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Abstract
The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins constitute the vast majority of total blood protein mass. Various separation, depletion, enrichment, and quantitative developments coupled with improvements in gel-based protein quantification technologies, specifically fluorescence two-dimensional difference gel electrophoresis (2D-DIGE), have contributed to significant improvements in the detection and identification of lower abundance proteins. One of these enrichment technologies, ProteoMiner, is the focus of this chapter. The ProteoMiner technology utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but at the same time suppresses the concentration of high-abundance proteins in subsequent analysis.
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Affiliation(s)
- Sandra Murphy
- Charles River Laboratories, Saffron Walden, Essex, United Kingdom
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Boschetti E, Zilberstein G, Righetti PG. Combinatorial peptides: A library that continuously probes low-abundance proteins. Electrophoresis 2021; 43:355-369. [PMID: 34498305 DOI: 10.1002/elps.202100131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/31/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
After a decade of experimental applications, it is the objective of this review to make a point on combinatorial peptide ligand libraries dedicated to low-abundance proteins from animals to plants and to microorganism proteomics. It is, thus, at the light of the recent technical developments and applications that we will examine the state of the art, its usage within the scientific community, and its openness to unexplored fields. The improvements of the methodology and its implementation in connection with analytical determinations of combinatorial peptide ligand library (CPLL)-treated samples are extensively reviewed and commented upon. Relevant examples covering few critical aspects describe the performance of the technology. Finally, a reflection on the technological future is attempted in particular by involving new concepts adapted to the limited availability of certain biological samples.
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Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
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Panachan J, Chokchaichamnankit D, Weeraphan C, Srisomsap C, Masaratana P, Hatairaktham S, Panichkul N, Svasti J, Kalpravidh RW. Differentially expressed plasma proteins of β-thalassemia/hemoglobin E patients in response to curcuminoids/vitamin E antioxidant cocktails. ACTA ACUST UNITED AC 2019; 24:300-307. [PMID: 30661467 DOI: 10.1080/16078454.2019.1568354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Iron overload and oxidative stress are the major causes of serious complications and mortality in thalassemic patients. Our previous work supports the synergistic effects of antioxidant cocktails (curcuminoids or vitamin E, N-acetylcysteine, and deferiprone) in treatment of β-thalassemia/Hb E patients. This further 2-DE-based proteomic study aimed to identify the plasma proteins that expressed differentially in response to antioxidant cocktails. METHODS Frozen plasma samples of ten normal subjects and ten β-thalassemia/Hb E patients at three-time points (baseline, month 6, and month 12) were reduced the dynamic range of proteome using ProteoMiner kit and separated proteins by two-dimensional gel electrophoresis. Differentially expressed proteins were identified using tandem mass spectrometry. Several plasma proteins were validated by ELISA and Western blot analysis. RESULTS Thirteen and 11 proteins were identified with altered expression levels in the curcuminoids- and vitamin E cocktail groups, respectively. The associations between vitronectin (VTN) expression and total bilirubin levels, as well as between serum paraoxonase/arylesterase 1 (PON1) expression and blood reactive oxygen species were observed. Validation results were consistent with proteomics results. DISCUSSION AND CONCLUSIONS These plasma proteins may provide better understanding of the mechanisms underlying the therapeutic effects of antioxidant cocktails in thalassemic patients.
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Affiliation(s)
- Jirawan Panachan
- a Department of Biochemistry, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand
| | | | - Churat Weeraphan
- b Laboratory of Biochemistry , Chulabhorn Research Institute , Bangkok , Thailand.,c Department of Molecular Biotechnology and Bioinformatics, Faculty of Science , Prince of Songkla University , Songkla , Thailand
| | - Chantragan Srisomsap
- b Laboratory of Biochemistry , Chulabhorn Research Institute , Bangkok , Thailand
| | - Patarabutr Masaratana
- a Department of Biochemistry, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand
| | - Suneerat Hatairaktham
- a Department of Biochemistry, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand
| | - Narumol Panichkul
- a Department of Biochemistry, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand
| | - Jisnuson Svasti
- b Laboratory of Biochemistry , Chulabhorn Research Institute , Bangkok , Thailand.,d Applied Biological Sciences Program, Chulabhorn Research Institute , Bangkok , Thailand
| | - Ruchaneekorn W Kalpravidh
- a Department of Biochemistry, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok , Thailand
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4
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Abstract
The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins constitute the vast majority of total blood protein mass. Various separation, depletion, enrichment, and quantitative developments coupled with improvements in gel-based protein quantification technologies, specifically difference gel electrophoresis (DIGE), have contributed to significant improvements in the detection and identification of lower abundance proteins. One of these enrichment technologies, Proteominer, will be the focus of this chapter. The Proteominer technology a utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but at the same time suppressing the concentration of high-abundance proteins in subsequent analysis.
