201
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Wheeler JX, Vipond C, Feavers IM. Exploring the proteome of meningococcal outer membrane vesicle vaccines. Proteomics Clin Appl 2007; 1:1198-210. [DOI: 10.1002/prca.200700204] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Indexed: 11/06/2022]
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202
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Gupta N, Shankernarayan NP, Dharmalingam K. Serum Proteome of Leprosy Patients Undergoing Erythema Nodosum Leprosum Reaction: Regulation of Expression of the Isoforms of Haptoglobin. J Proteome Res 2007; 6:3669-79. [PMID: 17658739 DOI: 10.1021/pr070223p] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Validated proteome profile allows better understanding of disease progression, subtype classification, susceptibility patterns, and disease prognosis. Leprosy is a spectral disease, with clinically, histologically, immunologically, and bacteriologically distinguishable subtypes. In addition, a significant fraction of patients undergo immune mediated reactions even after multidrug therapy (MDT). Erythema nodosum leprosum (ENL) is an immune complex mediated reactional condition in leprosy, characterized by a systemic inflammatory condition afflicting borderline lepromatous (BL) and lepromatous leprosy patients (LL). In this study, we have analyzed serum proteome of leprosy patients undergoing ENL reactions and compared it with that of healthy noncontact controls. Depletion of albumin and immunoglobulin G (IgG) was optimized using Aurum serum protein mini kit (Bio-Rad), and then two-dimensional gel electrophoresis (2-DE) of these serum samples was performed. Differentially expressed proteins were identified by MALDI-TOF and MALDI-TOF MS/MS mass spectrometry. Significant increase in one of the isoforms of alpha2 chain of haptoglobin was observed in ENL condition. In addition, haptoglobin phenotype was determined for healthy controls and leprosy patients. Hp 0-0 phenotype was detected in 21.4% of the ENL patients undergoing treatment, which on follow up examination showed typable phenotype, thus showing a condition of acquired anhaptoglobinemia. Since ENL still remains a threat to leprosy disease management, the above findings may provide new insights in understanding the development and progression of this inflammatory condition.
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Affiliation(s)
- Nishma Gupta
- Department of Genetic Engineering, School of Biotechnology, Madurai Kamaraj University, Madurai-625021, Tamil Nadu, India
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203
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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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204
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Bermúdez-Crespo J, López JL. A better understanding of molecular mechanisms underlying human disease. Proteomics Clin Appl 2007; 1:983-1003. [PMID: 21136752 DOI: 10.1002/prca.200700086] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Indexed: 01/06/2023]
Abstract
This review summarises and discusses the degree to which proteomics is contributing to medical care, providing examples and signspots for future directions. Why do genomic approaches provide a limited view of gene expression? Because of the multifactorial nature of many diseases, proteomics enables us to understand the molecular basis of disease, not only at the organism, whole-cell or tissue levels, but also in subcellular structures, protein complexes and biological fluids. The application of proteomics in medicine is expected to have a major impact by providing an integrated view of individual disease processes. This review describes several proteomic platforms and examines the role of proteomics as a tool for clinical biomarker discovery, the identification of prognostic and earlier diagnostic markers, their use in monitoring the effects of drug treatments and eventually find more efficient and safer therapeutics for a wide range of pathologies.
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Affiliation(s)
- José Bermúdez-Crespo
- Department of Genetics, Faculty of Biology, University of Santiago de Compostela, Santiago de Compostela, Spain
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205
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Drake RR, Cazares L, Semmes OJ. Mining the low molecular weight proteome of blood. Proteomics Clin Appl 2007; 1:758-68. [DOI: 10.1002/prca.200700175] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Indexed: 01/08/2023]
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206
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Gianazza E, Rocco AG, Marchetto A, Vergani L. IPG with electrodic plateaus (and other unusual procedures for 2-DE). Electrophoresis 2007; 28:2953-6. [PMID: 17640092 DOI: 10.1002/elps.200600722] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We describe some simple changes to the geometry of the IPG strips that make them suitable to the loading of very large sample volumes and of high-salt solutions. Of special relevance is the possibility of using strips with immobilized plateau(s) to either side of the gradient, or to both, also in connection with in-gel rehydration protocols and focusing in stock trays. The only requirement to achieve this is to leave the all-ready-made attitude and go back to custom polymerization of the IPGs in one's laboratory.
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Affiliation(s)
- Elisabetta Gianazza
- Gruppo di Studio per la Proteomica e la Struttura delle Proteine, Dipartimento di Scienze Farmacologiche, Università degli Studi, Milano, Italia.
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207
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Zhang J. Proteomics of human cerebrospinal fluid - the good, the bad, and the ugly. Proteomics Clin Appl 2007; 1:805-19. [PMID: 21136735 DOI: 10.1002/prca.200700081] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2007] [Indexed: 12/16/2022]
Abstract
The development of MALDI ESI in the late 1980s has revolutionized the biological sciences and facilitated the emergence of a new discipline called proteomics. Application of proteomics to human cerebrospinal fluid (CSF) has greatly hastened the advancement of characterizing the CSF proteome as well as revealing novel protein biomarkers that are diagnostic of various neurological diseases. While impressive progressions have been made in this field, it has become increasingly clear that proteomics results generated by various laboratories are highly variable. The underlying issues are vast, including limitations and complications with heterogeneity of patients/testing subjects, experimental design, sample processing, as well as current proteomics technology. Accordingly, this review not only summarizes the current status of characterization of the human CSF proteome and biomarker discovery for major neurodegenerative disorders, i.e., Alzheimer's disease and Parkinson's disease, but also addresses a few essential caveats involved in several steps of CSF proteomics that may contribute to the variable/contradicting results reported by different laboratories. The potential future directions of CSF proteomics are also discussed with this analysis.
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Affiliation(s)
- Jing Zhang
- Division of Neuropathology, Department of Pathology, University of Washington School of Medicine, Seattle, WA, USA.
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208
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Barelli S, Crettaz D, Thadikkaran L, Rubin O, Tissot JD. Plasma/serum proteomics: pre-analytical issues. Expert Rev Proteomics 2007; 4:363-70. [PMID: 17552920 DOI: 10.1586/14789450.4.3.363] [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: 11/08/2022]
Abstract
High-throughput proteomics technologies tend to provide highly sensitive information about living tissues and biological fluids. Analytes are characterized by intrinsic and extrinsic properties, the latter depending on each phase of their preparation, sometimes adding artifacts with crucial repercussions in result reliability and interpretation. This review aims to address some issues that can be encountered when handling plasma and serum in experimental and clinical proteomic settings.
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Affiliation(s)
- Stefano Barelli
- Service Régional Vaudois de Transfusion Sanguine, Lausanne, Switzerland.
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209
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Harezlak J, Wang M, Christiani D, Lin X. Quantitative quality-assessment techniques to compare fractionation and depletion methods in SELDI-TOF mass spectrometry experiments. Bioinformatics 2007; 23:2441-8. [PMID: 17626063 DOI: 10.1093/bioinformatics/btm346] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Mass spectrometry (MS), such as the surface-enhanced laser desorption and ionization time-of-flight (SELDI-TOF) MS, provides a potentially promising proteomic technology for biomarker discovery. An important matter for such a technology to be used routinely is its reproducibility. It is of significant interest to develop quantitative measures to evaluate the quality and reliability of different experimental methods. RESULTS We compare the quality of SELDI-TOF MS data using unfractionated, fractionated plasma samples and abundant protein depletion methods in terms of the numbers of detected peaks and reliability. Several statistical quality-control and quality-assessment techniques are proposed, including the Graeco-Latin square design for the sample allocation on a Protein chip, the use of the pairwise Pearson correlation coefficient as the similarity measure between the spectra in conjunction with multi-dimensional scaling (MDS) for graphically evaluating similarity of replicates and assessing outlier samples; and the use of the reliability ratio for evaluating reproducibility. Our results show that the number of peaks detected is similar among the three sample preparation technologies, and the use of the Sigma multi-removal kit does not improve peak detection. Fractionation of plasma samples introduces more experimental variability. The peaks detected using the unfractionated plasma samples have the highest reproducibility as determined by the reliability ratio. AVAILABILITY Our algorithm for assessment of SELDI-TOF experiment quality is available at http://www.biostat.harvard.edu/~xlin. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jaroslaw Harezlak
- Department of Biostatistics, Harvard School of Public Health 655 Huntington Avenue Boston, MA 02115, USA.
