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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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2
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Güray MZ, Zheng S, Doucette AA. Mass Spectrometry of Intact Proteins Reveals +98 u Chemical Artifacts Following Precipitation in Acetone. J Proteome Res 2017; 16:889-897. [PMID: 28088865 DOI: 10.1021/acs.jproteome.6b00841] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein precipitation in acetone is frequently employed ahead of mass spectrometry for sample preconcentration and purification. Unfortunately, acetone is not chemically inert; mass artifacts have previously been observed on glycine-containing peptides when exposed to acetone under acidic conditions. We herein report a distinct chemical modification occurring at the level of intact proteins when incubated in acetone. This artifact manifests as one or more satellite peaks in the MS spectrum of intact protein, spaced 98 u above the mass of the unmodified protein. Other artifacts (+84, +112 u) also appear upon incubation of proteins or peptides in acetone. The reaction is pH-sensitive, being suppressed when proteins are exposed to acetone under acidic conditions. The +98 u artifact is speculated to originate through an intermediate product of aldol condensation of acetone to form diacetone alcohol and mesityl oxide. A +98 u product could originate from nucleophilic attack on mesityl oxide or through condensation with diacetone alcohol. Given the extent of modification possible upon exposure of proteins to acetone, particularly following overnight solvent exposure or incubation at room temperature, an awareness of the variables influencing this novel modification is valued by proteomics researchers who employ acetone precipitation for protein purification.
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Affiliation(s)
- Melda Z Güray
- Department of Chemistry, Dalhousie University , PO Box 15000, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Shi Zheng
- Department of Chemistry, Dalhousie University , PO Box 15000, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University , PO Box 15000, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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3
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Streamlined Membrane Proteome Preparation for Shotgun Proteomics Analysis with Triton X-100 Cloud Point Extraction and Nanodiamond Solid Phase Extraction. MATERIALS 2016; 9:ma9050385. [PMID: 28773508 PMCID: PMC5503057 DOI: 10.3390/ma9050385] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/28/2016] [Accepted: 05/11/2016] [Indexed: 12/19/2022]
Abstract
While mass spectrometry (MS) plays a key role in proteomics research, characterization of membrane proteins (MP) by MS has been a challenging task because of the presence of a host of interfering chemicals in the hydrophobic protein extraction process, and the low protease digestion efficiency. We report a sample preparation protocol, two-phase separation with Triton X-100, induced by NaCl, with coomassie blue added for visualizing the detergent-rich phase, which streamlines MP preparation for SDS-PAGE analysis of intact MP and shot-gun proteomic analyses. MP solubilized in the detergent-rich milieu were then sequentially extracted and fractionated by surface-oxidized nanodiamond (ND) at three pHs. The high MP affinity of ND enabled extensive washes for removal of salts, detergents, lipids, and other impurities to ensure uncompromised ensuing purposes, notably enhanced proteolytic digestion and down-stream mass spectrometric (MS) analyses. Starting with a typical membranous cellular lysate fraction harvested with centrifugation/ultracentrifugation, MP purities of 70%, based on number (not weight) of proteins identified by MS, was achieved; the weight-based purity can be expected to be much higher.
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4
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Rusmili MRA, Tee TY, Mustafa MR, Othman I, Hodgson WC. Isolation and characterization of α-elapitoxin-Bf1b, a postsynaptic neurotoxin from Malaysian Bungarus fasciatus venom. Biochem Pharmacol 2014; 88:229-36. [DOI: 10.1016/j.bcp.2014.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 01/03/2014] [Accepted: 01/07/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Muhamad Rusdi Ahmad Rusmili
- Monash Venom Group, Department of Pharmacology, Faculty of Medicine, Nursing and Health Sciences, 3168 Clayton, Victoria, Australia; Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus, 46150 Bandar Sunway, Malaysia
| | - Ting Yee Tee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus, 46150 Bandar Sunway, Malaysia
| | - Mohd Rais Mustafa
- Department of Pharmacology, Faculty of Medicine, University of Malaya, 59100 Kuala Lumpur, Malaysia
| | - Iekhsan Othman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Sunway Campus, 46150 Bandar Sunway, Malaysia
| | - Wayne C Hodgson
- Monash Venom Group, Department of Pharmacology, Faculty of Medicine, Nursing and Health Sciences, 3168 Clayton, Victoria, Australia.
