presents technical challenges, biological mass spectrometry has been applied to all aspects of membrane protein chemistry and biology, including analysis of primary, secondary, tertiary, and quaternary structures as well as the dynamics that accompany functional cycles and catalysis.
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Affiliation(s)
- Julian P Whitelegge
- The Pasarow Mass Spectrometry Laboratory, The NPI-Semel Institute for Neuroscience and Human Behavior, The David Geffen School of Medicine, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, California 90095, United States.
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21
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Ning Z, Seebun D, Hawley B, Chiang CK, Figeys D. From cells to peptides: "one-stop" integrated proteomic processing using amphipols. J Proteome Res 2013; 12:1512-9. [PMID: 23394071 DOI: 10.1021/pr301064z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In proteomics, detergents and chaotropes are indispensable for proteome analysis, not only for protein extraction, but also for protein digestion. To increase the protein extraction efficiency, detergents are usually added in the lysis buffer to extract membrane proteins out of membrane structure and to maintain protein in solutions. In general, these detergents need to be removed prior to protein digestion, usually by precipitation or ultrafiltration. Digestion often takes place in the presence of chaotropic reagents, such as urea, which often need to be removed prior to mass spectrometry. The addition and removal of detergents and chaotropes require multiple steps that are time-consuming and can cause sample losses. Amphipols (APols) are a different class of detergents that have physical and solubilization properties that are distinct from conventional detergents. They have primarily been used in protein structure analysis for membrane protein trapping and stabilization. Here, we demonstrate a simple and rapid protocol for total and membrane proteome preparation using APols. We demonstrate that APols added for cell lysis help maintain the proteome in solution, are compatible with protein digestion using trypsin, and can readily be removed prior to mass spectrometry by a one-step acidification and centrifugation. This protocol is much faster, can be performed in a single tube, and can readily replace the conventional detergent/chaotrope approaches for total and membrane proteome analysis.
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Affiliation(s)
- Zhibin Ning
- Ottawa Institute of Systems Biology, Department of Biochemistry, Immunology and Microbiology, University of Ottawa, Ontario, Canada
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22
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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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23
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Rao Kadiyala CS, Mullangi V, Zhou X, Vukoti KM, Miyagi M. Rapid and effective removal of perfluorooctanoic acid from proteomics samples. Proteomics 2012; 12:2271-5. [DOI: 10.1002/pmic.201100546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | | | - Xiang Zhou
- Department of Chemistry; Cleveland State University; Cleveland; OH; USA
| | - Krishna M. Vukoti
- Case Center for Proteomics and Bioinformatics, Case Western Reserve University; Cleveland; OH; USA
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Yuan Y, Kadiyala CS, Ching TT, Hakimi P, Saha S, Xu H, Yuan C, Mullangi V, Wang L, Fivenson E, Hanson RW, Ewing R, Hsu AL, Miyagi M, Feng Z. Enhanced energy metabolism contributes to the extended life span of calorie-restricted Caenorhabditis elegans. J Biol Chem 2012; 287:31414-26. [PMID: 22810224 DOI: 10.1074/jbc.m112.377275] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Caloric restriction (CR) markedly extends life span and improves the health of a broad number of species. Energy metabolism fundamentally contributes to the beneficial effects of CR, but the underlying mechanisms that are responsible for this effect remain enigmatic. A multidisciplinary approach that involves quantitative proteomics, immunochemistry, metabolic quantification, and life span analysis was used to determine how CR, which occurs in the Caenorhabditis elegans eat-2 mutants, modifies energy metabolism of the worm, and whether the observed modifications contribute to the CR-mediated physiological responses. A switch to fatty acid metabolism as an energy source and an enhanced rate of energy metabolism by eat-2 mutant nematodes were detected. Life span analyses validated the important role of these previously unknown alterations of energy metabolism in the CR-mediated longevity of nematodes. As observed in mice, the overexpression of the gene for the nematode analog of the cytosolic form of phosphoenolpyruvate carboxykinase caused a marked extension of the life span in C. elegans, presumably by enhancing energy metabolism via an altered rate of cataplerosis of tricarboxylic acid cycle anions. We conclude that an increase, not a decrease in fuel consumption, via an accelerated oxidation of fuels in the TCA cycle is involved in life span regulation; this mechanism may be conserved across phylogeny.