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Gianazza E, Miller I, Palazzolo L, Parravicini C, Eberini I. With or without you — Proteomics with or without major plasma/serum proteins. J Proteomics 2016; 140:62-80. [DOI: 10.1016/j.jprot.2016.04.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 12/26/2022]
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Comparison of serum fractionation methods by data independent label-free proteomics. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Dittrich J, Becker S, Hecht M, Ceglarek U. Sample preparation strategies for targeted proteomics via proteotypic peptides in human blood using liquid chromatography tandem mass spectrometry. Proteomics Clin Appl 2014; 9:5-16. [PMID: 25418444 DOI: 10.1002/prca.201400121] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/29/2014] [Accepted: 11/18/2014] [Indexed: 11/07/2022]
Abstract
The simultaneous quantification of protein concentrations via proteotypic peptides in human blood by liquid chromatography coupled to quadrupole MS/MS is an important field of bioanalytical research with a high potential for routine diagnostic applications. This review summarizes currently available sample preparation procedures and trends for absolute protein quantification in blood using LC-MS/MS. It discusses approaches of transferring established qualitative protocols to a quantitative analysis regarding their reliability and reproducibility. Techniques used to enhance method sensitivity such as the depletion of high-abundant proteins or the immunoaffinity enrichment of proteins and peptides are described. Furthermore, workflows for (i) protein denaturation, (ii) disulfide bridge reduction and (iii) thiol alkylation as well as (iv) enzymatic digestion for absolute protein quantification are presented. The main focus is on the tryptic digestion as a bottleneck of protein quantification via proteotypic peptides. Conclusively, requirements for a high-throughput application are discussed.
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Affiliation(s)
- Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
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Guo X, Hao Y, Kamilijiang M, Hasimu A, Yuan J, Wu G, Reyimu H, Kadeer N, Abudula A. Potential predictive plasma biomarkers for cervical cancer by 2D-DIGE proteomics and Ingenuity Pathway Analysis. Tumour Biol 2014; 36:1711-20. [PMID: 25427637 DOI: 10.1007/s13277-014-2772-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 10/23/2014] [Indexed: 11/27/2022] Open
Abstract
The current methods available for screening and detecting cervical squamous cell carcinoma (CSCC) have insufficient sensitivity and specificity. As a result, many patients suffered from erroneous and missed diagnosis. Because CSCC is usually asymptomatic at potentially curative stages, identification of biomarkers is an urgent need for the early detection of CSCC. Comparative proteomics based on two-dimensional differential in-gel electrophoresis (2D-DIGE) was employed to quantitatively analyze plasma proteins of healthy Uyghur women and with early stage cervical carcinoma. The 2D-DIGE image were analyzed statistically using DeCyder™ 2D software. The statistical analysis of proteomic data revealed that 43 protein spots showed significantly different expression (ratio > 1.5, P < 0.01). A further identification of these protein spots by MALDI-TOF-MS found out 16 different proteins. Bioinformatic analysis within the framework of Ingenuity Pathway Analysis (IPA(@)) showed that 10 plasma proteins as candidate biomarker were screened, mainly including lipid metabolism-related proteins (APOA4, APOA1, APOE), complement (EPPK1, CFHR1), metabolic enzymes (CP, F2, MASP2), glycoprotein (CLU), and immune function-related proteins (IGK@). Networks involved in lipid metabolism, molecular transport, and small molecule biochemistry were dysfunctional in CSCC. Acute phase response signaling and JAK/Stat signaling and IL-4 signaling, etc., were identified as the canonical pathways that are overrepresented in CSCC. Furthermore, the expression of three proteins (APOA1, APOE, CLU) were validated using ELISA in plasma of patients with different stage cervical lesion. With the combined proteomic and bioinformatic approach, this study was successful in identifying biomarker signatures for cervical cancer and might provide new insights into the mechanism of CSCC progression, potentially leading to the design of novel diagnostic and therapeutic strategies.