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210
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Luque-Garcia JL, Neubert TA. Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry. J Chromatogr A 2007; 1153:259-76. [PMID: 17166507 PMCID: PMC7094463 DOI: 10.1016/j.chroma.2006.11.054] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2006] [Revised: 11/06/2006] [Accepted: 11/16/2006] [Indexed: 01/14/2023]
Abstract
In this article, we present an overview of the different strategies for sample preparation for identification by mass spectrometry (MS) of biomarkers from serum and/or plasma. We consider the effects of the variables involved in sample collection, handling and storage, and describe different approaches for removal of high abundance proteins and serum/plasma fractionation. We review the advantages and disadvantages of such techniques as centrifugal ultrafiltration, different formats for solid phase extraction, organic solvent extraction, gel and capillary electrophoresis, and liquid chromatography. We also discuss a variety of current proteomic methods and their main applications for biomarker-related studies.
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Affiliation(s)
| | - Thomas A. Neubert
- Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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211
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Falk R, Ramström M, Ståhl S, Hober S. Approaches for systematic proteome exploration. ACTA ACUST UNITED AC 2007; 24:155-68. [PMID: 17376740 DOI: 10.1016/j.bioeng.2007.01.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 01/24/2007] [Accepted: 01/25/2007] [Indexed: 10/23/2022]
Abstract
With the completion of the human genome project (HUGO) during recent years, gene function, protein abundance and expression patterns in tissues and cell types have emerged as central areas for the scientific community. A mapped human proteome will extend the value of the genome sequence and large-scale efforts aiming at elucidating protein localization, abundance and function are invaluable for biomarker and drug discovery. This research area, termed proteomics, is more demanding than any genome sequencing effort and to perform this on a wide scale is a highly diverse task. Therefore, the proteomics field employs a range of methods to examine different aspects of proteomics including protein localization, protein-protein interactions, posttranslational modifications and alteration of protein composition (e.g. differential expression) in tissues and body fluids. Here, some of the most commonly used methods, including chromatographic separations together with mass spectrometry and a number of affinity proteomics concepts are discussed and exemplified.
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Affiliation(s)
- Ronny Falk
- Royal Institute of Technology, Albanova University Center, School of Biotechnology, SE-106 91 Stockholm, Sweden
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212
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Millioni R, Puricelli L, Iori E, Tessari P. Rapid, simple and effective technical procedure for the regeneration of IgG and HSA affinity columns for proteomic analysis. Amino Acids 2007; 34:507-9. [PMID: 17514490 DOI: 10.1007/s00726-007-0556-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2007] [Accepted: 04/11/2007] [Indexed: 11/30/2022]
Abstract
In plasma and serum, the presence of high-abundance proteins can overwhelm the signals of low-abundance proteins, which then become undetectable either by two-dimensional gels or chromatographic techniques. Therefore, depletion of abundant proteins is a prerequisite to detect low-abundance components. Furthermore, the regeneration of pre-purification tools could be money-saving. We applied an affinity chromatography kit to remove albumin and the immunoglobulin chains from plasma and propose a simple and effective technical procedure for the regeneration of these affinity columns.
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Affiliation(s)
- R Millioni
- Department of Clinical and Experimental Medicine, Chair of Metabolism, University of Padova, Padova, Italy
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213
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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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214
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Maltman DJ, Przyborski SA. Application of proteomic technology to neural stem cell science and neurology. FUTURE NEUROLOGY 2007. [DOI: 10.2217/14796708.2.3.285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There is widespread recognition of the potential that stem cells hold for the treatment and repair of a large number of disorders affecting the human CNS. Therefore, stem cell research will go hand in hand with progress in specific areas of neuroscience. Proteomics has great potential to make important contributions to the basic understanding of neurological processes, and to deliver much needed cellular biomarkers in both of these fields. This review focuses on the importance of proteomic research in neuroscience, in particular the application of biomarker discovery in stem cells and degenerative diseases of the CNS.
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Affiliation(s)
- Daniel J Maltman
- University of Durham, School of Biological & Biomedical Science, South Road, Durham DH1 3LE, UK and, ReInnervate Limited, Old Shire Hall, Old Elvet, Durham DH1 3HP, UK
| | - Stefan A Przyborski
- University of Durham, School of Biological & Biomedical Science, South Road, Durham DH1 3LE, UK and, ReInnervate Limited, Old Shire Hall, Old Elvet, Durham DH1 3HP, UK
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215
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Rieux L, Bischoff R, Verpoorte E, Niederländer HAG. Restricted-access material-based high-molecular-weight protein depletion coupled on-line with nano-liquid chromatography–mass spectrometry for proteomics applications. J Chromatogr A 2007; 1149:169-77. [PMID: 17418220 DOI: 10.1016/j.chroma.2007.02.118] [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: 08/16/2006] [Revised: 01/22/2007] [Accepted: 02/23/2007] [Indexed: 11/18/2022]
Abstract
Proteomics samples often contain both abundant proteins and low-level proteins and peptides. Highly abundant proteins can mask and/or bind those of lower abundance and thereby hinder their analysis. In particular, we were concerned with samples containing large amounts of albumin (up to 4.0 microM). In this study, a novel set-up for multidimensional nano-liquid chromatography-mass spectrometry (nanoLC-MS) with three columns coupled on-line was developed and characterised. A 1-mm-I.D. restricted-access-material (RAM) cartridge and a 100-microm-I.D. reversed-phase trap column are coupled in forward-flush mode to remove albumin before on-line separation on a 50 microm I.D. reversed-phase capillary analytical column. Volumes up to 100 microL of a complex matrix (containing 0.4 or 4.0 microM albumin) could be injected onto this system, enabling a 5000-fold volume reduction. Up to 99.7% of the albumin present in samples could be efficiently removed over the RAM cartridge. The total analysis time was about 40 min. Using Substance P as a model peptide, separations were efficient, with a peak width of 10s at half height. Moreover, separations were highly reproducible (relative standard deviation (RSD) on retention time approximately 3% over 1 week). The set-up proved to be robust and was used for about 750 analyses without exchanging one of the columns. Flexibility with respect to the stationary phase material in the sample preparation cartridge allows for other separation modes to be applied as well.
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Affiliation(s)
- Laurent Rieux
- Pharmaceutical Analysis Group, University Centre for Pharmacy, University of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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216
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Kim MR, Kim CW. Human blood plasma preparation for two-dimensional gel electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:203-10. [PMID: 17174613 PMCID: PMC7105212 DOI: 10.1016/j.jchromb.2006.11.046] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Revised: 11/17/2006] [Accepted: 11/20/2006] [Indexed: 12/29/2022]
Abstract
Human plasma consists of mainly large proteins, which vary in terms of both composition and concentration with the physiological state of the individual. Alterations in protein concentrations reflect the current state of the individual's health and thus may be utilized as valuable biomarkers for a specific biological process or disease. Two-dimensional gel electrophoresis (2-DE) has proven to be a valuable method for the separation and comparison of complex protein mixtures, for example, from disease and healthy states, as this method provides information regarding the variation, relative quantities, and structures of the intact proteins. The procedures utilized for the preparation of samples for 2-DE are critical to the acquisition of high-quality results for the discovery of biomarkers. The objective of this study was to review the preparation methods of plasma for 2-DE, particularly those designed to improve the detection of proteins in low abundance in plasma on 2-DE. The use of anticoagulants and protease inhibitors during the collection of blood, the removal of abundant proteins using multicomponent immunodepletion system, and desalting procedure allow us to compile profiles of proteins occurring in low concentrations in the plasma and to improve the pattern generated during 2-DE.
