51
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Ouvry-Patat SA, Torres MP, Quek HH, Gelfand CA, O'Mullan P, Nissum M, Schroeder GK, Han J, Elliott M, Dryhurst D, Ausio J, Wolfenden R, Borchers CH. Free-flow electrophoresis for top-down proteomics by Fourier transform ion cyclotron resonance mass spectrometry. Proteomics 2008; 8:2798-808. [DOI: 10.1002/pmic.200800079] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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52
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Balgley BM, Wang W, Song T, Fang X, Yang L, Lee CS. Evaluation of confidence and reproducibility in quantitative proteomics performed by a capillary isoelectric focusing-based proteomic platform coupled with a spectral counting approach. Electrophoresis 2008; 29:3047-54. [DOI: 10.1002/elps.200800050] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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53
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Kwon KH, Park GW, Kim JY, Lee SK, Lee JH, Kim YH, Kim SY, Park YM, Yoo JS. Island clustering analysis for the comparison of the membrane and the soluble protein fractions of human brain proteome. Proteomics 2008; 8:1149-61. [PMID: 18283667 DOI: 10.1002/pmic.200700756] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A protein identified in multiple separate bands of a 1-D gel reflects variation in the molecular weight caused by alternative splicing, endoproteolytic cleavage, or PTMs, such as glycosylation or ubiquitination. To characterize such a protein distribution over the bands, we defined an entity called an 'island' as the band region including the bands of the same protein identified sequentially. We quantified the island distribution using a new variable called an Iscore. Previously, as described in Park et al.. (Proteomics 2006, 6, 4978-4986.), we analyzed human brain tissue using a multidimensional MS/MS separation method. Here, the new method of island analysis was applied to the previous proteome data. The soluble and membrane protein fractions of human brain tissue were reanalyzed using the island distribution. The proteome of the soluble fraction exhibited more variation in island positions than that of the membrane fraction. Through the island analysis, we identified protein modifications and protein complexes over the 1-D gel bands.
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54
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Manabe T, Jin Y. Noncovalent interactions in human plasma proteins analyzed by the comparison of nondenaturing and denaturing micro‐2‐D gel electrophoresis patterns after polypeptide assignment using matrix‐assisted laser desorption/ionization‐mass spectrometry and peptide mass fingerprinting. Electrophoresis 2008; 29:2672-88. [DOI: 10.1002/elps.200700893] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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55
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Reinhardt T, Lippolis J. Developmental Changes in the Milk Fat Globule Membrane Proteome During the Transition from Colostrum to Milk. J Dairy Sci 2008; 91:2307-18. [DOI: 10.3168/jds.2007-0952] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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56
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Liu J, Liu X, Baeyens WRG, Delanghe JR, Ouyang J. A Novel Probe Au(III) for Chemiluminescent Image Detection of Protein Blots on Nitrocellulose Membranes. J Proteome Res 2008; 7:1884-90. [DOI: 10.1021/pr700616u] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jia Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Xia Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Willy R. G. Baeyens
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Joris R. Delanghe
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
| | - Jin Ouyang
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China, Department of Pharmaceutical Analysis, Faculty of Pharmaceutical Sciences, Ghent University, Harelbekestraat 72, B-9000 Ghent, Belgium, and Department of Clinical Chemistry, Microbiology and Immunology, Ghent University Hospital, De Pintelaan 185, B-9000 Ghent, Belgium
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57
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Two-dimensional separation of human plasma proteins using iterative free-flow electrophoresis. Proteomics 2008; 7:4218-27. [PMID: 17973290 DOI: 10.1002/pmic.200700166] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Blood plasma is the most complex human-derived proteome, containing other tissue proteomes as subsets. This proteome has only been partially characterized due to the extremely wide dynamic range of the plasma proteins of more than ten orders of magnitude. Thus, the reduction in sample complexity prior to mass spectrometric analysis is particularly important and alternative separation methodologies are required to more effectively mine the lower abundant plasma proteins. Here, we demonstrated a novel separation approach using 2-D free-flow electrophoresis (FFE) separating proteins and peptides in solution according to their pI prior to LC-MS/MS. We used the combination of sequential protein and peptide separation by first separating the plasma proteins into specific FFE fractions. Tryptic digests of the separated proteins were generated and subsequently separated using FFE. The protein separation medium was optimized to segregate albumin into specific fractions containing only few other proteins. An optimization of throughput for the protein separation reduced the separation time of 1 mL of plasma to approximately 3 h providing sufficient material for digestion and the subsequent peptide separation. Our approach revealed low-abundant proteins (e.g., L-selectin at 17 ng/mL and vascular endothelial-cadherin precursor at 30 ng/mL) and several tissue leakage products, thus providing a powerful orthogonal separation step in the proteomics workflow.
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58
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Simpson RJ, Bernhard OK, Greening DW, Moritz RL. Proteomics-driven cancer biomarker discovery: looking to the future. Curr Opin Chem Biol 2008; 12:72-7. [PMID: 18295612 DOI: 10.1016/j.cbpa.2008.02.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 02/01/2008] [Accepted: 02/11/2008] [Indexed: 11/29/2022]
Abstract
Availability of a suite of biomarkers for early detection, stratification into distinct subtypes, and monitoring progression or response to therapy promises significant improvements in clinical outcomes for cancer patients. However, despite the recent progress in proteomics technologies based on mass spectrometry (MS), discovery of novel clinical assessment tools has been slow. This is, partly due to the inherent difficulties in working with blood as the biospecimen for candidate discovery. A better understanding of the limitations of blood for comparative protein profiling and a better appreciation of the advantages of cancer tissue or cancer cell secretomes have the potential to greatly enhance the progress.
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Affiliation(s)
- Richard J Simpson
- Joint Proteomics Laboratory, Ludwig Institute for Cancer Research and the Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3055, Australia.