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5
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Pham MD, Yu SSF, Han CC, Chan SI. Improved Mass Spectrometric Analysis of Membrane Proteins Based on Rapid and Versatile Sample Preparation on Nanodiamond Particles. Anal Chem 2013; 85:6748-55. [DOI: 10.1021/ac400713g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Minh D. Pham
- Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Steve S.-F. Yu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chau-Chung Han
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Sunney I. Chan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
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6
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Sodium laurate, a novel protease- and mass spectrometry-compatible detergent for mass spectrometry-based membrane proteomics. PLoS One 2013; 8:e59779. [PMID: 23555778 PMCID: PMC3610932 DOI: 10.1371/journal.pone.0059779] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/18/2013] [Indexed: 11/22/2022] Open
Abstract
The hydrophobic nature of most membrane proteins severely complicates their extraction, proteolysis and identification. Although detergents can be used to enhance the solubility of the membrane proteins, it is often difficult for a detergent not only to have a strong ability to extract membrane proteins, but also to be compatible with the subsequent proteolysis and mass spectrometric analysis. In this study, we made evaluation on a novel application of sodium laurate (SL) to the shotgun analysis of membrane proteomes. SL was found not only to lyse the membranes and solubilize membrane proteins as efficiently as SDS, but also to be well compatible with trypsin and chymotrypsin. Furthermore, SL could be efficiently removed by phase transfer method from samples after acidification, thus ensuring not to interfere with the subsequent CapLC-MS/MS analysis of the proteolytic peptides of proteins. When SL was applied to assist the digestion and identification of a standard protein mixture containing bacteriorhodoposin and the proteins in rat liver plasma membrane-enriched fractions, it was found that, compared with other two representative enzyme- and MS-compatible detergents RapiGest SF (RGS) and sodium deoxycholate (SDC), SL exhibited obvious superiority in the identification of membrane proteins particularly those with high hydrophobicity and/or multiple transmembrane domains.
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7
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Huang C, Mohanty S, Banerjee M. A novel method of production and biophysical characterization of the catalytic domain of yeast oligosaccharyl transferase. Biochemistry 2010; 49:1115-26. [PMID: 20047336 DOI: 10.1021/bi902181v] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Oligosaccharyl transferase (OT) is a multisubunit enzyme that catalyzes N-linked glycosylation of nascent polypeptides in the lumen of the endoplasmic reticulum. In the case of Saccharomyces cerevisiae, OT is composed of nine integral membrane protein subunits. Defects in N-linked glycosylation cause a series of disorders known as congenital disorders of glycosylation (CDG). The C-terminal domain of the Stt3p subunit has been reported to contain the acceptor protein recognition site and/or catalytic site. We report here the subcloning, overexpression, and a robust but novel method of production of the pure C-terminal domain of Stt3p at 60-70 mg/L in Escherichia coli. CD spectra indicate that the C-terminal Stt3p is highly helical and has a stable tertiary structure in SDS micelles. The well-dispersed two-dimensional (1)H-(15)N HSQC spectrum in SDS micelles indicates that it is feasible to determine the atomic structure by NMR. The effect of the conserved D518E mutation on the conformation of the C-terminal Stt3p is particularly interesting. The replacement of a key residue, Asp(518), located within the WWDYG signature motif (residues 516-520), led to a distinct tertiary structure, even though both proteins have similar overall secondary structures, as demonstrated by CD, fluorescence and NMR spectroscopies. This observation strongly suggests that Asp(518) plays a critical structural role, in addition to the previously proposed catalytic role. Moreover, the activity of the protein was confirmed by saturation transfer difference and nuclear magnetic resonance titration studies.
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Affiliation(s)
- Chengdong Huang
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA
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8
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Breugelmans P, Leroy B, Bers K, Dejonghe W, Wattiez R, De Mot R, Springael D. Proteomic study of linuron and 3,4-dichloroaniline degradation by Variovorax sp. WDL1: evidence for the involvement of an aniline dioxygenase-related multicomponent protein. Res Microbiol 2010; 161:208-18. [DOI: 10.1016/j.resmic.2010.01.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 01/06/2010] [Accepted: 01/21/2010] [Indexed: 11/25/2022]
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9
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Mandal SM, Dey S, Mandal M, Maria-Neto S, Franco OL. Comparative analyses of different surfactants on matrix-assisted laser desorption/ionization mass spectrometry peptide analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:567-575. [PMID: 20814080 DOI: 10.1255/ejms.1097] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been extensively used for proteomics and peptidomics analysis. Nevertheless, these analyses, when focused on low molecular mass proteins, show some limitation due to background interference from surfactant ions. Surfactants are routinely used as a solubilizing or denaturing agents for proteins and peptides. In this report, an evaluation and further comparison of the effects of an ionic surfactant, sodium dodecyl sulfate (SDS), and a non-ionic surfactant, tergitol, on MALDI-MS analyses of the amphipathic peptides, angiotensin and bradykinin, were carried out. At concentrations > or = 10 mmol L(-1), SDS deteriorates the MALDI spectral quality by reducing the signal and intensity of the analyte ions. In particular, it affects the hydrophobic peptide where the signal of surfactant-interfering ions suppresses the analyte ion signal. Whereas, the non-ionic surfactant, tergitol, improves the MALDI-MS analysis of peptide mixtures or hydrophobic peptides by reducing interference from the surfactant itself in positive ion mode analysis. Three-dimensional molecular modeling of two different peptides in complex to tergitol NP-40 and SDS were conducted in order to explain the molecular effects of both agents. In summary, while SDS must be removed from the sample solution to avoid interference of ions from SDS and suppression of analyte ion signal, tergitol at low concentrations may be used as an additive with sample solution for MALDI-MS analysis of peptides. Finally, molecular modeling analyses associated with docking were used in order to explain experimental biochemical data.