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Affiliation(s)
| | - Chan-Wha Kim
- School of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
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217
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Plavina T, Wakshull E, Hancock WS, Hincapie M. Combination of abundant protein depletion and multi-lectin affinity chromatography (M-LAC) for plasma protein biomarker discovery. J Proteome Res 2007; 6:662-71. [PMID: 17269723 DOI: 10.1021/pr060413k] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on the development of a robust and relatively high-throughput method for in-depth proteomic analysis of human plasma suitable for biomarker discovery. The method consists of depletion of albumin and IgG and multi-lectin affinity chromatography (M-LAC), followed by nanoLC-MS/MS analysis of digested proteins and label-free comparative quantitation of proteins. The performance of the method is monitored by multiple quality control points to ensure reproducibility of the analysis. The method identifies proteins that are reported to be present in normal plasma at concentrations of 10-100 ng/mL and that may be of particular interest when studying a variety of disease conditions. Numerous tissue leakage proteins of potentially even lower concentrations are also identified. When the method was used in a study to identify potential biomarkers of psoriasis, the differential abundance of proteins present at low mug/mL level was quantitated and later verified by ELISA measurements.
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218
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Henrich S, Cordwell SJ, Crossett B, Baker MS, Christopherson RI. The nuclear proteome and DNA-binding fraction of human Raji lymphoma cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:413-32. [PMID: 17369005 DOI: 10.1016/j.bbapap.2006.12.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2006] [Revised: 11/26/2006] [Accepted: 12/20/2006] [Indexed: 12/17/2022]
Abstract
Purification of organelles and analysis of their proteins is an important initial step for biological proteomics, simplifying the proteome prior to analysis by established techniques such as two-dimensional liquid chromatography (2-DLC) or two-dimensional gel electrophoresis (2-DE). Nuclear proteins play a central role in regulating gene expression, but are often under-represented in proteomic studies due to their lower abundance in comparison to cellular 'housekeeping' metabolic enzymes and structural proteins. A reliable procedure for separation and proteomic analysis of nuclear proteins would be useful for investigations of cell proliferation and differentiation during disease processes (e.g., human cancer). In this study, we have purified nuclei from the human Burkitt's lymphoma B-cell line, Raji, using sucrose density gradient centrifugation. The integrity and purity of the nuclei were assessed by light microscopy and proteins from the nuclear fractions were separated by 2-DE and identified using matrix assisted laser desorption ionization mass spectrometry (MALDI-MS). A total of 124 unique proteins were identified, of which 91% (n=110) were predicted to be nuclear using PSORT. Proteins from the nuclear fraction were subjected to affinity chromatography on DNA-agarose to isolate DNA-binding proteins. From this purified fraction, 131 unique proteins were identified, of which 69% (n=90) were known or predicted DNA-binding proteins. Purification of nuclei and subsequent enrichment of DNA-binding proteins allowed identification of a total of 209 unique proteins, many involved in transcription and/or correlated with lymphoma, leukemia or cancer in general. The data obtained should be valuable for identification of biomarkers and targets for cancer therapy, and for furthering our understanding of the molecular mechanisms underlying lymphoma development and progression.
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Affiliation(s)
- Silke Henrich
- School of Molecular and Microbial Biosciences, University of Sydney, Sydney, NSW, Australia
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219
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Villar-Garea A, Griese M, Imhof A. Biomarker discovery from body fluids using mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 849:105-14. [PMID: 17097359 DOI: 10.1016/j.jchromb.2006.09.017] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2006] [Revised: 08/22/2006] [Accepted: 09/08/2006] [Indexed: 11/18/2022]
Abstract
Systems analysis of body fluids by mass spectrometry (MS) is an upcoming field of biomarker research. This approach is extremely attractive because it does not require biomarker candidates and the sample preparation is simple. However, during the development of the technique strong critical comments were made on the poor reproducibility, the special characteristics of blood as a source of peptides and on the frequent non-adequate statistical analysis of the data. Here we discuss the efforts made in the last few years to develop suitable protocols, which could lead to biomarker discovery from body fluids by mass spectrometry. Our review focuses on the systems analysis of non-digested blood serum or plasma samples by MALDI-TOF and SELDI-TOF.
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Affiliation(s)
- Ana Villar-Garea
- Histone modifications group, Adolf-Butenandt Institute, Ludwig-Maximilians University of Munich, Schillerstr 44, 80336 Munich, Germany
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220
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Chen J, Anderson M, Misek DE, Simeone DM, Lubman DM. Characterization of apolipoprotein and apolipoprotein precursors in pancreatic cancer serum samples via two-dimensional liquid chromatography and mass spectrometry. J Chromatogr A 2007; 1162:117-25. [PMID: 17434173 PMCID: PMC2692198 DOI: 10.1016/j.chroma.2007.03.096] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Revised: 03/25/2007] [Accepted: 03/27/2007] [Indexed: 01/06/2023]
Abstract
Major advances in cancer control depend upon early detection, early diagnosis and efficacious treatment modalities. Current existing markers of pancreatic ductal adenocarcinoma, generally incurable by available treatment modalities, are inadequate for early diagnosis or for distinguishing between pancreatic cancer and chronic pancreatitis. We have used a proteomic approach to identify proteins that are differentially expressed in sera from pancreatic cancer patients, as compared to control. Normal, chronic pancreatitis and pancreatic cancer serum samples were depleted of high molecular weight proteins by acetonitrile precipitation. Each sample was separated by chromatofocusing, and then further resolved by reversed-phase (RP)-HPLC. Effluent from the RP-HPLC column was split into two streams with one directly interfaced to an electrospray time-of-flight (ESI-TOF) mass spectrometer for molecular weight (MW) determination of the intact proteins. The remainder went through a UV detector with the corresponding peaks collected with a fraction collector, subsequently used for MS/MS analysis. The ion intensities of proteins with the same MW obtained from ESI-TOF-MS analysis were compared, with the differentially expressed proteins determined. An 8915 Da protein was found to be up-regulated while a 9422 Da protein was down-regulated in the pancreatic cancer sera. Both proteins were identified by MS and MS/MS as proapolipoprotein C-II and apolipoprotein C-III(1), respectively. The MS/MS data of proapolipoprotein C-II was searched using "semi-trypsin" as the search enzyme, thus confirming that the protein at 8915 Da was proapolipoprotein C-II. In order to confirm the identity of the protein at 9422 Da, we initially identified a protein of 8765 Da with a similar mass spectral pattern. Based on MS and MS/MS, its intact molecular weight and "semi-trypsin" database search, the protein at 8765 Da was identified as apolipoprotein C-III(0). The MS and MS/MS data of the proteins at 8765 Da and 942 Da were similar, thus confirming the protein at 9422 Da as being apolipoprotein C-III(1). The detection of differentially expressed proapolipoprotein C-II and apolipoprotein C-III(1) in the sera of pancreatic cancer patients may have utility for detection of this deadly malignancy.
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Affiliation(s)
- Jianzhong Chen
- Department of Surgery, University of Michigan, Ann Arbor, MI, USA
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221
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Archakov AI, Ivanov YD, Lisitsa AV, Zgoda VG. AFM fishing nanotechnology is the way to reverse the Avogadro number in proteomics. Proteomics 2007; 7:4-9. [PMID: 17154275 DOI: 10.1002/pmic.200600467] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Future development of proteomics may be hindered by limitations in the concentration sensitivity of widespread technological approaches. The concentration sensitivity limit (CSL) of currently used approaches, like 2-DE/LC separation coupled with MS detection, etc., varies from 10(-9) to 10(-12) M. Therefore, proteomic technologies enable detection of up to 20% of the protein species present in the plasma. New technologies, like atomic force microscopy (AFM molecular detector), enable the counting of single molecules, whereas biospecific fishing can be used to capture these molecules from the biomaterial. At the same time, fishing also has thermodynamic limitations due to the reversibility of the binding. In cases where the fishing becomes irreversible, its combination with an AFM detector enables the registration of single protein molecules, and that opens up a way to lower the CSL down to the reverse Avogadro number.
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Affiliation(s)
- Alexander Ivanovich Archakov
- Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Pogodinskaya Street, Moscow, Russia.