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59
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Liu J, Ouyang J, Baeyens WRG, Delanghe JR, Wang Z, Liu J, Zhang H. A novel probe for chemiluminescent image detection of proteins in two-dimensional gel electrophoresis. Electrophoresis 2008; 29:716-25. [DOI: 10.1002/elps.200700424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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60
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Abstract
Prefractionation of complex protein samples prior to mass spectrometry provides a method for the isolation of low-abundance proteins into specific fractions thereby enabling their identification. Free-flow electrophoresis in the isoelectric focusing mode (IEF-FFE) presents a complementary approach to established prefractionation methodologies. Proteins are separated in solution according to their isoelectric point (pI) with a high throughput of sample volume. The separation may be performed under denaturing or nondenaturing conditions and detergents may be added to promote protein solubilization. A protocol covering the pH range from pH 3 to 9 under denaturing conditions was used to illustrate the method of IEF-FFE including sample preparation prior to reversed-phase liquid chromatography and tandem mass spectrometry. The IEF-FFE separation was applied to a sample of human urine.
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61
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Greening DW, Glenister KM, Kapp EA, Moritz RL, Sparrow RL, Lynch GW, Simpson RJ. Comparison of human platelet membrane-cytoskeletal proteins with the plasma proteome: Towards understanding the platelet-plasma nexus. Proteomics Clin Appl 2008; 2:63-77. [DOI: 10.1002/prca.200780067] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Indexed: 11/06/2022]
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62
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Wang J, Gutierrez P, Edwards N, Fenselau C. Integration of 18O labeling and solution isoelectric focusing in a shotgun analysis of mitochondrial proteins. J Proteome Res 2007; 6:4601-7. [PMID: 17994687 PMCID: PMC2562304 DOI: 10.1021/pr070401e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Forward and reverse (18)O labeling are integrated with solution isoelectric focusing and capillary LC-tandem mass spectrometry to evaluate a new strategy for quantitative proteomics and to study abundance changes in mitochondrial proteins associated with drug resistance in MCF-7 human cancer cells. Galectin-3 binding protein, which is involved in apoptosis, was detected only in the resistant cell line, as a result of reverse labeling. Among 278 proteins identified, 12 were detected with abundances altered at least 2-fold.
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Affiliation(s)
- Jinshan Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Peter Gutierrez
- Greenebaum Cancer Center, University of Maryland Medical School, Baltimore, Maryland 21201
| | - Nathan Edwards
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland 20742
| | - Catherine Fenselau
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
- Greenebaum Cancer Center, University of Maryland Medical School, Baltimore, Maryland 21201
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63
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Chen Y, Guo Z, Wang X, Qiu C. Sample preparation. J Chromatogr A 2007; 1184:191-219. [PMID: 17991475 DOI: 10.1016/j.chroma.2007.10.026] [Citation(s) in RCA: 252] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 10/08/2007] [Accepted: 10/10/2007] [Indexed: 11/17/2022]
Abstract
A panorama of sample preparation methods has been composed from 481 references, with a highlight of some promising methods fast developed during recent years and a somewhat brief introduction on most of the well-developed methods. All the samples were commonly referred to molecular composition, being extendable to particles including cells but not to organs, tissues and larger bodies. Some criteria to evaluate or validate a sample preparation method were proposed for reference. Strategy for integration of several methods to prepare complicated protein samples for proteomic studies was illustrated and discussed.
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Affiliation(s)
- Yi Chen
- Beijing National Laboratory of Molecular Science, Laboratory of Analytical Chemistry for Life Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, China.
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64
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Ahn SM, Simpson RJ. Body fluid proteomics: Prospects for biomarker discovery. Proteomics Clin Appl 2007; 1:1004-15. [PMID: 21136753 DOI: 10.1002/prca.200700217] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Indexed: 12/22/2022]
Abstract
Many diseases are caused by perturbations of cellular signaling pathways and related pathway networks as a result of genetic aberrations. These perturbations are manifested by altered cellular protein profiles in the fluids bathing tissue/organs (i.e., the tissue interstitial fluid, TIF). A major challenge of clinical chemistry is to quantitatively map these perturbed protein profiles - the so-called "signatures of disease" - using modern proteomic technologies. This information can be utilized to design protein biomarkers for the early detection of disease, monitoring disease progression and efficacy of drug action. Here, we discuss the use of body fluids in the context of prospective biomarker discovery, and the marked 1000-1500-fold dilution of body fluid proteins, during their passage from TIF to the circulatory system. Further, we discuss proteomics strategies aimed at depleting major serum proteins, especially albumin, in order to focus on low-abundance protein/peptides in plasma. A major limitation of depletion strategies is the removal of low-molecular weight protein/peptides which specifically bind major plasma proteins. We present a prototype model, using albumin, for understanding the multifaceted nature of biomarker research, highlighting the involvement of albumin in Alzheimer's disease. This model underscores the need for a system-level understanding for biomarker research and personalized medicine.
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Affiliation(s)
- Sung-Min Ahn
- Joint ProteomicS Laboratory, Ludwig Institute for Cancer Research, Walter and Eliza Hall Institute of Medical Research, Royal Melbourne Hospital Parkville, Victoria, Australia; Gachon Institute for Systems Medicine, Gachon University of Medicine and Science, Incheon, Korea
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65
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Wang W, Guo T, Song T, Lee CS, Balgley BM. Comprehensive yeast proteome analysis using a capillary isoelectric focusing-based multidimensional separation platform coupled with ESI-MS/MS. Proteomics 2007; 7:1178-87. [PMID: 17366490 DOI: 10.1002/pmic.200600722] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As demonstrated in this study, a CIEF-based multidimensional separation platform not only is compatible with the detergent-based membrane protein preparation protocol, but also achieves both the largest yeast membrane proteome coverage and the most comprehensive analysis of the yeast proteome to date. By using a 1% false discovery rate for total peptide identifications, a total of 2513 distinct yeast proteins are identified from the SDS-solubilized fraction with an average of 5.4 peptides leading to each protein identification. Among proteins identified from the SDS-solubilized fraction, 407 proteins are predicted to contain at least two or more transmembrane domains using TMHMM (www.cbs.dtu.dk/services/TMHMM-2.0/), corresponding to 46% yeast membrane proteome coverage. Only four additional membrane proteins are identified in the soluble and urea-solubilized fractions, affirming the utility of SDS extraction for enriching the membrane proteome. By combining proteome results obtained from the soluble, urea-solubilized, and SDS-solubilized fractions, a single yeast proteome analysis yields the identification of 3632 distinct yeast proteins, corresponding to 55% theoretical yeast proteome coverage or 70% of proteins predicted to be expressed during log-phase growth in rich media.