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Affiliation(s)
- Santi M Mandal
- Indian Institute of Technology, Kharagpur 721 302, West Bengal, India
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10
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Asanuma M, Fukuzawa S, Matsuda T, Hirota H. The effect of sodium dodecyl sulfate and anion-exchange silica gel on matrix-assisted laser desorption/ionization mass spectrometric analysis of proteins. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:1647-1653. [PMID: 19418491 DOI: 10.1002/rcm.4051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Sodium dodecyl sulfate (SDS), an anionic surfactant, is widely used in peptide and protein sample preparation. When the sample is analyzed by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), this surfactant can often cause signal suppression. We have previously reported an on-probe sample preparation method using a suspension of anion-exchange silica gel and sinapinic acid (i.e., gel-SA suspension) as a matrix, thereby greatly improving the MALDI signal detection of the protein solutions containing SDS. In this study, we found that a certain amount of SDS enhanced the MALDI signal intensity for protein samples. This effect was also observed when using sodium decyl sulfate and sodium tetradecyl sulfate instead of SDS. Furthermore, this on-probe sample preparation method using both SDS and the gel-SA suspension improved the detection limit of protein samples in the MALDI-MS analysis by about ten-fold as compared to that of protein samples without SDS and the gel-SA suspension. This method can be applied not only to the MALDI-MS analysis of samples containing SDS, but also to the examination of proteins at femtomole levels or insoluble proteins such as membrane proteins.
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Affiliation(s)
- Miwako Asanuma
- RIKEN Genomic Sciences Center, Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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11
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Seelert H, Krause F. Preparative isolation of protein complexes and other bioparticles by elution from polyacrylamide gels. Electrophoresis 2008; 29:2617-36. [PMID: 18494038 DOI: 10.1002/elps.200800061] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Due to its unmatched resolution, gel electrophoresis is an indispensable tool for the analysis of diverse biomolecules. By adaptation of the electrophoretic conditions, even fragile protein complexes as parts of intracellular networks migrate through the gel matrix under sustainment of their integrity. If the thickness of such native gels is significantly increased compared to the analytical version, also high sample loads can be processed. However, the cage-like network obstructs an in-depth analysis for deciphering structure and function of protein complexes and other species. Consequently, the biomolecules have to be removed from the gel matrix into solution. Several approaches summarized in this review tackle this problem. While passive elution relies on diffusion processes, electroelution employs an electric field to force biomolecules out of the gel. An alternative procedure requires a special electrophoresis setup, the continuous elution device. In this apparatus, molecules migrate in the electric field until they leave the gel and were collected in a buffer stream. Successful isolation of diverse protein complexes like photosystems, ATP-dependent enzymes or active respiratory supercomplexes and some other bioparticles demonstrates the versatility of preparative electrophoresis. After liberating particles out of the gel cage, numerous applications are feasible. They include elucidation of the individual components up to high resolution structures of protein complexes. Therefore, preparative electrophoresis can complement standard purification methods and is in some cases superior to them.
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Affiliation(s)
- Holger Seelert
- Department of Chemistry, Physical Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany.