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Affiliation(s)
- Xia Guo
- Xinjiang Key Laboratory of Molecular Biology and Endemic Diseases, Central Laboratory of XinJiang Medical University/Collaborative Innovation Center, Xinjiang Medical University, Urumqi, 830011, People's Republic of China,
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Halim A, Westerlind U, Pett C, Schorlemer M, Rüetschi U, Brinkmalm G, Sihlbom C, Lengqvist J, Larson G, Nilsson J. Assignment of saccharide identities through analysis of oxonium ion fragmentation profiles in LC-MS/MS of glycopeptides. J Proteome Res 2014; 13:6024-32. [PMID: 25358049 DOI: 10.1021/pr500898r] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein glycosylation plays critical roles in the regulation of diverse biological processes, and determination of glycan structure-function relationships is important to better understand these events. However, characterization of glycan and glycopeptide structural isomers remains challenging and often relies on biosynthetic pathways being conserved. In glycoproteomic analysis with liquid chromatography-tandem mass spectrometry (LC-MS/MS) using collision-induced dissociation (CID), saccharide oxonium ions containing N-acetylhexosamine (HexNAc) residues are prominent. Through analysis of beam-type CID spectra and ion trap CID spectra of synthetic and natively derived N- and O-glycopeptides, we found that the fragmentation patterns of oxonium ions characteristically differ between glycopeptides terminally substituted with GalNAcα1-O-, GlcNAcβ1-O-, Galβ3GalNAcα1-O-, Galβ4GlcNAcβ-O-, and Galβ3GlcNAcβ-O- structures. The difference in the oxonium ion fragmentation profiles of such glycopeptides may thus be used to distinguish among these glycan structures and could be of importance in LC-MS/MS-based glycoproteomic studies.
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Affiliation(s)
- Adnan Halim
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, ‡Department of Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg , SE-41345 Gothenburg, Sweden
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Mukherjee S, Jagadeeshaprasad MG, Banerjee T, Ghosh SK, Biswas M, Dutta S, Kulkarni MJ, Pattari S, Bandyopadhyay A. Proteomic analysis of human plasma in chronic rheumatic mitral stenosis reveals proteins involved in the complement and coagulation cascade. Clin Proteomics 2014; 11:35. [PMID: 25379033 PMCID: PMC4193131 DOI: 10.1186/1559-0275-11-35] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 08/14/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Rheumatic fever in childhood is the most common cause of Mitral Stenosis in developing countries. The disease is characterized by damaged and deformed mitral valves predisposing them to scarring and narrowing (stenosis) that results in left atrial hypertrophy followed by heart failure. Presently, echocardiography is the main imaging technique used to diagnose Mitral Stenosis. Despite the high prevalence and increased morbidity, no biochemical indicators are available for prediction, diagnosis and management of the disease. Adopting a proteomic approach to study Rheumatic Mitral Stenosis may therefore throw some light in this direction. In our study, we undertook plasma proteomics of human subjects suffering from Rheumatic Mitral Stenosis (n = 6) and Control subjects (n = 6). Six plasma samples, three each from the control and patient groups were pooled and subjected to low abundance protein enrichment. Pooled plasma samples (crude and equalized) were then subjected to in-solution trypsin digestion separately. Digests were analyzed using nano LC-MS(E). Data was acquired with the Protein Lynx Global Server v2.5.2 software and searches made against reviewed Homo sapiens database (UniProtKB) for protein identification. Label-free protein quantification was performed in crude plasma only. RESULTS A total of 130 proteins spanning 9-192 kDa were identified. Of these 83 proteins were common to both groups and 34 were differentially regulated. Functional annotation of overlapping and differential proteins revealed that more than 50% proteins are involved in inflammation and immune response. This was corroborated by findings from pathway analysis and histopathological studies on excised tissue sections of stenotic mitral valves. Verification of selected protein candidates by immunotechniques in crude plasma corroborated our findings from label-free protein quantification. CONCLUSIONS We propose that this protein profile of blood plasma, or any of the individual proteins, could serve as a focal point for future mechanistic studies on Mitral Stenosis. In addition, some of the proteins associated with this disorder may be candidate biomarkers for disease diagnosis and prognosis. Our findings might help to enrich existing knowledge on the molecular mechanisms involved in Mitral Stenosis and improve the current diagnostic tools in the long run.