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222
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Jmeian Y, El Rassi Z. Tandem affinity monolithic microcolumns with immobilized protein A, protein G', and antibodies for depletion of high abundance proteins from serum samples: integrated microcolumn-based fluidic system for simultaneous depletion and tryptic digestion. J Proteome Res 2007; 6:947-54. [PMID: 17291024 DOI: 10.1021/pr060660o] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Affinity monolithic microcolumns with immobilized affinity ligands including protein A, protein G' and polyclonal antibodies were developed for the microscale depletion of the top eight most abundant proteins in human serum. These various affinity microcolumns were evaluated for their sample loading capacities with the standard protein substrates. In general, the sample loading capacity of protein A and protein G' was about 7-25 fold higher than that of the antibody-based affinity columns. The macroporous nature of the monolithic columns, which offers high permeability in pressure-driven flow, allowed the design of long tandem affinity columns for the simultaneous depletion of the top eight most abundant proteins in a single run. The tandem format could be extended to include additional affinity monolithic columns to deplete other proteins for which specific antibodies are available without running into high inlet pressure. Furthermore, the tandem affinity columns were integrated with immobilized trypsin monolithic columns to achieve the simultaneous depletion and digestion of proteins. The various formats investigated in this study could be down scaled to achieve nanoLC or up scaled to perform conventional HPLC depending on the size of the proteomic samples.
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Affiliation(s)
- Yazen Jmeian
- Department of Chemistry, Oklahoma State University, Stillwater, Oklahoma 74078-3071, USA
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223
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Dekker LJ, Bosman J, Burgers PC, van Rijswijk A, Freije R, Luider T, Bischoff R. Depletion of high-abundance proteins from serum by immunoaffinity chromatography: A MALDI-FT-MS study. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 847:65-9. [PMID: 17049934 DOI: 10.1016/j.jchromb.2006.09.038] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2006] [Revised: 09/13/2006] [Accepted: 09/20/2006] [Indexed: 11/28/2022]
Abstract
Immunodepletion of high-abundance proteins from serum is a widely used initial step in biomarker discovery studies. In the present work we have investigated the reproducibility of the depletion step by comparing 250 serum samples from prostate cancer patients. All samples were depleted on a single immunoaffinity column over a time period of 6 weeks with automated peak detection and fraction collection. Reproducibility in terms of surface area of the depleted serum protein peak at 280nm was below 7% relative standard deviation (R.S.D.) and the collected volume of the relevant fraction was 0.97mL (4.5% R.S.D.). Proteins in the depleted serum fraction were subsequently digested with trypsin and analyzed by MALDI-FT-MS. The degree of the depletion of albumin, transferrin and alpha-1-antitrypsin was determined by comparing the intensity of peptide peaks before and after depletion of 11 samples taken at regular time intervals from amongst the 250 depleted, randomized samples. As a positive control we evaluated peaks of apolipoprotein A1 (the most abundant serum protein remaining after depleteion) showing a clear increase in intensity of these peaks in the depleted samples. From this study we conclude that the depletion of the 250 serum samples was complete and reproducible over a period of 6 weeks.
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224
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Karataş M, Akgöl S, Yavuz H, Say R, Denizli A. Immunoglobulin G depletion from human serum with metal-chelated beads under magnetic field. Int J Biol Macromol 2007; 40:254-60. [PMID: 16978689 DOI: 10.1016/j.ijbiomac.2006.08.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Revised: 08/07/2006] [Accepted: 08/07/2006] [Indexed: 11/15/2022]
Abstract
Magnetic poly(ethylene glycol dimethacrylate-N-methacryloyl-(L)-histidine methyl ester) [mag-poly(EGDMA-MAH) beads, 50-100 microm in diameter, were produced by suspension polymerization for affinity depletion of immunoglobulin G (IgG) from human serum. Cu2+ ions were complexed directly via MAH groups (Cu2+ loading: 4.1 micromol/g). IgG depletion studies were performed by magnetically stabilized fluidized bed column. Acetate, Tris-HCl, MES and phosphate buffers all allow adsorption of similar quantities of IgG (27.3-45.6 mg/g). MOPS and HEPES allow higher adsorption quantities (79.6 mg/g and 74.1mg/g, respectively). Maximum adsorption capacities in MOPS buffer were 46.8 mg/g for mag-poly(EGDMA-MAH) and 102.1mg/g for Cu2+ chelated mag-poly(EGDMA-MAH) beads. The adsorption capacity decreased drastically from 102.1mg/g to 30.7 mg/g with the increase of the flow rate from 0.2 ml/min to 3.5 ml/min. The elution studies were performed by 1.0M NaCl. The elution results demonstrated that the adsorption of IgG to the adsorbent was reversible. To test the efficiency of IgG depletion from human serum, proteins in the serum and eluted portion were analyzed by two-dimensional gel electrophoresis. The depletion efficiency for IgG was above 99.4%. Eluted proteins include mainly IgG, and a small number of non-albumin proteins such as apo-lipoprotein A1, sero-transferrin, haptoglobulin and alpha1-antitrypsin. When anti-HSA-sepharose adsorbent is used together with our metal-chelated mag-beads, IgG and HSA can be depleted in a single step.
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Affiliation(s)
- Melike Karataş
- Department of Chemistry, Biochemistry Division, Hacettepe University, Ankara, Turkey
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225
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Bertile F, Robert F, Delval-Dubois V, Sanglier S, Schaeffer C, Van Dorsselaer A. Endogenous Plasma Peptide Detection and Identification in the Rat by a Combination of Fractionation Methods and Mass Spectrometry. Biomark Insights 2007. [DOI: 10.1177/117727190700200002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Mass spectrometry-based analyses are essential tools in the field of biomarker research. However, detection and characterization of plasma low abundance and/or low molecular weight peptides is challenged by the presence of highly abundant proteins, salts and lipids. Numerous strategies have already been tested to reduce the complexity of plasma samples. The aim of this study was to enrich the low molecular weight fraction of rat plasma. To this end, we developed and compared simple protocols based on membrane filtration, solid phase extraction, and a combination of both. As assessed by UV absorbance, an albumin depletion >99% was obtained. The multistep fractionation strategy (including reverse phase HPLC) allowed detection, in a reproducible manner (CV < 30%-35%), of more than 450 peaks below 3000 Da by MALDI-TOF/MS. A MALDI-TOF/MS-determined LOD as low as 1 fmol/μL was obtained, thus allowing nanoLC-Chip/MS/MS identification of spiked peptides representing ~10–6% of total proteins, by weight. Signal peptide recovery ranged between 5%-100% according to the spiked peptide considered. Tens of peptide sequence tags from endogenous plasma peptides were also obtained and high confidence identifications of low abundance fibrinopeptide A and B are reported here to show the efficiency of the protocol. It is concluded that the fractionation protocol presented would be of particular interest for future differential (high throughput) analyses of the plasma low molecular weight fraction.
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Affiliation(s)
- Fabrice Bertile
- Institut Pluridisciplinaire Hubert Curien, Département Sciences Analytiques, Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS-ULP UMR 7178, ECPM, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France
| | - Flavie Robert
- Institut Pluridisciplinaire Hubert Curien, Département Sciences Analytiques, Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS-ULP UMR 7178, ECPM, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France
| | - Véronique Delval-Dubois
- Institut Pluridisciplinaire Hubert Curien, Département Sciences Analytiques, Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS-ULP UMR 7178, ECPM, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France
| | - Sarah Sanglier
- Institut Pluridisciplinaire Hubert Curien, Département Sciences Analytiques, Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS-ULP UMR 7178, ECPM, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France
| | - Christine Schaeffer
- Institut Pluridisciplinaire Hubert Curien, Département Sciences Analytiques, Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS-ULP UMR 7178, ECPM, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France
| | - Alain Van Dorsselaer
- Institut Pluridisciplinaire Hubert Curien, Département Sciences Analytiques, Laboratoire de Spectrométrie de Masse Bio-Organique, CNRS-ULP UMR 7178, ECPM, 25 rue Becquerel, 67087 Strasbourg Cedex 2, France
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226
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Gundry RL, Fu Q, Jelinek CA, Van Eyk JE, Cotter RJ. Investigation of an albumin-enriched fraction of human serum and its albuminome. Proteomics Clin Appl 2007; 1:73-88. [PMID: 20204147 PMCID: PMC2831644 DOI: 10.1002/prca.200600276] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Indexed: 11/07/2022]
Abstract
The removal of albumin and other high abundance proteins is a routine first step in the analysis of serum and plasma proteomes. However, as albumin can bind proteins and peptides, there is a universal concern as to how the serum proteome is changed by the removal of albumin. To address this concern, the current study was designed to identify proteins and peptides removed from the serum during albumin depletion; to determine which of these are bound to albumin (rather than copurified) and whether the bound proteins are intact proteins or peptide fragments. Sequential, independent analyses including both anti-albumin antibody (anti-HSA) affinity chromatography and SEC were used to isolate albumin-bound proteins. RP-HPLC and 1-D SDS-PAGE were then used to further separate the proteins prior to identification by MS/MS. Finally, whole protein molecular weight (MW) MS measurements coupled with protein coverage obtained by MS were combined to assess whether the bound proteins were intact or peptide fragments. Combining the results from multiple approaches, 35 proteins, of which 24 are intact, were found to be associated with albumin, and they include both known high and low abundance proteins.