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12
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Riederer BM. Non-covalent and covalent protein labeling in two-dimensional gel electrophoresis. J Proteomics 2008; 71:231-44. [DOI: 10.1016/j.jprot.2008.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Revised: 05/03/2008] [Accepted: 05/06/2008] [Indexed: 12/16/2022]
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13
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Yassine MM, Guo N, Zhong H, Li L, Lucy CA. Off-line coupling of preparative capillary zone electrophoresis with microwave-assisted acid hydrolysis and matrix-assisted laser desorption ionization mass spectrometry for protein sequencing. Anal Chim Acta 2007; 597:41-9. [PMID: 17658311 DOI: 10.1016/j.aca.2007.05.054] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Revised: 05/25/2007] [Accepted: 05/31/2007] [Indexed: 11/16/2022]
Abstract
An off-line coupling of capillary electrophoresis (CE) with microwave-assisted acid hydrolysis/matrix-assisted laser desorption ionization mass spectrometry (MAAH/MALDI) has been developed for protein identification and characterization. Preparative scale protein separations enable collection of 10-50 pmol of purified cytochrome c for subsequent sequencing using MAAH/MALDI. To reduce protein adsorption onto the silica surface, the cationic surfactant-based coatings, dimethylditetradecylammonium bromide and dimethyldioctadecylammonium bromide, are employed. The choice of the buffer conditions is critical for both the preparative CE and MAAH/MALDI method. The use of high buffer concentrations (100 mM Bis-tris) reduces electromigration dispersion, but suppressed MALDI ionization such that a peptide sequence coverage of only 80% was achieved at a sample loading of 40 g L(-1) of each cytochrome c. By reducing the buffer concentration to 25 mM Bis-tris, the sequence coverage increased to 95% at a sample loading of 40 g L(-1).
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Affiliation(s)
- Mahmoud M Yassine
- Department of Chemistry, Gunning/Lemieux Chemistry Centre, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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14
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Geng T, Seitz PK, Thomas ML, Xu B, Soman KV, Kurosky A, Luxon BA, Cunningham KA. Use of surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) to study protein expression in a rat model of cocaine withdrawal. J Neurosci Methods 2006; 158:1-12. [PMID: 16766040 DOI: 10.1016/j.jneumeth.2006.04.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2006] [Revised: 03/21/2006] [Accepted: 04/18/2006] [Indexed: 11/20/2022]
Abstract
Surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) is an analytical technology for proteomic analysis that combines chromatography and mass spectrometry. At present, this technology is most commonly being exploited for the simultaneous measurement of numerous proteins in serum, but has also been utilized in organ tissue, although rarely in the brain. We applied SELDI-TOF MS technology to study protein expression in the brain of rats withdrawn from repeated cocaine exposure. Our goals were to optimize sample preparation and ProteinChip Array protocols for brain tissue, to verify the reproducibility of SELDI-TOF mass spectra and to determine whether SELDI-TOF MS detects differentially expressed proteins in cocaine- versus saline-treated rats. Consequently, we have developed an optimal protocol and generated a reproducible spectral pattern with six dominant peaks in all test samples. We have detected two smaller peaks (m/z: 5179, 5030) that were significantly increased (p < 0.05) in cocaine-treated rats compared to saline-treated rats. In summary, the application of SELDI-TOF MS to the study of protein expression in a rat model of cocaine withdrawal is feasible and has the potential to generate new hypotheses.
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Affiliation(s)
- Tao Geng
- Center for Addiction Research, Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Blvd., Galveston, TX 77555-1031, United States
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15
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Goncharuk VD, Buijs RM, Mactavish D, Jhamandas JH. Neuropeptide FF distribution in the human and rat forebrain: a comparative immunohistochemical study. J Comp Neurol 2006; 496:572-93. [PMID: 16572434 DOI: 10.1002/cne.20927] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Neuropeptide FF (NPFF) is an octapeptide implicated in a variety of physiological functions, including nociception, cardiovascular responses, and neuroendocrine regulation. The NPFF gene and its mRNA are highly conserved across species. A comparative study of NPFF distribution in the human and rat forebrain was carried out by using single NPFF and double NPFF + vasopressin (VP) immunohistochemistry. NPFF is extensively localized within neurochemical circuits of human and rat forebrain. Semiquantitative analysis revealed that the densities of NPFF cells and fibers in many forebrain nuclei in the human correlate well with those observed for the same structures in the rat. High numbers of NPFF positive neurons in the dorsomedial hypothalamic nucleus and a dense plexus of NPFF fibers surrounding the fornix within the bed nucleus of the stria terminalis were identified in the human and rat forebrain. Within the hypothalamus of both species, dense NPFF innervation was observed in the perinuclear zone of the supraoptic nucleus (SO) just dorsolateral to the VP-positive neurons. Extensive NPFF innervation of ventricular ependyma and brain microvasculature were common for both species. At the same time, obvious differences in NPFF localization between the two species were also apparent. For example, in contrast to the rat SO, no NPFF- or NPFF- + VP-immunostained cells were observed in the human SO. Knowledge of NPFF neuroanatomical localization in the human brain and the relationship of these observations to those in the rat brain may provide insight into the role of this peptide in central cardiovascular and neuroendocrine regulation.