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Affiliation(s)
- Somaditya Mukherjee
- />Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032 India
| | | | - Tanima Banerjee
- />Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032 India
| | - Sudip K Ghosh
- />General Medicine Department, Medical College, Kolkata, India
| | - Monodeep Biswas
- />Department of Cardiology, Geisinger Community Medical Center & Wright Center for graduate medical education, Scranton, PA 18510 USA
| | - Santanu Dutta
- />Department of Cardio-thoracic and Vascular Surgery, Institute of Post Graduate Medical Education and Research, SSKM Hospital, Kolkata, 700020 India
| | - Mahesh J Kulkarni
- />Proteomics Facility, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, 411008 India
| | - Sanjib Pattari
- />Rabindranath Tagore International Institute of Cardiac Sciences, Kolkata, 700099 India
| | - Arun Bandyopadhyay
- />Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata, 700032 India
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Álvarez-Chaver P, Otero-Estévez O, Páez de la Cadena M, Rodríguez-Berrocal FJ, Martínez-Zorzano VS. Proteomics for discovery of candidate colorectal cancer biomarkers. World J Gastroenterol 2014; 20:3804-3824. [PMID: 24744574 PMCID: PMC3983438 DOI: 10.3748/wjg.v20.i14.3804] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/24/2014] [Accepted: 03/10/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer-related deaths in Europe and other Western countries, mainly due to the lack of well-validated clinically useful biomarkers with enough sensitivity and specificity to detect this disease at early stages. Although it is well known that the pathogenesis of CRC is a progressive accumulation of mutations in multiple genes, much less is known at the proteome level. Therefore, in the last years many proteomic studies have been conducted to find new candidate protein biomarkers for diagnosis, prognosis and as therapeutic targets for this malignancy, as well as to elucidate the molecular mechanisms of colorectal carcinogenesis. An important advantage of the proteomic approaches is the capacity to look for multiple differentially expressed proteins in a single study. This review provides an overview of the recent reports describing the different proteomic tools used for the discovery of new protein markers for CRC such as two-dimensional electrophoresis methods, quantitative mass spectrometry-based techniques or protein microarrays. Additionally, we will also focus on the diverse biological samples used for CRC biomarker discovery such as tissue, serum and faeces, besides cell lines and murine models, discussing their advantages and disadvantages, and summarize the most frequently identified candidate CRC markers.
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Lichtenauer AM, Herzog R, Tarantino S, Aufricht C, Kratochwill K. Equalizer technology followed by DIGE-based proteomics for detection of cellular proteins in artificial peritoneal dialysis effluents. Electrophoresis 2014; 35:1387-94. [DOI: 10.1002/elps.201300499] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 01/17/2014] [Accepted: 02/21/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Anton Michael Lichtenauer
- Department of Pediatrics and Adolescent Medicine; Medical University of Vienna; Austria
- Zytoprotec GmbH; Vienna Austria
| | - Rebecca Herzog
- Department of Pediatrics and Adolescent Medicine; Medical University of Vienna; Austria
- Zytoprotec GmbH; Vienna Austria
| | - Silvia Tarantino
- Department of Pediatrics and Adolescent Medicine; Medical University of Vienna; Austria
| | - Christoph Aufricht
- Department of Pediatrics and Adolescent Medicine; Medical University of Vienna; Austria
| | - Klaus Kratochwill
- Department of Pediatrics and Adolescent Medicine; Medical University of Vienna; Austria
- Zytoprotec GmbH; Vienna Austria
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Desoubeaux G, Jourdan ML, Valera L, Jardin B, Hem S, Caille A, Cormier B, Marchand-Adam S, Bailly É, Diot P, Chandenier J. Proteomic demonstration of the recurrent presence of inter-alpha-inhibitor H4 heavy-chain during aspergillosis induced in an animal model. Int J Med Microbiol 2013; 304:327-38. [PMID: 24360996 DOI: 10.1016/j.ijmm.2013.11.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 11/07/2013] [Accepted: 11/25/2013] [Indexed: 11/30/2022] Open
Abstract
Invasive pulmonary aspergillosis remains a matter of great concern in oncology/haematology, intensive care units and organ transplantation departments. Despite the availability of various diagnostic tools with attractive features, new markers of infection are required for better medical care. We therefore looked for potential pulmonary biomarkers of aspergillosis, by carrying out two-dimensional (2D) gel electrophoresis comparing the proteomes of bronchial-alveolar lavage fluids (BALF) from infected rats and from control rats presenting non-specific inflammation, both immunocompromised. A bioinformatic analysis of the 2D-maps revealed significant differences in the abundance of 20 protein spots (ANOVA P-value<0.01; q-value<0.03; power>0.8). One of these proteins, identified by mass spectrometry, was considered of potential interest: inter-alpha-inhibitor H4 heavy-chain (ITIH4), characterised for the first time in this infectious context. Western blotting confirmed its overabundance in all infected BALF, particularly at early stages of murine aspergillosis. Further investigations were carried on rat serum, and confirmed that ITIH4 levels increased during experimental aspergillosis. Preliminary results in human samples strengthened this trend. To our knowledge, this is the first description of the involvement of ITIH4 in aspergillosis.