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Affiliation(s)
- Yiyuan Yuan
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, USA
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Doucette AA, Tran JC, Wall MJ, Fitzsimmons S. Intact proteome fractionation strategies compatible with mass spectrometry. Expert Rev Proteomics 2012; 8:787-800. [PMID: 22087661 DOI: 10.1586/epr.11.67] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Proteome fractionation refers to separation at the level of intact proteins. Proteome fractionation may precede sample digestion and subsequent peptide-level separation and detection (i.e., bottom-up mass spectrometry [MS]). For top-down MS, proteome fractionation acts as a stand-alone separation platform, since intact proteins are directly analyzed by the mass spectrometer. Regardless of the MS identification strategy, separation of intact proteins has clear benefits as a result of decreasing sample complexity. However, this stage of the workflow also creates considerable challenges, which are generally absent from the counterpart peptide separation experiment. For example, maintaining protein solubility is a key concern before, during and after separation. To this end, surfactants such as sodium dodecyl sulfate may be employed during fractionation, so long as they are eliminated prior to MS. In this article, current strategies for proteome fractionation in a MS-compatible format are reviewed, illustrating the challenges and outlooks on this important aspect of proteomics.
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Affiliation(s)
- Alan A Doucette
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS, B3H 4R2, Canada.
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26
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Vieira DB, Crowell AMJ, Doucette AA. Perfluorooctanoic acid and ammonium perfluorooctanoate: volatile surfactants for proteome analysis? RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2012; 26:523-531. [PMID: 22302492 DOI: 10.1002/rcm.6127] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RATIONALE Fluorinated surfactants are being explored as mass spectrometry (MS)-friendly alternatives to sodium dodecyl sulfate (SDS) for proteome analysis. Previous work demonstrates perfluorooctanoic acid (PFOA) to be compatible with electrospray ionization (ESI)-MS. The high volatility of PFOA provides an intrinsic approach to potentially eliminate the surfactant during ESI, or alternatively through solvent evaporation prior to MS. The ammonium salt of PFOA, ammonium perfluorooctanoate (APFO), is likely favored for proteome experiments; the MS and liquid chromatography (LC)/MS tolerance of APFO has not been established for proteome applications. METHODS Standard proteins and peptides, as well as a yeast proteome mixture, were individually spiked with surfactants (APFO, PFOA, SDS), and subjected to direct infusion ESI-MS, LC/MS/MS and LC/UV. The level of fluorinated surfactant remaining after solvent evaporation under varying conditions (time, pH, salt and protein content) was quantified and compared to the threshold tolerance level of the surfactant in an MS experiment (determined herein). RESULTS Whereas PFOA is found ineffective at assisting protein solubilization, APFO is as effective as SDS for resolubilization of acetone-precipitated yeast proteins (~100% recovery). Unfortunately, the LC and MS threshold tolerance of APFO is only minimally greater than SDS (~2-fold higher concentration to cause 50% suppression). Nonetheless, the benefits of APFO in a proteome experiment are realized following a one-step evaporation protocol for removal of the surfactant in acidified solvent. CONCLUSIONS APFO is considered a favoured alternative to SDS for proteome solubilization. Strictly speaking, APFO is not an 'MS-friendly' surfactant for proteome characterization; the detergent not only suppresses ESI signals at high concentration, but also perturbs reversed phase separation. However, the simplicity of APFO removal ahead of LC/MS justifies its use over the conventional SDS.
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Affiliation(s)
- Douglas B Vieira
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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28
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Abstract
Proteomic analysis requires the combination of an extensive suite of technologies including protein processing and separation, micro-flow HPLC, MS and bioinformatics. Although proteomic technologies are still in flux, approaches that bypass gel electrophoresis (gel-free approaches) are dominating the field of proteomics. Along with the development of gel-free proteomics, came the development of devices for the processing of proteomic samples termed proteomic reactors. These microfluidic devices provide rapid, robust and efficient pre-MS sample procession by performing protein sample preparation/concentration, digestion and peptide fractionation. The proteomic reactor has advanced in two major directions: immobilized enzyme reactor and ion exchange-based proteomic reactor. This review summarizes the technical developments and biological applications of the proteomic reactor over the last decade.
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Affiliation(s)
- Hu Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, ON, Canada
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29
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Ning Z, Zhou H, Wang F, Abu-Farha M, Figeys D. Analytical Aspects of Proteomics: 2009–2010. Anal Chem 2011; 83:4407-26. [DOI: 10.1021/ac200857t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Hu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Fangjun Wang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China 116023
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