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Affiliation(s)
- Rebekah L. Gundry
- Department of Pharmacology and Molecular Sciences, Middle Atlantic Mass Spectrometry Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins NHLBI Proteomics Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Qin Fu
- Department of Medicine, Johns Hopkins NHLBI Proteomics Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christine A. Jelinek
- Department of Pharmacology and Molecular Sciences, Middle Atlantic Mass Spectrometry Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jennifer E. Van Eyk
- Department of Medicine, Johns Hopkins NHLBI Proteomics Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert J. Cotter
- Department of Pharmacology and Molecular Sciences, Middle Atlantic Mass Spectrometry Laboratory, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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227
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Akgöl S, Özkara S, Uzun L, Yılmaz F, Denizli A. Pseudospecific magnetic affinity beads for immunoglobulin-G depletion from human serum. J Appl Polym Sci 2007. [DOI: 10.1002/app.26771] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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228
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Kalenka A, Feldmann RE, Otero K, Maurer MH, Waschke KF, Fiedler F. Changes in the serum proteome of patients with sepsis and septic shock. Anesth Analg 2006; 103:1522-6. [PMID: 17122233 DOI: 10.1213/01.ane.0000242533.59457.70] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Sepsis is still the leading cause of death in the intensive care unit. Our goal was to elucidate potential early differences in serum between survivors (SURV) and non-survivors (NON-SURV) on day 28. METHODS We applied proteomic technology to serum samples of patients with sepsis and septic shock. Serum samples from 18 patients with sepsis and septic shock were obtained during the first 12 h after diagnosis of septic shock. Patients were grouped into SURV and NON-SURV on day 28. RESULTS Seven patients survived and 11 patients died. Using proteome analysis, two-dimensional gel electrophoresis detected more than 200 spots per gel. A differential protein expression was discovered between SURV and NON-SURV, whereby protein alterations not yet described in sepsis were revealed. CONCLUSIONS Our results show that proteomic profiling is a useful approach for detecting protein expression dynamics in septic patients, and may bring us closer to achieving a comprehensive molecular profiling compared with genetic studies alone.
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Affiliation(s)
- Armin Kalenka
- Department of Anesthesiology and Critical Care Medicine, Faculty of Clinical Medicine Mannheim, University of Heidelberg, Theodor Kutzer Ufer 1-3, 68167 Mannheim, Germany.
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229
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Abstract
The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human disease biomarker discovery. We aim to summarize the proteomics technologies currently used for global identification and quantification of body fluid proteins, and elaborate the putative biomarkers discovered for a variety of human diseases through human body fluid proteome (HBFP) analysis. Some critical concerns and perspectives in this emerging field are also discussed. With the advances made in proteomics technologies, the impact of HBFP analysis in the search for clinically relevant disease biomarkers would be realized in the future.
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Affiliation(s)
- Shen Hu
- School of Dentistry, Division of Oral Biology and Medicine, Dental Research Institute, University of California, Los Angeles, CA 90095, USA.
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230
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Vercauteren FGG, Arckens L, Quirion R. Applications and current challenges of proteomic approaches, focusing on two-dimensional electrophoresis. Amino Acids 2006; 33:405-14. [PMID: 17136510 DOI: 10.1007/s00726-006-0460-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2006] [Accepted: 10/10/2006] [Indexed: 01/23/2023]
Abstract
Since the formulation of the concept of "proteomics" in 1995, a plethora of proteomic technologies have been developed in order to study proteomes of tissues, cells and organelles. The powerful new technologies enabled by proteomic approaches have lead to the application of these methods to an exponentially increasing variety of biological questions for highly complex protein mixtures. Continuous technical optimization allows for an ever-increasing sensitivity of proteomic techniques. In this review, a brief overview of currently available proteomic techniques and their applications is given, followed by a more detailed description of advantages and technical challenges of two-dimensional electrophoresis (2-DE). Some solutions to circumvent currently encountered technical difficulties for 2-DE analyses are proposed.
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Affiliation(s)
- F G G Vercauteren
- Douglas Hospital Research Center, Department of Psychiatry, McGill University, Montréal, Québec, Canada
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231
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Lambrecht S, Deforce D, Elewaut D. Entering the era of proteomics in rheumatology. Expert Opin Drug Discov 2006; 1:539-48. [DOI: 10.1517/17460441.1.6.539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Stijn Lambrecht
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University Hospital, Harelbekestraat 72, 9000, Ghent, Belgium
| | - Dirk Elewaut
- Laboratory for Molecular Immunology and Inflammation, Division of Rheumatology, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
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232
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Babac C, Yavuz H, Galaev IY, Pişkin E, Denizli A. Binding of antibodies to concanavalin A-modified monolithic cryogel. REACT FUNCT POLYM 2006. [DOI: 10.1016/j.reactfunctpolym.2006.03.007] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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233
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Tanaka Y, Akiyama H, Kuroda T, Jung G, Tanahashi K, Sugaya H, Utsumi J, Kawasaki H, Hirano H. A novel approach and protocol for discovering extremely low-abundance proteins in serum. Proteomics 2006; 6:4845-55. [PMID: 16878292 DOI: 10.1002/pmic.200500774] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The proteomic analysis of serum (plasma) has been a major approach to determining biomarkers essential for early disease diagnoses and drug discoveries. The determination of these biomarkers, however, is analytically challenging since the dynamic concentration range of serum proteins/peptides is extremely wide (more than 10 orders of magnitude). Thus, the reduction in sample complexity prior to proteomic analyses is essential, particularly in analyzing low-abundance protein biomarkers. Here, we demonstrate a novel approach to the proteomic analyses of human serum that uses an originally developed serum protein separation device and a sequentially linked 3-D-LC-MS/MS system. Our hollow-fiber-membrane-based serum pretreatment device can efficiently deplete high-molecular weight proteins and concentrate low-molecular weight proteins/peptides automatically within 1 h. Four independent analyses of healthy human sera pretreated using this unique device, followed by the 3-D-LC-MS/MS successfully produced 12 000-13 000 MS/MS spectra and hit around 1800 proteins (>95% reliability) and 2300 proteins (>80% reliability). We believe that the unique serum pretreatment device and proteomic analysis protocol reported here could be a powerful tool for searching physiological biomarkers by its high throughput (3.7 days per one sample analysis) and high performance of finding low abundant proteins from serum or plasma samples.
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Affiliation(s)
- Yoshinori Tanaka
- Toray Industries, Inc., New Frontiers Research Laboratories, Kamakura, Kanagawa, Japan
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234
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Morelle W, Canis K, Chirat F, Faid V, Michalski JC. The use of mass spectrometry for the proteomic analysis of glycosylation. Proteomics 2006; 6:3993-4015. [PMID: 16786490 DOI: 10.1002/pmic.200600129] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Of all protein PTMs, glycosylation is by far the most common, and is a target for proteomic research. Glycosylation plays key roles in controlling various cellular processes and the modifications of the glycan structures in diseases highlight the clinical importance of this PTM. Glycosylation analysis remains a difficult task. MS, in combination with modern separation methodologies, is one of the most powerful and versatile techniques for the structural analysis of glycoconjugates. This review describes methodologies based on MS for detailed characterization of glycoconjugates in complex biological samples at the sensitivity required for proteomic work.