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Affiliation(s)
- Weijie Wang
- Calibrant Biosystems, Gaithersburg, MD 20878, USA
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66
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Smith JC, Lambert JP, Elisma F, Figeys D. Proteomics in 2005/2006: developments, applications and challenges. Anal Chem 2007; 79:4325-43. [PMID: 17477510 DOI: 10.1021/ac070741j] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jeffrey C Smith
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ontario, Canada K1H 8M5
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67
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Lam HT, Josserand J, Lion N, Girault HH. Modeling the Isoelectric Focusing of Peptides in an OFFGEL Multicompartment Cell. J Proteome Res 2007; 6:1666-76. [PMID: 17397209 DOI: 10.1021/pr0606023] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In proteomic analysis of complex samples at the peptide level (termed shotgun proteomics), an effective prefractionation is crucial to decrease the complexity of the peptide mixture for further analysis. In this perspective, the high-resolving power of the IEF fractionation step is a determining parameter, in order to obtain well-defined fractions and correct information on peptide isoelectric points, to provide an additional filter for protein identification. Here, we explore the resolving power of OFFGEL IEF as a prefractionation tool to separate peptides. By modeling the peak width evolution versus the peptide charge gradient at pI, we demonstrate that for the three proteomes considered in silico (Deinococcus radiodurans, Saccharomyces cerevisiae, and Homo sapiens), 90% of the peptides should be correctly focused and recovered in two wells at most. This result strongly suggests OFFGEL to be used as a powerful fractionation tool in shotgun proteomics. The influence of the height and shape of the compartments is also investigated, to give the optimal cell dimensions for an enhanced peptide recovery and fast focusing time.
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Affiliation(s)
- Hoang-Trang Lam
- Laboratoire d'Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland
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68
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Guo T, Wang W, Rudnick PA, Song T, Li J, Zhuang Z, Weil RJ, DeVoe DL, Lee CS, Balgley BM. Proteome analysis of microdissected formalin-fixed and paraffin-embedded tissue specimens. J Histochem Cytochem 2007; 55:763-72. [PMID: 17409379 DOI: 10.1369/jhc.7a7177.2007] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Targeted proteomics research, based on the enrichment of disease-relevant proteins from isolated cell populations selected from high-quality tissue specimens, offers great potential for the identification of diagnostic, prognostic, and predictive biological markers for use in the clinical setting and during preclinical testing and clinical trials, as well as for the discovery and validation of new protein drug targets. Formalin-fixed and paraffin-embedded (FFPE) tissue collections, with attached clinical and outcome information, are invaluable resources for conducting retrospective protein biomarker investigations and performing translational studies of cancer and other diseases. Combined capillary isoelectric focusing/nano-reversed-phase liquid chromatography separations equipped with nano-electrospray ionization-tandem mass spectrometry are employed for the studies of proteins extracted from microdissected FFPE glioblastoma tissues using a heat-induced antigen retrieval (AR) technique. A total of 14,478 distinct peptides are identified, leading to the identification of 2733 non-redundant SwissProt protein entries. Eighty-three percent of identified FFPE tissue proteins overlap with those obtained from the pellet fraction of fresh-frozen tissue of the same patient. This large degree of protein overlapping is attributed to the application of detergent-based protein extraction in both the cell pellet preparation protocol and the AR technique.
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Affiliation(s)
- Tong Guo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
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69
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Xie H, Bandhakavi S, Griffin TJ. Evaluating preparative isoelectric focusing of complex peptide mixtures for tandem mass spectrometry-based proteomics: a case study in profiling chromatin-enriched subcellular fractions in Saccharomyces cerevisiae. Anal Chem 2007; 77:3198-207. [PMID: 15889909 DOI: 10.1021/ac0482256] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have evaluated the use of free-flow electrophoresis, an emerging separation method for preparative isoelectric focusing of complex peptide mixtures, as a tool for high-throughput tandem mass spectrometry-based proteomic analysis. In this study, we investigated the ability of free-flow electrophoresis to resolve and fractionate complex peptide mixtures and also the effectiveness of using peptide isoelectric point in conjunction with peptide match probability scoring in sequence database searching. As a model system for this study, we analyzed a chromatin-enriched fraction from the yeast Saccharomyces cerevisiae. This mixture was fractionated using preparative isoelectric focusing by free-flow electrophoresis, followed by online capillary liquid chromatography electrospray tandem mass spectrometry and sequence database searching. Our results demonstrate that (1) FFE effectively resolves and fractionates complex peptide mixtures on the basis of peptide isoelectric point and (2) the introduction of peptide pI is effective in minimizing both false positive and false negative sequence matches in sequence database searching of tandem mass spectrometry data.
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Affiliation(s)
- Hongwei Xie
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, 6-155 Jackson Hall, Minneapolis, Minnesota 55455, USA
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70
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Chi A, Huttenhower C, Geer LY, Coon JJ, Syka JEP, Bai DL, Shabanowitz J, Burke DJ, Troyanskaya OG, Hunt DF. Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A 2007; 104:2193-8. [PMID: 17287358 PMCID: PMC1892997 DOI: 10.1073/pnas.0607084104] [Citation(s) in RCA: 456] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present a strategy for the analysis of the yeast phosphoproteome that uses endo-Lys C as the proteolytic enzyme, immobilized metal affinity chromatography for phosphopeptide enrichment, a 90-min nanoflow-HPLC/electrospray-ionization MS/MS experiment for phosphopeptide fractionation and detection, gas phase ion/ion chemistry, electron transfer dissociation for peptide fragmentation, and the Open Mass Spectrometry Search Algorithm for phosphoprotein identification and assignment of phosphorylation sites. From a 30-microg (approximately 600 pmol) sample of total yeast protein, we identify 1,252 phosphorylation sites on 629 proteins. Identified phosphoproteins have expression levels that range from <50 to 1,200,000 copies per cell and are encoded by genes involved in a wide variety of cellular processes. We identify a consensus site that likely represents a motif for one or more uncharacterized kinases and show that yeast kinases, themselves, contain a disproportionately large number of phosphorylation sites. Detection of a pHis containing peptide from the yeast protein, Cdc10, suggests an unexpected role for histidine phosphorylation in septin biology. From diverse functional genomics data, we show that phosphoproteins have a higher number of interactions than an average protein and interact with each other more than with a random protein. They are also likely to be conserved across large evolutionary distances.