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16
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Distler AM, Kerner J, Peterman SM, Hoppel CL. A targeted proteomic approach for the analysis of rat liver mitochondrial outer membrane proteins with extensive sequence coverage. Anal Biochem 2006; 356:18-29. [PMID: 16876102 DOI: 10.1016/j.ab.2006.03.053] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2005] [Revised: 03/23/2006] [Accepted: 03/31/2006] [Indexed: 11/19/2022]
Abstract
Membrane proteins play an important role in cellular function. However, their analysis by mass spectrometry often is hindered by their hydrophobicity and/or low abundance. In this article, we present a method for the mass spectrometric analysis of membrane proteins based on the isolation of the resident membranes, isolation of the proteins by gel electrophoresis, and electroelution followed by enzymatic digestion by both trypsin and proteinase K. With this method, we have achieved 82-99% sequence coverage for the membrane proteins carnitine palmitoyltransferase-I (CPT-I), long-chain acyl-CoA synthetase (LCAS), and voltage-dependent anion channel (VDAC), isolated from rat liver mitochondrial outer membranes, including the transmembrane domains of these integral membrane proteins. This high sequence coverage allowed the identification of the isoforms of the proteins under study. This methodology provides a targeted approach for examining membrane proteins in detail.
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Affiliation(s)
- Anne M Distler
- Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
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17
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Chang CY, Liao HK, Juo CG, Chen SH, Chen YJ. Improved analysis of membrane protein by PVDF-aided, matrix-assisted laser desorption/ionization mass spectrometry. Anal Chim Acta 2006; 556:237-46. [PMID: 17723354 DOI: 10.1016/j.aca.2005.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Revised: 07/13/2005] [Accepted: 07/14/2005] [Indexed: 11/30/2022]
Abstract
Characterization of membrane proteins remains an analytical challenge because of difficulties associated with tedious isolation and purification. This study presents the utility of the polyvinylidene difluoride (PVDF) membrane for direct sub-proteome profiling and membrane protein characterization by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). The hydrophobic adsorption of protein, particularly membrane proteins, on the PVDF surface enables efficient on-PVDF washing to remove high concentrations of detergents and salts, such as up to 5% sodium dodecyl sulfate (SDS). The enhanced spectrum quality for MALDI detection is particularly notable for high molecular weight proteins. By using on-PVDF washing prior to MALDI detection, we obtained protein profiles of the detergent-containing and detergent-insoluble membrane fractions from Methylococcus capsulatus (Bath). Similar improvements of signal-to-noise ratios were shown on the MALDI spectra for proteins electroblotted from SDS-polyacrylamide gel electrophoresis (SDS-PAGE) onto the PVDF membrane. We have applied this strategy to obtain intact molecular weights of the particulate methane monooxygenase (pMMO) composed of three intrinsic membrane-bound proteins, PmoA, PmoB, and PmoC. Together with peptide sequencing by tandem mass spectrometry, post-translational modifications including N-terminal acetylation of PmoA and PmoC and alternative C-terminal truncation of PmoB were identified. The above results show that PVDF-aided MALDI-MS can be an effective approach for profiling and characterization of membrane proteins.
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Affiliation(s)
- Chih-Yang Chang
- Institute of Chemistry, Academia Sinica, 128 Sec. 2, Academia Road, Nankang, Taipei 11529, Taiwan, ROC
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18
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Hachmann JP, Amshey JW. Models of protein modification in Tris-glycine and neutral pH Bis-Tris gels during electrophoresis: effect of gel pH. Anal Biochem 2005; 342:237-45. [PMID: 15935323 DOI: 10.1016/j.ab.2005.04.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 04/09/2005] [Accepted: 04/12/2005] [Indexed: 11/16/2022]
Abstract
The pH of conventional Tris-glycine SDS-PAGE gels during a run is determined to be 9.5, in contrast to Bis-Tris-Mes gels where the pH is 7.2. Concentrations of free acrylamide are determined to be less than 10mM in commercial gels of both types, and it is found that of the major components in these gels, only glycine and protein amine or sulfhydryl functions are likely to react with residual acrylamide during the time frame of typical separations. The addition of acrylamide to sulfhydryl groups on proteins is modeled using glutathione and cysteine at acrylamide concentrations found in the commercial gels. Rate constants are determined for these reactions as well as for reaction with glycine at the pH that proteins will encounter in these gel types. The half-life for glutathione sulfhydryl at 10mM acrylamide and pH 7.2 is more than 4h at room temperature. Rates are significantly lower in Bis-Tris-Mes gels than in Tris-glycine gels, reducing the risk of adventitious protein modification. Commercial Bis-Tris-Mes gels provide a sample reduction buffer at pH 8.5 versus the conventional pH 6.8 of Tris-glycine gels. It is shown that significantly less protein degradation occurs during sample preparation at the higher pH used with Bis-Tris gels.