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Affiliation(s)
- Willy Morelle
- Unité Mixte de Recherche CNRS/USTL 8576, Université des Sciences et Technologies de Lille 1, Villeneuve d'Ascq Cedex, France.
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235
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Roche S, Tiers L, Provansal M, Piva MT, Lehmann S. Interest of major serum protein removal for Surface-Enhanced Laser Desorption/Ionization - Time Of Flight (SELDI-TOF) proteomic blood profiling. Proteome Sci 2006; 4:20. [PMID: 17022823 PMCID: PMC1613235 DOI: 10.1186/1477-5956-4-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Accepted: 10/05/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Surface-Enhanced Laser Desorption/Ionization - Time Of Flight (SELDI-TOF) has been proposed as new approach for blood biomarker discovery. However, results obtained so far have been often disappointing as this technique still has difficulties to detect low-abundant plasma and serum proteins. RESULTS We used a serum depletion scheme using chicken antibodies against various abundant proteins to realized a pre-fractionation of serum prior to SELDI-TOF profiling. Depletion of major serum proteins by immunocapture was confirmed by 1D and 2D gel electrophoresis. SELDI-TOF analysis of bound and unbound (depleted) serum fractions revealed that this approach allows the detection of new low abundant protein peaks with satisfactory reproducibility. CONCLUSION The combination of immunocapture and SELDI-TOF analysis opens new avenues into proteomic profiling for the discovery of blood biomarkers.
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Affiliation(s)
- Stéphane Roche
- Institut de Génétique Humaine du CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
- CHU Montpellier, Laboratoire de Biochimie, Hôpital St. Eloi, 80, av A. Fliche, 34295 Montpellier Cedex 5, France
| | - Laurent Tiers
- Institut de Génétique Humaine du CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Monique Provansal
- Institut de Génétique Humaine du CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
- Faculté de Médecine Montpellier – Nîmes, UM1 – UFR Médecine, 2, rue École de Médecine, 34060 Montpellier, France
| | - Marie-Thérèse Piva
- CHU Montpellier, Laboratoire de Biochimie, Hôpital St. Eloi, 80, av A. Fliche, 34295 Montpellier Cedex 5, France
- Faculté de Médecine Montpellier – Nîmes, UM1 – UFR Médecine, 2, rue École de Médecine, 34060 Montpellier, France
| | - Sylvain Lehmann
- Institut de Génétique Humaine du CNRS, 141 rue de la Cardonille, 34396 Montpellier, France
- CHU Montpellier, Laboratoire de Biochimie, Hôpital St. Eloi, 80, av A. Fliche, 34295 Montpellier Cedex 5, France
- Faculté de Médecine Montpellier – Nîmes, UM1 – UFR Médecine, 2, rue École de Médecine, 34060 Montpellier, France
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236
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Queloz PA, Thadikkaran L, Crettaz D, Rossier JS, Barelli S, Tissot JD. Proteomics and transfusion medicine: Future perspectives. Proteomics 2006; 6:5605-14. [PMID: 16972297 DOI: 10.1002/pmic.200600179] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Limited number of important discoveries have greatly contributed to the progresses achieved in the blood transfusion; ABO histo-blood groups, citrate as anticoagulant, fractionation of plasma proteins, plastic bags and apheresis machines. Three major types of blood products are transfused to patients: red cell concentrates, platelet concentrates and fresh frozen plasma. Several parameters of these products change during storage process and they have been well studied over the years. However, several aspects have completely been ignored; in particular those related to peptide and protein changes. This review presents what has been done using proteomic tools and the potentials of proteomics for transfusion medicine.
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237
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Greco M, Chiriacò F, Del Boccio P, Tagliaferro L, Acierno R, Menegazzi P, Pinca E, Pignatelli F, Storelli C, Federici G, Urbani A, Maffia M. A proteomic approach for the characterization of C677T mutation of the human gene methylenetetrahydrofolate reductase. Proteomics 2006; 6:5350-61. [PMID: 16955529 DOI: 10.1002/pmic.200600130] [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: 11/12/2022]
Abstract
Methylenetetrahydrofolate reductase (MTHFR) catalyzes the conversion of methylenetetrahydrofolate (CH2H4folate) to methyltetrahydrofolate (CH3H4folate). The C677T mutation is a common polymorphism of the human enzyme that leads to the replacement of Ala222Val, thermolability of MTHFR, and mild elevation of plasma homocysteine levels. A mild hyperhomocysteinemia is known to be risk factor for cardiovascular and thrombotic diseases, ischemic stroke, neural tube defects, late on-set dementia, and pregnancy complications. Human plasma of subjects carrying the C677T mutation in the MTHFR gene has been investigated for their protein pattern in order to identify novel molecular hallmarks. 2-D analysis of the plasma protein allowed the identification of a specific pattern associated with the TT mutant genotype. Noteworthy, we found one spot shifted to a more basic pI in mutant individuals, and MS identification corresponded to vitamin D-binding protein (DBP or group component (Gc) globulin). MS/MS peptide sequencing allowed to discriminate different allelic variants in the investigated clinical groups. These data confirmed by molecular genetic analysis highlight the novel association between the C677T MTHFR genotype with the Gc2 polymorphism of the DBP. Moreover, we found a quantitative reduction of Apolipoprotein A-I in mutant individuals, which was associated, in previous studies by others to an increased cardiovascular risk.
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Affiliation(s)
- Marilena Greco
- Department of Biological and Environmental Sciences and Technologies, University of Lecce, Lecce, Italy
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238
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Shen Z, Want EJ, Chen W, Keating W, Nussbaumer W, Moore R, Gentle TM, Siuzdak G. Sepsis Plasma Protein Profiling with Immunodepletion, Three-Dimensional Liquid Chromatography Tandem Mass Spectrometry, and Spectrum Counting. J Proteome Res 2006; 5:3154-60. [PMID: 17081067 DOI: 10.1021/pr060327k] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Sepsis is a systemic, often fatal inflammatory response whose biochemical pathways are not fully understood and with no single biomarker capable of its reliable prediction. Increased interest in protein profiling to reveal fundamental biochemical events as well as disease diagnosis has grown considerably, largely due to advances in mass spectrometry and related front-end technologies. In this study, patients with sepsis and systemic inflammatory response syndrome (SIRS) were examined using plasma protein profiling following immunodepletion treatment to remove the most abundant proteins, serum albumin, transferrin, haptoglobin, anti-trypsin, IgG, and IgA. These proteins cause significant signal suppression, and their removal allows for lower abundance proteins to be examined through improved ion signal. Analyses after immunodepletion were performed using 3-dimensional reverse phase/strong cation exchange/reverse phase liquid chromatography with electrospray ion trap mass spectrometry (3D LC-MS/MS) and spectrum counting for comparative quantitation. The results revealed a major theme in immune system activity, including activation of the complement and coagulation pathways. Additionally, lipid transport may prove to be important in distinguishing sepsis from SIRS. Specifically, significant multi-fold changes were observed in 10 proteins and are now being investigated for the early diagnosis of sepsis.
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Affiliation(s)
- Zhouxin Shen
- Mass Consortium Corporation, San Diego, California, USA
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239
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Ramachandran P, Boontheung P, Xie Y, Sondej M, Wong DT, Loo JA. Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry. J Proteome Res 2006; 5:1493-503. [PMID: 16740002 DOI: 10.1021/pr050492k] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycoproteins make up a major and important part of the salivary proteome and play a vital role in maintaining the health of the oral cavity. Because changes in the physiological state of a person are reflected as changes in the glycoproteome composition, mapping the salivary glycoproteome will provide insights into various processes in the body. Salivary glycoproteins were identified by the hydrazide coupling and release method. In this approach, glycoproteins were coupled onto a hydrazide resin, the proteins were then digested and formerly N-glycosylated peptides were selectively released with the enzyme PNGase F and analyzed by LC-MS/MS. Employing this method, coupled with in-solution isoelectric focusing separation as an additional means for pre-fractionation, we identified 84 formerly N-glycosylated peptides from 45 unique N-glycoproteins. Of these, 16 glycoproteins have not been reported previously in saliva. In addition, we identified 44 new sites of N-linked glycosylation on the proteins.