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71
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Zhu K, Zhao J, Lubman DM, Miller FR, Barder TJ. Protein pI shifts due to posttranslational modifications in the separation and characterization of proteins. Anal Chem 2007; 77:2745-55. [PMID: 15859589 DOI: 10.1021/ac048494w] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins from breast cancer cell lines are characterized using a 2-D liquid separation technique in which protein pI is used as the first-dimension separation parameter. To effect this protein pI separation, chromatofocusing(CF) is employed whereby a pH gradient is generated on-column using a weak anion exchange medium with the intact proteins fractionated and collected every 0.2 pH unit. It is demonstrated that the pI for expressed intact proteins as generated by CF is an important parameter for identification and characterization of the actual protein modifications occurring in the cancer cell. For most proteins, the experimentally determined pI is very close to that predicted by the databases. In other cases, however, where the pI is observed to be shifted from the expected value, it is shown that this shift is often correlated to protein modifications. The modifications that cause such shifts include truncations and deletions often observed in cancer cells or phosphorylations that can shift the pI by several pH units. It is also shown that the effects of phosphorylation on the observed shift can vary depending upon the protein and the amount of phosphorylation. Moreover, large changes in the pI are often observed for proteins with a pI above 7.0 upon phosphorylation, whereas little change is observed for proteins with a pI of approximately 5.0. The expressed protein's pI value thus becomes an important parameter together with the intact MW value, peptide map, and MS/MS results for identification of the presence and type of posttranslational modifications occurring in the cancer cell.
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Affiliation(s)
- Kan Zhu
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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72
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Balgley BM, Wang W, De Voe DL, Lee CS. Mass spectrometry-based tissue proteomics for cancer biomarker discovery. Per Med 2007; 4:45-58. [PMID: 29793304 DOI: 10.2217/17410541.4.1.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There is an urgent need for the development of technologies that allow the monitoring of protein expression and processing in tumor tissues resulting from development, physiology and disease state. To address the issue of cell heterogeneity in the tissue section, several microdissection techniques have been developed to provide a rapid and straightforward method for isolating selected subpopulations of cells for downstream molecular analysis. Development and demonstration of an effective discovery-based proteome platform, Gemini, are particularly highlighted for its capabilities of achieving ultrasensitive and comprehensive analysis of minute proteins extracted from targeted cells in tissue specimens. The greatest expectations for targeted proteomics research using enriched nonmalignant and malignant cells from high-quality fresh-frozen, formalin-fixed and paraffin-embedded specimens reside in the identification of diagnostic, prognostic and predictive biological markers in the clinical setting, as well as the discovery and validation of new protein targets in the biopharmaceutical industry.
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Affiliation(s)
- Brian M Balgley
- Calibrant Biosystems, 910 Clopper Road, Suite 220N, Gaithersburg, MD 20878, USA.
| | - Weijie Wang
- Calibrant Biosystems, 910 Clopper Road, Suite 220N, Gaithersburg, MD 20878, USA.
| | - Don L De Voe
- Department of Mechanical Engineering and Bioengineering Program, University of Maryland, College Park, MD 20742, USA.
| | - Cheng S Lee
- Calibrant Biosystems, 910 Clopper Road, Suite 220N, Gaithersburg, MD 20878, USA. .,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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73
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Wang W, Guo T, Rudnick PA, Song T, Li J, Zhuang Z, Zheng W, Devoe DL, Lee CS, Balgley BM. Membrane Proteome Analysis of Microdissected Ovarian Tumor Tissues Using Capillary Isoelectric Focusing/Reversed-Phase Liquid Chromatography−Tandem MS. Anal Chem 2006; 79:1002-9. [PMID: 17263328 DOI: 10.1021/ac061613i] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work expands our tissue proteome capabilities from the analysis of soluble proteins in previous studies to the examination of membrane proteins within the pellets of enriched and selectively isolated tumor cells procured from microdissected tissue specimens. The pellets of targeted ovarian tumor cells are treated by two different membrane protein extraction methods, including the use of detergent and organic solvent. The detergent-based membrane protein preparation protocol not only extracts proteins effectively from cell pellets but also is compatible with subsequent proteome analysis using combined capillary isoelctric focusing/nano reversed-phase liquid chromatography separations coupled with nano electrospray ionization mass spectrometry. Among proteins identified from an amount of pellet equivalent to 20 000 cells, 773 proteins are predicted to contain one or more transmembrane domains, corresponding to 22% membrane proteome coverage within the SwissProt Human protein sequence entries.
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Affiliation(s)
- Weijie Wang
- Calibrant Biosystems, 910 Clopper Road, Suite 220N, Gaithersburg, Maryland 20878, USA
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74
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Malmström J, Lee H, Nesvizhskii AI, Shteynberg D, Mohanty S, Brunner E, Ye M, Weber G, Eckerskorn C, Aebersold R. Optimized Peptide Separation and Identification for Mass Spectrometry Based Proteomics via Free-Flow Electrophoresis. J Proteome Res 2006; 5:2241-9. [PMID: 16944936 DOI: 10.1021/pr0600632] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multidimensional LC-MS based shotgun proteomics experiments at the peptide level have traditionally been carried out by ion exchange in the first dimension and reversed-phase liquid chromatography in the second. Recently, it has been shown that isoelectric focusing (IEF) is an interesting alternative approach to ion exchange separation of peptides in the first dimension. Here we present an improved protocol for peptide separation by continuous free-flow electrophoresis (FFE) as the first dimension in a two-dimensional peptide separation work flow. By the use of a flat pI gradient and a mannitol and urea based separation media we were able to perform high-throughput proteome analysis with improved interfacing between FFE and RPLC-MS/MS. The developed protocol was applied to a cytosolic fraction from Schneider S2 cells from Drosophila melanogaster, resulting in the identification of more than 10,000 unique peptides with high probability. To improve the accuracy of the peptide identification following FFE-IEF we incorporated the pI information as an additional parameter into a statistical model for discrimination between correct and incorrect peptide assignments to MS/MS spectra.