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19
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Norris JL, Hangauer MJ, Porter NA, Caprioli RM. Nonacid cleavable detergents applied to MALDI mass spectrometry profiling of whole cells. JOURNAL OF MASS SPECTROMETRY : JMS 2005; 40:1319-26. [PMID: 16220468 DOI: 10.1002/jms.914] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Although cleavable detergents were first synthesized a number of years ago, they have only recently been successfully applied to problems involving biological molecules. Recent reports have demonstrated that these compounds are useful for applications involving both 2D PAGE and mass spectrometry. However, most cleavable surfactants have utilized acid-labile functional groups to affect cleavage. In applications where extreme pH is required, acid cleavable detergents have limited usefulness. We report the synthesis of fluoride cleavable silane compounds and photolabile cinnamate esters as cleavable detergents having alternative cleavage chemistries than previously reported cleavable detergents. These compounds were applied to whole cell analysis using MALDI mass spectrometry, and it was demonstrated that their use results in an increase in the number of proteins analyzed by increasing protein solubility.
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Affiliation(s)
- Jeremy L Norris
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232-8575, USA
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Distler AM, Allison J, Hiser C, Qin L, Hilmi Y, Ferguson-Miller S. Mass spectrometric detection of protein, lipid and heme components of cytochrome c oxidase from R. sphaeroides and the stabilization of non-covalent complexes from the enzyme. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2004; 10:295-308. [PMID: 15103107 DOI: 10.1255/ejms.594] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The cytochrome c oxidase enzyme from the Rhodobacter sphaeroides bacteria exists as a complex of four peptide subunits, two hemes, and a variety of lipids and metal ions held together by non-covalent forces. While the native enzyme functions as an associated unit, this complex usually dissociates during MALDI- TOF analysis. Through the use of matrix additives such as sucrose, the complete complex and partial complexes can be stabilized in the MALDI-TOF experiment. The dissociation of the complex allows for the detection of the components of the enzyme. The direct detection of associated lipids from an aqueous solution of the intact enzyme may eliminate the need for enzyme disruption and lipid extraction. The partial dissociation of multisubunit enzymes in such experiments may allow for the determination of subunit-subunit and subunit-lipid interactions
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Affiliation(s)
- Anne M Distler
- Department of Chemistry, Michigan State University, East Lansing, MI 48824-1322, USA
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21
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Kalume DE, Kieffer S, Rafn K, Skou L, Andersen SO, Roepstorff P. Sequence determination of three cuticular proteins and isoforms from the migratory locust, Locusta migratoria, using a combination of Edman degradation and mass spectrometric techniques. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1645:152-63. [PMID: 12573245 DOI: 10.1016/s1570-9639(02)00531-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The cuticle (exoskeleton) is a characteristic structure of insects and other arthropods. It is an extracellular layer which surrounds and protects the insect, and it is composed of proteins, lipids, water molecules, phenolic materials and chitin. Four proteins isolated from the thorax and femur cuticle of pharate adult migratory locust, Locusta migratoria, have been purified by ion-exchange chromatography and reversed-phase high performance liquid chromatography (RP-HPLC). Their amino acid sequences were determined by combined use of mass spectrometry and automated Edman degradation. The cuticular extract was also separated by two-dimensional gel electrophoresis. In order to localize and identify the position of the proteins in the gel, a number of gel spots were excised and the proteins electroeluted. The molecular mass of some of the electroeluted proteins was determined by means of matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) as well as by electrospray mass spectrometry (ESI-MS). Two of the sequenced proteins exist as pairs of closely related isoforms; one of the pairs contains the conserved 68-residue RR-2 motif, common for proteins from solid cuticles, and the other proteins contain the short motif Ala-Ala-Pro-Ala/Val repeatedly throughout the sequence.
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Affiliation(s)
- Dário Eluan Kalume
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, 55 DK-5230 Odense M, Denmark
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22
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Keller BO, Wang Z, Li L. Low-mass proteome analysis based on liquid chromatography fractionation, nanoliter protein concentration/digestion, and microspot matrix-assisted laser desorption ionization mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 782:317-29. [PMID: 12458015 DOI: 10.1016/s1570-0232(02)00565-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HPLC fractionation combined with mass spectrometry can become a powerful tool for analyzing the proteome in the mass range below 15 kDa where efficient protein separation by gel electrophoresis can be difficult. For sensitive and high-resolution separation of the low-mass proteome, the use of analytical rather than preparative HPLC columns is preferred. However, individual fractions collected by a conventional HPLC separation usually contain a small amount of proteins whose concentrations may not be sufficiently high for subsequent enzyme digestion and protein identification by mass spectrometry. In this work, we present a high sensitivity nanoliter sample handling technique to analyze proteins fractionated by HPLC. In this technique, an individual HPLC fraction in hundreds of microliter volume is pre-concentrated to several microliters. About 700 pl of the pre-concentrated fraction is then drawn into a 20-microm I.D. capillary and dried in a small region near the capillary's entrance. This process can be repeated many times to concentrate a sufficient amount of protein to the small region of the capillary. After protein concentration, protein digestion is achieved by drawing 1 nl of chemical or enzymatic reagent into the capillary and placing it in the same region where the dried protein sits. The resulting peptides are then deposited onto a microspot in a MALDI probe for mass analysis. The performance of this technique is demonstrated with the use of a standard protein solution. This technique is applied to the identification of low-mass proteins separated by HPLC from a complex mixture of an E. coli extract.