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Affiliation(s)
- Prasanna Ramachandran
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California, USA
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240
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Gong Y, Li X, Yang B, Ying W, Li D, Zhang Y, Dai S, Cai Y, Wang J, He F, Qian X. Different immunoaffinity fractionation strategies to characterize the human plasma proteome. J Proteome Res 2006; 5:1379-87. [PMID: 16739989 DOI: 10.1021/pr0600024] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Plasma proteins may often serve as indicators of disease and are a rich source for biomarker discovery. However, the intrinsic large dynamic range of plasma proteins makes the analysis very challenging because a large number of low abundance proteins are often masked by a few high abundance proteins. The use of prefractionation methods, such as depletion of higher abundance proteins before protein profiling, can assist in the discovery and detection of less abundant proteins that may ultimately prove to be informative biomarkers. But there are few studies on comprehensive investigation of the proteins both in the fractions depleted and remainder. In the present study, two different immunoaffinity fractionation columns for the top-6 or the top-12 proteins in plasma were investigated and both the proteins in column-bound and flow-through fractions were subsequently analyzed. A two-dimensional peptide separation strategy, utilizing chromatographic separation techniques, combined with tandem mass spectrometry (MS/MS) was employed for proteomic analysis of the four fractions. Using the established HUPO PPP criteria, a total of 2401 unique plasma proteins were identified. The Multiple Affinity Removal System yielded 921 and 725 unique proteins from the flow-through and bound fractions, respectively, whereas the Seppro MIXED 12 column yielded identification of 897 and 730 unique proteins from the flow-through and bound fractions, respectively. When more stringent criteria, based on searching against the reversed database, were implemented, 529 unique proteins were identified from the four fractions with the confidence in peptide identification increased from 73.6% to 99%. To determine whether the presence of nontarget proteins in the immunoaffinity-bound fraction could be attributed to their interaction with high abundance proteins, co-immunoprecipitation analysis with an antibody to human plasma albumin was performed, which resulted in an identification of 40 unique proteins from the coimmunoprecipitate with the more stringent criteria. This study illustrated that combining the column-bound and flow-through fractions from immunoaffinity separation affords more extensive profiling of the protein content of human plasma. The presence of nontarget proteins in the column-bound fractions may be induced by their binding to the higher abundance proteins targeted by the immunoaffinity column.
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Affiliation(s)
- Yan Gong
- Department of Genomics and Proteomics, Beijing Institute of Radiation Medicine, 27 Taiping Road, Beijing 100850, People's Republic of China
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241
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Brand J, Haslberger T, Zolg W, Pestlin G, Palme S. Depletion efficiency and recovery of trace markers from a multiparameter immunodepletion column. Proteomics 2006; 6:3236-42. [PMID: 16645986 DOI: 10.1002/pmic.200500864] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The selective removal of high-abundance proteins is considered to be an important prerequisite for a sensitive proteome analysis in plasma. In this study, we examined the "multiaffinity removal system", an immunoaffinity depletion column targeted against six plasma proteins. As determined by sandwich ELISA, the depletion rate for each target protein is >99% over 200 cycles of regeneration. Our data give evidence that two column antibodies are slowly inactivated during the repeated use of the column; however, the individual depletion rate meets the specification of the manufacturer. To estimate a potential loss of analytes after the immunodepletion, we performed spiking/recovery experiments with a selection of tumor markers at concentrations in the lower to medium ng/mL range. The average recovery of 9 out of 11 markers is 78%. A significant proportion of two other markers binds to the column. Based on the average marker recovery and a depletion of ;85% of the total protein we estimate a five-fold enrichment of a potential biomarker by the use of this depletion column. We conclude that the selective depletion of plasma proteins by immunoaffinity chromatography is a valid strategy for the enrichment of potential biomarkers sought by proteomics methodologies.
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242
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Okano T, Kondo T, Kakisaka T, Fujii K, Yamada M, Kato H, Nishimura T, Gemma A, Kudoh S, Hirohashi S. Plasma proteomics of lung cancer by a linkage of multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis. Proteomics 2006; 6:3938-48. [PMID: 16767791 DOI: 10.1002/pmic.200500883] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
To investigate aberrant plasma proteins in lung cancer, we compared the proteomic profiles of serum from five lung cancer patients and from four healthy volunteers. Immuno-affinity chromatography was used to deplete highly abundant plasma proteins, and the resulting plasma samples were separated into eight fractions by anion-exchange chromatography. Quantitative protein profiles of the fractionated samples were generated by two-dimensional difference gel electrophoresis, in which the experimental samples and the internal control samples were labeled with different dyes and co-separated by two-dimensional polyacrylamide gel electrophoresis. This approach succeeded in resolving 3890 protein spots. For 364 of the protein spots, the expression level in lung cancer was more than twofold different from that in the healthy volunteers. These differences were statistically significant (Student's t-test, p-value less than 0.05). Mass spectrometric protein identification revealed that the 364 protein spots corresponded to 58 gene products, including the classical plasma proteins and the tissue-leakage proteins catalase, clusterin, ficolin, gelsolin, lumican, tetranectin, triosephosphate isomerase and vitronectin. The combination of multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis provides a valuable tool for serum proteomics in lung cancer.
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Affiliation(s)
- Tetsuya Okano
- Proteome Bioinformatics Project, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
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243
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Govorukhina NI, Reijmers TH, Nyangoma SO, van der Zee AGJ, Jansen RC, Bischoff R. Analysis of human serum by liquid chromatography–mass spectrometry: Improved sample preparation and data analysis. J Chromatogr A 2006; 1120:142-50. [PMID: 16574134 DOI: 10.1016/j.chroma.2006.02.088] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 12/04/2005] [Accepted: 02/16/2006] [Indexed: 10/24/2022]
Abstract
Discovery of biomarkers is a fast developing field in proteomics research. Liquid chromatography coupled on line to mass spectrometry (LC-MS) has become a powerful method for the sensitive detection, quantification and identification of proteins and peptides in biological fluids like serum. However, the presence of highly abundant proteins often masks those of lower abundance and thus generally prevents their detection and identification in proteomics studies. To perform future comparative analyses of samples from a serum bank of cervical cancer patients in a longitudinal and cross-sectional manner, methodology based on the depletion of high-abundance proteins followed by tryptic digestion and LC-MS has been developed. Two sample preparation methods were tested in terms of their efficiency to deplete high-abundance serum proteins and how they affect the repeatability of the LC-MS data sets. The first method comprised depletion of human serum albumin (HSA) on a dye ligand chromatographic and immunoglobulin G (IgG) on an immobilized Protein A support followed by tryptic digestion, fractionation by cation-exchange chromatography, trapping on a C18 column and reversed-phase LC-MS. The second method included depletion of the six most abundant serum proteins based on multiple immunoaffinity chromatography followed by tryptic digestion, trapping on a C18 column and reversed-phase LC-MS. Repeatability of the overall procedures was evaluated in terms of retention time and peak area for a selected number of endogenous peptides showing that the second method, besides being less time consuming, gave more repeatable results (retention time: <0.1% RSD; peak area: <30% RSD). Application of an LC-MS component detection algorithm followed by principal component analysis (PCA) enabled discrimination of serum samples that were spiked with horse heart cytochrome C from non-spiked serum and the detection of a concentration trend, which correlated to the amount of spiked horse heart cytochrome C to a level of 5 pmol cytochrome C in 2 microl original serum.