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Affiliation(s)
- Johan Malmström
- Institute for Molecular Systems Molecular Biology, Swiss Federal Institute for Technology Zürich (ETH), Hoenggerberg 8093 Zürich, Switzerland
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75
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Immler D, Greven S, Reinemer P. Targeted proteomics in biomarker validation: detection and quantification of proteins using a multi-dimensional peptide separation strategy. Proteomics 2006; 6:2947-58. [PMID: 16619308 DOI: 10.1002/pmic.200500659] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Authentic biomarkers, distilling the essence of a complex, functionally significant process in a mammalian system into a precise, physicochemical measurement have been implicated as a tool of increasing importance for drug discovery and development. However, even in spite of recent technological advances, validating a new biomarker candidate, where generation of suitable antibodies is required, is still a long-lasting task. Methods to accelerate initial validation by MS approaches have been suggested, but all methods described so far are associated with serious drawbacks, finally leading to non-generic methods of detection and quantification. Moreover, when complex body fluids are used as samples, efficient debulking strategies are crucial to open a window of analytical sensitivity in the ng/mL range, where many diagnostically relevant analytes are present. Here we report the proof-of-principle of a multi-dimensional strategy for accelerated initial validation of biomarker candidates by MS, which promises to be generally applicable, sensitive and quantitative. The method presented employs a combination of electrophoretic and chromatographic steps on the peptide level, followed by MS quantification using isotopically labeled synthetic peptides as internal standards. Our proposed workflow includes up to four dimensions, finally resulting in a desired LOD sufficient to detect and quantify diagnostically relevant analytes from complex samples. Although the current state of the method only represents a starting point for further validation and development, it reveals great potential in biomarker validation.
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Affiliation(s)
- Dorian Immler
- Bayer Healthcare AG, PH-R&D-R-EU-ET, Wuppertal, Germany
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76
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Tang HY, Speicher DW. Complex proteome prefractionation using microscale solution isoelectrofocusing. Expert Rev Proteomics 2006; 2:295-306. [PMID: 16000077 DOI: 10.1586/14789450.2.3.295] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The proteomes of mammalian cells, tissues and biologic fluids are complex and consist of proteins present over a wide dynamic range. Current protein profiling technologies do not have the capacity to overcome the sample complexity for comprehensive analysis of complex proteomes. A common strategy to substantially expand protein profiling capacities is sample prefractionation. A prefractionation method developed in the authors' laboratory, microscale solution isoelectrofocusing, has resulted in a commercial product, the ZOOM IEF Fractionator, which provides a simple and convenient method for high-resolution separation of complex proteomes based upon their isoelectric points. Complex human samples such as cancer cells and biologic fluids can be fractionated into well-resolved fractions with minimal cross-contamination of proteins between adjacent fractions. This review focuses on the application of microscale solution isoelectrofocusing prefractionation and subsequent downstream strategies in expanding protein profiling capacities and mining low-abundance proteins of complex proteomes.
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Affiliation(s)
- Hsin-Yao Tang
- The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104, USA.
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77
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Gilson PR, Nebl T, Vukcevic D, Moritz RL, Sargeant T, Speed TP, Schofield L, Crabb BS. Identification and stoichiometry of glycosylphosphatidylinositol-anchored membrane proteins of the human malaria parasite Plasmodium falciparum. Mol Cell Proteomics 2006; 5:1286-99. [PMID: 16603573 DOI: 10.1074/mcp.m600035-mcp200] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most proteins that coat the surface of the extracellular forms of the human malaria parasite Plasmodium falciparum are attached to the plasma membrane via glycosylphosphatidylinositol (GPI) anchors. These proteins are exposed to neutralizing antibodies, and several are advanced vaccine candidates. To identify the GPI-anchored proteome of P. falciparum we used a combination of proteomic and computational approaches. Focusing on the clinically relevant blood stage of the life cycle, proteomic analysis of proteins labeled with radioactive glucosamine identified GPI anchoring on 11 proteins (merozoite surface protein (MSP)-1, -2, -4, -5, -10, rhoptry-associated membrane antigen, apical sushi protein, Pf92, Pf38, Pf12, and Pf34). These proteins represent approximately 94% of the GPI-anchored schizont/merozoite proteome and constitute by far the largest validated set of GPI-anchored proteins in this organism. Moreover MSP-1 and MSP-2 were present in similar copy number, and we estimated that together these proteins comprise approximately two-thirds of the total membrane-associated surface coat. This is the first time the stoichiometry of MSPs has been examined. We observed that available software performed poorly in predicting GPI anchoring on P. falciparum proteins where such modification had been validated by proteomics. Therefore, we developed a hidden Markov model (GPI-HMM) trained on P. falciparum sequences and used this to rank all proteins encoded in the completed P. falciparum genome according to their likelihood of being GPI-anchored. GPI-HMM predicted GPI modification on all validated proteins, on several known membrane proteins, and on a number of novel, presumably surface, proteins expressed in the blood, insect, and/or pre-erythrocytic stages of the life cycle. Together this work identified 11 and predicted a further 19 GPI-anchored proteins in P. falciparum.
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Affiliation(s)
- Paul R Gilson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3050, Australia
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78
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Cantin GT, Venable JD, Cociorva D, Yates JR. Quantitative phosphoproteomic analysis of the tumor necrosis factor pathway. J Proteome Res 2006; 5:127-34. [PMID: 16396503 PMCID: PMC2570265 DOI: 10.1021/pr050270m] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation has become a focus of many proteomic studies due to the central role that it plays in biology. We combine peptide-based gel-free isoelectric focusing and immobilized metal affinity chromatography to enhance the detection of phosphorylation events within complex protein samples using LC-MS. This method is then used to carry out a quantitative phosphoproteomic analysis of the tumor necrosis factor (TNF) pathway using HeLa cells metabolically labeled with 15N-containing amino acids, where 145 phosphorylation sites were found to be up-regulated upon the activation of the TNF pathway.