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Affiliation(s)
- Bernd O Keller
- Department of Chemistry, Faculty of Science, University of Alberta, E3-44 Chemistry Building, Edmonton, Canada
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23
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Kraft P, Mills J, Dratz E. Mass spectrometric analysis of cyanogen bromide fragments of integral membrane proteins at the picomole level: application to rhodopsin. Anal Biochem 2001; 292:76-86. [PMID: 11319820 DOI: 10.1006/abio.2001.5072] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Advances in time-of-flight mass spectrometry allow unit mass resolution of proteins and peptides up to about 6000 Da molecular weight. Identification of larger proteins and study of their posttranslational or experimental modifications by mass analysis is greatly enhanced by cleavage into smaller fragments. Most membrane proteins are difficult to mass analyze because of their high hydrophobicity, typical expression in low quantities, and because the detergents commonly used for solubilization may be deleterious to mass analysis. Cleavage with cyanogen bromide is beneficial for analysis of membrane proteins since the methionine cleavage sites are typically located in hydrophobic domains and cleavage at these points reduces the size of the hydrophobic fragments. Cyanogen bromide also gives high cleavage yields and introduces only volatile contaminants. Even after cleavage membrane proteins often contain fragments that are difficult to chromatograph. Matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) is capable of analyzing complex mixtures without chromatography. We present a MALDI MS method that quickly and reliably identifies the cyanogen bromide fragments and posttranslational modifications of reduced and alkylated bovine rhodopsin from as little as 30 pmol of rhodopsin in detergent-solubilized retinal rod disk membranes, using 1-5 pmol of digest per sample. The amino acid sequences of some of the peptides in the digest were confirmed by post source decomposition MS analysis of the same samples. The method appears to be general and applicable to the analysis of membrane proteins and the protein composition of membrane preparations.
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Affiliation(s)
- P Kraft
- Department of Chemistry and Biochemistry, Department of Microbiology, Montana State University, 108 Gaines Hall, Bozeman, Montana 59717, USA
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24
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Chen YC, Tsai MF. Using surfactants to enhance the analyte signals in activated carbon, surface-assisted laser desorption/ionization (SALDI) mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2000; 35:1278-1284. [PMID: 11114085 DOI: 10.1002/1096-9888(200011)35:11<1278::aid-jms59>3.0.co;2-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The effect of surface activity in surface-assisted laser desorption/ionization (SALDI) mass spectrometry was examined. Several surfactants, including p-tolunensulfonic acid (PTSA), sodium dodecyl sulfate and alkyltrimethylammonium bromide, were used as analytes or additives in the SALDI matrix to demonstrate the surface activity effect. The experimental results demonstrate that analytes that have good surface activity have good sensitivity. Adding suitable amounts of surfactants to the SALDI matrix can dramatically enhance the sensitivity of analytes lacking surface activity. We propose that the enhancement of analyte signals is due to the ionic interaction between ionic surfactants and analytes because non-ionic surfactant additives in the SALDI matrix do not affect the analyte signals. The detection limit of methylephedrine can be as low as 100 pg in the SALDI analysis of 0.5 M PTSA additive in the SALDI matrix. Although other surfactants can also be used as matrix additives to enhance the analyte signal, they do not improve the ion abundance as much as PTSA does.
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Affiliation(s)
- Y C Chen
- Institute of Toxicology, Tzu Chi University, Hualien 970, Taiwan.