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Affiliation(s)
- N I Govorukhina
- Department of Analytical Biochemistry, Centre for Pharmacy, University of Groningen, Ant. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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244
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Choe LH, Werner BG, Lee KH. Two-dimensional protein electrophoresis: from molecular pathway discovery to biomarker discovery in neurological disorders. NeuroRx 2006; 3:327-35. [PMID: 16815216 PMCID: PMC3593383 DOI: 10.1016/j.nurx.2006.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Two-dimensional protein electrophoresis (2-DE) has undergone many technical improvements in the past 30 years, resulting in an analytical method that is unparalleled in the resolution of complex protein mixtures and capable of quantifying changes in protein expression from a wide variety of tissues and samples. The technique has been applied in many studies of neurologic disease to identify changes in spot patterns that correlate with disease. The true power of the technique emerges when it is coupled to state-of-the-art methods in mass spectrometry, which enable identification of the protein or proteins contained within a spot of interest on a 2-DE map. Investigators have successfully applied the technique to gain improved understanding of neurologic disease mechanisms in humans and in animal models and to discover biomarkers that are useful in the clinical setting. An important extension to these efforts that has not been realized thus far is the desire to profile changes in protein expression that result from therapy to help relate disease-modifying effects at the molecular level with clinical outcomes. Here we review the major advances in 2-DE methods and discuss specific examples of its application in the study of neurologic diseases.
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Affiliation(s)
- Leila H. Choe
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, 14853-5201 Ithaca, NY
| | - Brenda G. Werner
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, 14853-5201 Ithaca, NY
| | - Kelvin H. Lee
- School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, 14853-5201 Ithaca, NY
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245
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Two-dimensional protein electrophoresis: From molecular pathway discovery to biomarker discovery in neurological disorders. Neurotherapeutics 2006. [DOI: 10.1007/bf03206656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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246
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Coyle EM, Blazer LL, White AA, Hess JL, Boyle MDP. Practical applications of high-affinity, albumin-binding proteins from a group G streptococcal isolate. Appl Microbiol Biotechnol 2006; 71:39-45. [PMID: 16317541 DOI: 10.1007/s00253-005-0097-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2005] [Revised: 07/08/2005] [Accepted: 07/10/2005] [Indexed: 11/24/2022]
Abstract
Binding proteins that have high affinities for mammalian plasma proteins that are expressed on the surface of bacteria have proven valuable for the purification and detection of several biologically important molecules from human and animal plasma or serum. In this study, we have isolated a high affinity albumin-binding molecule from a group G streptococcal isolate of bovine origin and have demonstrated that the isolated protein can be biotinylated without loss of binding activity and can be used as a tracer for quantification of human serum albumin (HSA). The binding protein can be immobilized and used as a selective capture reagent in a competitive ELISA format using a biotinylated HSA tracer. In this assay format, the sensitivity of detection for 50% inhibition of binding of HSA was less than 1 microg/ml. When attached to the bacterial surface, this binding protein can be used to deplete albumin from human plasma, as analyzed by surface-enhanced laser desorption ionization time of flight mass spectrometry.
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Affiliation(s)
- Emily M Coyle
- Department of Biology, Juniata College, 1700 Moore St., Huntingdon, PA 16652, USA
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247
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Chen WH, Lee SC, Sabu S, Fang HC, Chung SC, Han CC, Chang HC. Solid-Phase Extraction and Elution on Diamond (SPEED): A Fast and General Platform for Proteome Analysis with Mass Spectrometry. Anal Chem 2006; 78:4228-34. [PMID: 16771555 DOI: 10.1021/ac052085y] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper presents a new solid-phase extraction and elution platform based on surface-functionalized diamond nanocrystallites. Compared with conventional methods, the platform facilitates purification and concentration of intact proteins and their enzymatic digests for ensuing sodium dodecyl sulfate-polyacrylamide gel electrophoresis or matrix-assisted laser desorption/ionization mass spectrometry analysis without prior removal of the adsorbent. One-pot work flow involving reduction of disulfide bonds, protection of free cysteine residues, washing off residual chemicals, and proteolytic digestion of adsorbed proteins can be performed directly on the particles. The utility and versatility of this protein workup platform were demonstrated with liquid chromatography-electrospray ionization tandem mass spectrometry in proteome analysis of human urine. The proteome analysis of each urine sample can be completed in 8 h.
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Affiliation(s)
- Wei-Hao Chen
- Institute of Atomic and Molecular Sciences, Academia Sinica, P.O. Box 23-116, Taipei 106, Taiwan, ROC
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248
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Freeman WM, Lull ME, Guilford MT, Vrana KE. Depletion of abundant proteins from non-human primate serum for biomarker studies. Proteomics 2006; 6:3109-13. [PMID: 16619306 DOI: 10.1002/pmic.200500717] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Non-human primates are an important biomedical research model organism and offer great promise for serum biomarker proteomic studies. However, potential obstacles to these studies include affinity serum depletion methods based on human antigens, depletion methods altering quantitation, and incomplete non-human primate genome sequences for protein identification. In the present study, high-abundance protein removal from monkey serum using a human multiple affinity removal system (MARS) was shown to be specific and did not alter quantitation. Depleted serum also demonstrated greater sensitivity for previously masked, lower-abundance proteins.
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Affiliation(s)
- Willard M Freeman
- Department of Pharmacology H078, Penn State College of Medicine, 500 University Drive, Hershey, PA 17033, USA.
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249
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Holland JW, Deeth HC, Alewood PF. Resolution and characterisation of multiple isoforms of bovine κ-casein by 2-DE following a reversible cysteine-tagging enrichment strategy. Proteomics 2006; 6:3087-95. [PMID: 16619295 DOI: 10.1002/pmic.200500780] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Visualisation of multiple isoforms of kappa-casein on 2-D gels is restricted by the abundant alpha- and beta-caseins that not only limit gel loading but also migrate to similar regions as the more acidic kappa-casein isoforms. To overcome this problem, we took advantage of the absence of cysteine residues in alpha(S1)- and beta-casein by devising an affinity enrichment procedure based on reversible biotinylation of cysteine residues. Affinity capture of cysteine-containing proteins on avidin allowed the removal of the vast majority of alpha(S1)- and beta-casein, and on subsequent 2-D gel analysis 16 gel spots were identified as kappa-casein by PMF. Further analysis of the C-terminal tryptic peptide along with structural predictions based on mobility on the 2-D gel allowed us to assign identities to each spot in terms of genetic variant (A or B), phosphorylation status (1, 2 or 3) and glycosylation status (from 0 to 6). Eight isoforms of the A and B variants with the same PTMs were observed. When the casein fraction of milk from a single cow, homozygous for the B variant of kappa-casein, was used as the starting material, 17 isoforms from 13 gel spots were characterised. Analysis of isoforms of low abundance proved challenging due to the low amount of material that could be extracted from the gels as well as the lability of the PTMs during MS analysis. However, we were able to identify a previously unrecognised site, T(166), that could be phosphorylated or glycosylated. Despite many decades of analysis of milk proteins, the reasons for this high level of heterogeneity are still not clear.
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Affiliation(s)
- John W Holland
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia.
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250
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Palacios O, Ruiz Encinar J, Schaumlöffel D, Lobinski R. Fractionation of selenium-containing proteins in serum by multiaffinity liquid chromatography before size-exclusion chromatography–ICPMS. Anal Bioanal Chem 2006; 384:1276-83. [PMID: 16493548 DOI: 10.1007/s00216-005-0286-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2005] [Revised: 12/16/2005] [Accepted: 12/17/2005] [Indexed: 12/21/2022]
Abstract
Immunoaffinity chromatography has been investigated for fractionation of serum into selenoalbumin and true selenoproteins. Among several albumin-depletion kits tested, a multiaffinity column specifically binding albumin and five other major serum proteins provided the best results. It extracted ca 95% of both albumin and selenoalbumin, which enabled interference-free determination of glutathione peroxidase, selenoprotein P, and selenoalbumin by size-exclusion chromatography combined with inductively coupled plasma mass spectrometry (SEC-ICPMS). The efficiency of the multiaffinity column did not vary over a period of 18 months. The purity of fractions separated by immunoaffinity LC was confirmed by elution-volume matching with standards in SEC-ICPMS and by selenopeptide mapping in capillary HPLC-ICPMS. Quantification of the selenium distribution among the different proteins in human serum from a control group and from a person on a selenium-rich diet revealed that 67% of the supplemented selenium was incorporated into albumin, 30% into glutathione peroxidase, and 3% into selenoprotein P.
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Affiliation(s)
- Oscar Palacios
- Equipe de Chimie Analytique Bio-inorganique, CNRS UMR 5034, Hélioparc, 2, av. Pr. Angot, 64053, Pau, France
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