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Affiliation(s)
| | | | | | - John R. Yates
- To whom correspondence should be addressed. E-mail: . Tel: 858-784-8862. Fax: 858-784-8883
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79
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Yu T, Zhang Y, You C, Zhuang J, Wang B, Liu B, Kang Y, Tang Y. Controlled Nanozeolite-Assembled Electrode: Remarkable Enzyme-Immobilization Ability and High Sensitivity as Biosensor. Chemistry 2006; 12:1137-43. [PMID: 16250058 DOI: 10.1002/chem.200500562] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
An enzyme-immobilized nanozeolite-assembled electrode was prepared by controlled assembly of nanometer-sized Linder type-L zeolite (nano-LTL-zeolite) on an indium tin oxide (ITO) glass electrode surface, and subsequent immobilization of cytochrome c. Cyclic voltammetric (CV) and amperometric experiments showed that, relative to other reported electrodes, the enzyme-immobilized electrodes possess fast electron-transfer rates (2.2 s(-1)), a broad linear range (15-540 micromol L(-1)), a low detection limit (3.2 nmol L(-1)), a remarkably long lifetime (5 months), and high stability in the pH range 5-10. These characteristics could be due to the fact that nanozeolites assembled on ITO have high immobilization ability and facilitate interaction with enzymes. The function controllability of these enzyme electrodes, resulting from the facile manipulability of nanozeolite-assembled layers, may provide a possibility to rationally design biosensors.
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Affiliation(s)
- Tao Yu
- Department of Chemistry and Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, Fudan University, 200433, China
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80
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Moritz RL, Simpson RJ. Liquid-based free-flow electrophoresis-reversed-phase HPLC: a proteomic tool. Nat Methods 2005; 2:863-73. [PMID: 16278658 DOI: 10.1038/nmeth1105-863] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Robert L Moritz
- Joint Proteomics Laboratory, Ludwig Institute for Cancer Research (Melbourne Branch) and The Walter and Eliza Hall Institute of Medical Research, Parkville, 3050, Victoria, Australia
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81
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Xu A, Sluszny C, Yeung ES. Prototype for integrated two-dimensional gel electrophoresis for protein separation. J Chromatogr A 2005; 1087:177-82. [PMID: 16130711 DOI: 10.1016/j.chroma.2005.02.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Two-dimensional gel electrophoresis practitioners have long waited for a fully automated system. This article presents an integrated platform that is capable of complete automation from sample introduction to spots detection. The strip gel for the first dimensional separation is fixed on the edge of a discrete planar stage before separation. A pair of platinum pin electrodes for isoelectric focusing (IEF) makes contact from underneath the stage. IEF is performed directly after rehydration and protein loading. After the first dimensional separation, sodium dodecyl sulfate (SDS) equilibration is done on the same stage without moving the gel. The IEF stage is then moved horizontally to couple with a precast second dimensional gel. The <0.5 mm gap between the two gels is filled with poly (ethylene oxide) solution. After SDS-polyacrylamide gel electrohporesis separation, a charge-coupled device camera is used to detect spots via protein native fluorescence excited by a Hg (Xe) lamp with the gel inside the running cell. Potential for full automation is demonstrated with 0.5 microg of Escherichia coli proteins on this miniaturized platform. More than 240 spots are detected in a total experiment time of <2.5 h.
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Affiliation(s)
- Aoshuang Xu
- Ames Laboratory, US Department of Energy and Department of Chemistry, Iowa State University, Ames, IA 50011, USA
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82
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Kapp EA, Schütz F, Connolly LM, Chakel JA, Meza JE, Miller CA, Fenyo D, Eng JK, Adkins JN, Omenn GS, Simpson RJ. An evaluation, comparison, and accurate benchmarking of several publicly available MS/MS search algorithms: sensitivity and specificity analysis. Proteomics 2005; 5:3475-90. [PMID: 16047398 DOI: 10.1002/pmic.200500126] [Citation(s) in RCA: 286] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
MS/MS and associated database search algorithms are essential proteomic tools for identifying peptides. Due to their widespread use, it is now time to perform a systematic analysis of the various algorithms currently in use. Using blood specimens used in the HUPO Plasma Proteome Project, we have evaluated five search algorithms with respect to their sensitivity and specificity, and have also accurately benchmarked them based on specified false-positive (FP) rates. Spectrum Mill and SEQUEST performed well in terms of sensitivity, but were inferior to MASCOT, X!Tandem, and Sonar in terms of specificity. Overall, MASCOT, a probabilistic search algorithm, correctly identified most peptides based on a specified FP rate. The rescoring algorithm, PeptideProphet, enhanced the overall performance of the SEQUEST algorithm, as well as provided predictable FP error rates. Ideally, score thresholds should be calculated for each peptide spectrum or minimally, derived from a reversed-sequence search as demonstrated in this study based on a validated data set. The availability of open-source search algorithms, such as X!Tandem, makes it feasible to further improve the validation process (manual or automatic) on the basis of "consensus scoring", i.e., the use of multiple (at least two) search algorithms to reduce the number of FPs. complement.