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25
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Jeanville PM, Woods JH, Baird TJ, Estapé ES. Direct determination of ecgonine methyl ester and cocaine in rat plasma, utilizing on-line sample extraction coupled with rapid chromatography/quadrupole orthogonal acceleration time-of-flight detection. J Pharm Biomed Anal 2000; 23:897-907. [PMID: 11022914 DOI: 10.1016/s0731-7085(00)00362-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Our current experiments assess the applicability of on-line sample extraction with coupled rapid chromatography systems to quadrupole orthogonal acceleration time-of-flight (Q-TOF) detection for the quantitative analysis of cocaine (COC), and ecgonine methyl ester (EME) in rat plasma. Experiments were performed on a Q-TOF instrument, operated in the MS/MS mode. Quantitation was achieved utilizing the most prominent parent-daughter transition and internal standard calibration techniques (COC-d3: IS). The calibration curves produced for EME and COC ranged from 5.0 to 10,000 and 0.5 to 10,000 ng/ml, respectively. Equations of regression line and correlation coefficients for the pseudo-multiple reaction monitoring (MRM) ion abundance ratio and the corresponding calibration concentrations (r2) were as follows: y = 0.0003 + 0.0703x (r2 = 0.9921) for EME and y = 0.0032 + 0.0035x (r2 = 0.9997) for COC. The system repeatability, given as percent coefficient of variation (% CV) of mean peak-area ratios, was assessed using 50 injections of a rat plasma sample from the pharmacokinetic study. The analyses were performed over the course of 5 days, rendering % CVs for EME and COC of 0.73 and 0.58, respectively. This method suggests that on-line sample extraction coupled with fast liquid chromatography/quadrupole orthogonal time-of-flight mass spectrometry may be a viable alternative for quantitative analysis of EME and COC in rat plasma.
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Affiliation(s)
- P M Jeanville
- Drug Metabolism Technology Department, Pfizer Inc., Central Research Division, Groton, CT 06340, USA.
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Abstract
Mass spectrometry (MS) has become the technique of choice to identify proteins. This has been largely accomplished by the combination of high-resolution two-dimensional (2-D) gel separation with robotic sample preparation, automated MS measurement, data analysis, and database query. Developments during the last five years in MS associated with protein gel separation are reviewed.
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Affiliation(s)
- H W Lahm
- F. Hoffmann-LaRoche Ltd., Pharmaceutical Research, Roche Genetics, Basel, Switzerland.
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27
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Mirza UA, Liu YH, Tang JT, Porter F, Bondoc L, Chen G, Pramanik BN, Nagabhushan TL. Extraction and characterization of adenovirus proteins from sodium dodecylsulfate polyacrylamide gel electrophoresis by matrix-assisted laser desorption/ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2000; 11:356-361. [PMID: 10757173 DOI: 10.1016/s1044-0305(00)00101-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
A new methodology for the extraction and characterization of proteins from Coomassie-stained sodium dodecylsulfate polyacrylamide gel electrophoresis using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been described. The utility of this methodology was demonstrated in the characterization of adenovirus proteins. The key steps in the extraction and destaining process involve washing the excised band with a combination of solvents that include 10% acetic acid, acetonitrile, methanol, and formic acid:water:isopropanol mixture. By using this procedure, we determined adenovirus proteins with molecular weights ranging from 10,000 to 110,000 Da by MALDI-MS, obtaining a detection limit of approximately 6 pmol. Parallel experiments were successfully carried out to analyze adenovirus proteins from Cu-stained gels. It was observed that increase in laser intensity resulted in significant improvements in the quality of MALDI mass spectra for the analysis of inefficiently destained proteins from Cu-stained gels.
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Affiliation(s)
- U A Mirza
- Schering-Plough Research Institute, Kenilworth, New Jersey 07033, USA.
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28
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Galvani M, Bordini E, Piubelli C, Hamdan M. Effect of experimental conditions on the analysis of sodium dodecyl sulphate polyacrylamide gel electrophoresis separated proteins by matrix-assisted laser desorption/ ionisation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2000; 14:18-25. [PMID: 10623923 DOI: 10.1002/(sici)1097-0231(20000115)14:1<18::aid-rcm826>3.0.co;2-n] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Two mixtures of proteins having molecular weights in the range approximately 8-97 kDa were separated by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and examined by delayed extraction matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS). Part of our aim in this study is to gain more insight into the influence of the various experimental conditions on the overall quality of the acquired mass spectral data. Different protein extraction procedures, two staining agents, and extraction times, were among the parameters assessed. In terms of the overall quality of the acquired mass spectra and the speed of protein recovery, ultrasonic assisted passive elution, into a solvent mixture containing formic acid/acetonitrile/2-isopropanol/water, was found to be more efficient than other elution procedures. The higher resolution associated with the delayed extraction mode allowed the identification of a number of protein modifications, including multiple formylation provoked by formic acid, cysteine alkylation caused by unpolymerised acrylamide monomers, and complexation with the staining reagents. The detection of these modifications, however, was limited to proteins under 30 kDa. Analysis of a ubiquitin tryptic digest by reflectron MALDI time-of-flight (TOF) allowed reliable identification of a number of the formylation sites.
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Affiliation(s)
- M Galvani
- GlaxoWellcome Medicines Research Centre, via Fleming 4, Verona, 37135 Italy
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