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Affiliation(s)
- Eugene A Kapp
- Joint ProteomicS Laboratory, Ludwig Institute for Cancer Research (Melbourne Branch)/Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
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83
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Moritz RL, Clippingdale AB, Kapp EA, Eddes JS, Ji H, Gilbert S, Connolly LM, Simpson RJ. Application of 2-D free-flow electrophoresis/RP-HPLC for proteomic analysis of human plasma depleted of multi high-abundance proteins. Proteomics 2005; 5:3402-13. [PMID: 16052629 DOI: 10.1002/pmic.200500096] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Free-flow electrophoresis (FFE) and rapid (6 min) RP-HPLC was used to fractionate human citrate-treated plasma. Prior to analysis, the six most abundant proteins in plasma were removed by immunoaffinity chromatography; both depleted plasma and the fraction containing the six abundant proteins depleted were taken for MS-based analysis. Fractionated proteins were digested with trypsin and the generated peptides were subjected to MS-based peptide sequencing. To date, 78 plasma proteins have been unambiguously identified by manual validation from 16% (15/96 FFE total fractions) of the collected FFE pools; 55 identifications were based on > or = 2 tryptic peptides and 23 using single peptides. The molecular weight range of proteins and peptides isolated by this method ranged from approximately 190 K (e.g., Complement C3 and C4) to approximately 4-6 K (e.g., CRISPP and Apolipoprotein C1). This FFE/RP-HPLC approach reveals low-abundance proteins and peptides (e.g., L-Selectin approximately 17 ng/mL and the cancer-associated SCM-recognition, immunodefense suppression, and serine protease protection peptide (CRISPP) at approximately 0.5-1 ng/mL), where CRISPP was found in association with alpha-1-antitrypsin as a non-covalent complex, in the fraction containing the depleted high-abundance proteins. In contrast to shotgun proteomic approaches, the FFE/RP-HPLC method described here allows the identification of potentially interesting peptides to be traced back to their protein of origin, and for the first time, has confirmed the "protein sponge" hypothesis where the 35 residue CRISPP polypeptide is non-covalently complexed with the major circulating plasma protein alpha-1-antitrypsin.
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Affiliation(s)
- Robert L Moritz
- Joint Proteomics Laboratory, Ludwig Institute for Cancer Research (Melbourne Branch), The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
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84
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Abstract
The shotgun proteomic strategy based on digesting proteins into peptides and sequencing them using tandem mass spectrometry and automated database searching has become the method of choice for identifying proteins in most large scale studies. However, the peptide-centric nature of shotgun proteomics complicates the analysis and biological interpretation of the data especially in the case of higher eukaryote organisms. The same peptide sequence can be present in multiple different proteins or protein isoforms. Such shared peptides therefore can lead to ambiguities in determining the identities of sample proteins. In this article we illustrate the difficulties of interpreting shotgun proteomic data and discuss the need for common nomenclature and transparent informatic approaches. We also discuss related issues such as the state of protein sequence databases and their role in shotgun proteomic analysis, interpretation of relative peptide quantification data in the presence of multiple protein isoforms, the integration of proteomic and transcriptional data, and the development of a computational infrastructure for the integration of multiple diverse datasets.
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85
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Xie H, Rhodus NL, Griffin RJ, Carlis JV, Griffin TJ. A catalogue of human saliva proteins identified by free flow electrophoresis-based peptide separation and tandem mass spectrometry. Mol Cell Proteomics 2005; 4:1826-30. [PMID: 16103422 DOI: 10.1074/mcp.d500008-mcp200] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human saliva has great potential for clinical disease diagnostics. Constructing a comprehensive catalogue of saliva proteins using proteomic approaches is a necessary first step to identifying potential protein biomarkers of disease. However, because of the challenge presented in cataloguing saliva proteins with widely varying abundance, new proteomic approaches are needed. To this end, we used a newly developed approach coupling peptide separation using free flow electrophoresis with linear ion trap tandem mass spectrometry to identify proteins in whole human saliva. We identified 437 proteins with high confidence (false positive rate below 1%), producing the largest catalogue of proteins from a single saliva sample to date and providing new information on the composition and potential diagnostic utility of this fluid. The statistically validated, transparently presented, and annotated dataset provides a model for presenting large scale proteomic data of this type, which should facilitate better dissemination and easier comparisons of proteomic datasets from future studies in saliva.
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Affiliation(s)
- Hongwei Xie
- Department of Biochemistry, Molecular Biology, and Biophysics, School of Dentistry, University of Minnesota, Minneapolis 55455, USA
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86
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Moebius J, Zahedi RP, Lewandrowski U, Berger C, Walter U, Sickmann A. The human platelet membrane proteome reveals several new potential membrane proteins. Mol Cell Proteomics 2005; 4:1754-61. [PMID: 16081409 DOI: 10.1074/mcp.m500209-mcp200] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We present the first focused proteome study on human platelet membranes. Due to the removal of highly abundant cytoskeletal proteins a wide spectrum of known platelet membrane proteins and several new and hypothetical proteins were accessible. In contrast to other proteome studies we focused on prefractionation and purification of membranes from human platelets according to published protocols to reduce sample complexity and enrich interesting membrane proteins. Subsequently protein separation by common one-dimensional SDS-PAGE as well as the combined benzyldimethyl-n-hexadecylammonium chloride/SDS separation technique was performed prior to mass spectrometry analysis by nano-LC-ESI-MS/MS. We demonstrate that the application of both separation systems in parallel is required for maximization of protein tagging out of a complex sample. Furthermore the identification of several potential membrane proteins in human platelets yields new potential targets in functional platelet research.
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Affiliation(s)
- Jan Moebius
- Protein Mass Spectrometry and Functional Proteomics Group, Rudolf Virchow Center for Experimental Biomedicine, Julius Maximilians University of Wuerzburg, Versbacher Strasse 9, 97078 Wuerzburg, Germany
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87
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Ottens AK, Kobeissy FH, Wolper RA, Haskins WE, Hayes RL, Denslow ND, Wang KKW. A Multidimensional Differential Proteomic Platform Using Dual-Phase Ion-Exchange Chromatography−Polyacrylamide Gel Electrophoresis/Reversed-Phase Liquid Chromatography Tandem Mass Spectrometry. Anal Chem 2005; 77:4836-45. [PMID: 16053296 DOI: 10.1021/ac050478r] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Differential proteomic analysis has arisen as a large-scale means to discern proteome-wide changes upon treatment, injury, or disease. Tandem protein separation methods are required for large-scale differential proteomic analysis. Here, a novel multidimensional platform for resolving and differentially analyzing complex biological samples is presented. The platform, collectively termed CAX-PAGE/RPLC-MSMS, combines biphasic ion-exchange chromatography with polyacrylamide gel electrophoresis for protein separation, quantification, and differential band targeting, followed by capillary reversed-phase liquid chromatography and data-dependent tandem mass spectrometry for quantitative and qualitative peptide analysis. CAX-PAGE provides high protein resolving power with a theoretical peak capacity of 3570, extendable to 7600, a wide protein mass range verified from 16 to 273 kDa, and reproducible differential sample comparison without the added expense of fluorescent dyes and imaging equipment. Demonstrated using a neuroproteomic model, CAX-PAGE revealed an increased number of differential proteins, 137, compared with 82 found by 2D difference gel electrophoresis. When combined with RPLC-MSMS for protein identification, an additional quantification step is performed for internal validation, confirming a 2-fold or greater change in 89% of identified differential targets.
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Affiliation(s)
- Andrew K Ottens
- Center for Neuroproteomics and Biomarker Research, University of Florida, Gainesville, Florida 32610, USA.
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88
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Gulcicek EE, Colangelo CM, McMurray W, Stone K, Williams K, Wu T, Zhao H, Spratt H, Kurosky A, Wu B. Proteomics and the analysis of proteomic data: an overview of current protein-profiling technologies. CURRENT PROTOCOLS IN BIOINFORMATICS 2005; Chapter 13:Unit 13.1. [PMID: 18428746 PMCID: PMC3863626 DOI: 10.1002/0471250953.bi1301s10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In recent years, several proteomic methodologies have been developed that now make it possible to identify, characterize, and comparatively quantify the relative level of expression of hundreds of proteins that are coexpressed in a given cell type or tissue, or that are found in biological fluids such as serum. These advances have resulted from the integration of diverse scientific disciplines including molecular and cellular biology, protein/peptide chemistry, bioinformatics, analytical and bioanalytical chemistry, and the use of instrumental and software tools such as multidimensional electrophoretic and chromatographic separations and mass spectrometry. In this unit, some of the common protein-profiling technologies are reviewed, along with the accompanying data-analysis tools.
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89
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Obermaier C, Jankowski V, Schmutzler C, Bauer J, Wildgruber R, Infanger M, Köhrle J, Krause E, Weber G, Grimm D. Free-flow isoelectric focusing of proteins remaining in cell fragments following sonication of thyroid carcinoma cells. Electrophoresis 2005; 26:2109-16. [PMID: 15861465 DOI: 10.1002/elps.200410422] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The method of preparing protein mixtures for electrophoretic analysis of membrane-associated cell proteins was improved. By sonication, about one-half of the proteins of thyroid cells were released into the supernatant, while the other half preferentially comprising membrane proteins still remained in cell fragments, which could be sedimented by centrifugation. After sonication, even those proteins which remained in cell fragments, could completely be dissolved by free-flow isoelectric focusing media. They migrated through the free-flow electrophoresis chamber without forming precipitates. Because of these improvements, it was possible to show that the two thyroid cancer cell lines ML-1 and ONCO-DG1 express cytokeratin 8 at similar rates, but cytokeratins 7 and 18 differently. In addition, the presence of inorganic pyrophosphatase, tubulin-beta-5, and tubulin-beta-1 chains in human thyroid cells was proved for the first time.
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90
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Holm A, Storbråten E, Mihailova A, Karaszewski B, Lundanes E, Greibrokk T. Combined solid-phase extraction and 2D LC–MS for characterization of the neuropeptides in rat-brain tissue. Anal Bioanal Chem 2005; 382:751-9. [PMID: 15889243 DOI: 10.1007/s00216-005-3146-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2004] [Revised: 01/24/2005] [Accepted: 02/04/2005] [Indexed: 10/25/2022]
Abstract
A comprehensive two-dimensional capillary liquid chromatographic (2D LC) method has been established for determination of neuropeptides in rat brain tissue. Rats were exposed to different levels of stress before sacrificing and the aim of this study was to design a powerful separation and detection technique capable of characterizing differences between cerebral neuropeptide expression as a function of stress level. Rat brain samples were homogenized and subjected to clean-up by solid-phase extraction (SPE) on both a reversed-phase (C(18)) and a weak cation-exchange (CBA) cartridge. The samples were divided in two fractions (A and B) depending on retention on the CBA column. Subsequently, 50 microL of the sample were injected on to a strong cation exchanger (SCX) at a mobile phase pH of 3, which enabled preconcentration of positively charged compounds. The trapped compounds were eluted using step gradients of ammonium formate in water-ACN (90:10, v/v). Before enrichment in the second dimension, the eluate from the first dimension was diluted with water containing 0.1% TFA. The compounds eluting from the first dimension were trapped in the second dimension using a dual precolumn system consisting of two short capillary columns packed with Kromasil C(18), 10 microm particles. Subsequently, the trapped compounds were backflushed on to a 10 cm long, 320 microm I.D. analytical column packed with Kromasil C(18) 3.5 microm particles, on which they were efficiently separated. Detection was performed using an ion-trap mass spectrometer (ITMS) in both the MS and the MS-MS mode. Comparison of base-peak chromatograms (BPC) from MS analysis of stressed and non-stressed rats clearly revealed several differences in neuropeptide expression. The MS-MS data obtained combined with Mascot software were employed for peptide identification.
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Affiliation(s)
- Anders Holm
- Institute of Immunology, Rikshospitalet University Hospital, 0027 Oslo, Norway.
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91
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Resing KA, Ahn NG. Proteomics strategies for protein identification. FEBS Lett 2005; 579:885-9. [PMID: 15680968 DOI: 10.1016/j.febslet.2004.12.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2004] [Revised: 12/03/2004] [Accepted: 12/03/2004] [Indexed: 01/04/2023]
Abstract
The information from genome sequencing provides new approaches for systems-wide understanding of protein networks and cellular function. DNA microarray technologies have advanced to the point where nearly complete monitoring of gene expression is feasible in several organisms. An equally important goal is to comprehensive survey cellular proteomes and profile protein changes under different cellular states. This presents a complex analytical problem, due to the chemical variability between proteins and peptides. Here, we discuss strategies to improve accuracy and sensitivity of peptide identification, distinguish represented protein isoforms, and quantify relative changes in protein abundance.
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Affiliation(s)
- Katheryn A Resing
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309-0215, USA
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92
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2448604 DOI: 10.1002/cfg.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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