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Affiliation(s)
- Guillaume Desoubeaux
- CHU de Tours, Service de Parasitologie - Mycologie - Médecine tropicale, Tours, France; Université François Rabelais, CEPR UMR-INSERM U1100/E.A. 6305, Faculté de Médecine, Tours, France.
| | - Marie-Lise Jourdan
- CHU de Tours, Service d'Hématologie Biologique, Tours, France; Université François Rabelais, INSERM U1069/N2C, Faculté de Médecine, Tours, France
| | - Lionel Valera
- Sysdiag, CNRS UMR 3145 Bio-Rad, Cap Delta, Montpellier, France
| | | | - Sonia Hem
- Plateforme de spectrométrie de masse protéomique - MSPP, Laboratoire de Protéomique Fonctionnelle, INRA UR1199, Montpellier, France
| | - Agnès Caille
- CHU de Tours, Centre d'Investigation Clinique, Tours, France; Université François Rabelais, INSERM 202, Faculté de Médecine, Tours, France
| | - Bénédicte Cormier
- CHU de Tours, Service d'Anatomie et Cytologie Pathologiques, Tours, France
| | - Sylvain Marchand-Adam
- Université François Rabelais, CEPR UMR-INSERM U1100/E.A. 6305, Faculté de Médecine, Tours, France; CHU de Tours, Service de Pneumologie, Tours, France
| | - Éric Bailly
- CHU de Tours, Service de Parasitologie - Mycologie - Médecine tropicale, Tours, France
| | - Patrice Diot
- Université François Rabelais, CEPR UMR-INSERM U1100/E.A. 6305, Faculté de Médecine, Tours, France; CHU de Tours, Service de Pneumologie, Tours, France
| | - Jacques Chandenier
- CHU de Tours, Service de Parasitologie - Mycologie - Médecine tropicale, Tours, France; Université François Rabelais, CEPR UMR-INSERM U1100/E.A. 6305, Faculté de Médecine, Tours, France
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Zhang X, Zhang J, Li Q, Wu X, Wang T, Wang Y. SELDI-TOF-MS in chronic obstructive pulmonary disease. CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-012-5460-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Ma D, Li L. Searching for reliable premortem protein biomarkers for prion diseases: progress and challenges to date. Expert Rev Proteomics 2013; 9:267-80. [PMID: 22809206 DOI: 10.1586/epr.12.20] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prion diseases are a unique family of fatal neurodegenerative diseases caused by abnormal folding of normal cellular prion proteins in the brain. Due to the high risk of prion disease transmission and the lack of effective treatment to cure or delay the disease progression, prion diseases pose a serious threat to public health. To control and prevent prion diseases, an early diagnosis is urgently needed. Proteomic analysis has emerged as a powerful technology to decipher biological and pathophysiological processes and identify protein biomarkers indicative of disease. In this article, the authors review the use of the latest proteomic technologies for the identification of promising prion disease biomarkers, the challenges that exist in biomarker development pipelines and the new directions for utilizing proteomics for future biomarker discovery in the context of prion disease diagnostics.
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Affiliation(s)
- Di Ma
- School of Pharmacy, University of Wisconsin at Madison, 777 Highland Avenue, Madison, WI 53705, USA
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Gil-Dones F, Darde VM, Vivanco F, Barderas MG. A comparative study of immunodepletion and equalization methods for aortic stenosis human plasma. Methods Mol Biol 2013; 1005:245-56. [PMID: 23606263 DOI: 10.1007/978-1-62703-386-2_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Calcified aortic valve disease is a slowly progressive disorder that ranges from mild valve thickening with no obstruction of blood flow, known as aortic sclerosis, to severe calcification with impaired leaflet motion or aortic stenosis. Until now, aortic stenosis (AS) was thought to result from aging and "wear and tear" of the aortic valve, but nowadays, it is known that it presents the same risk factors as atherosclerosis and cardiovascular diseases.A proteomic analysis of plasma could permit to identify the changes in protein expression induced by AS in this biological sample. However, the characterization of human plasma proteome is a very complicated task, due to the wide dynamic range of concentration that separates the most abundant proteins and the less common ones (10-12 orders of magnitude). For this reason, plasma analysis requires pre-fractionation methods, and several such techniques are currently used to deplete albumin and other abundant plasma proteins.In this work we describe two different and optimized protocols to decrease the plasma proteome complexity for proteomic analysis. With this, comprehensive and systematic characterization of the plasma proteome in the healthy and diseased aortic stenosis (AS) state will greatly facilitate the development of "useful" biomarkers for early disease detection, clinical diagnosis, and therapy.
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Affiliation(s)
- Felix Gil-Dones
- Department of Vascular Physiopathology, Hospital Nacional de Paraplejicos, SESCAM, Toledo, Spain
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Zhu G, Zhao P, Deng N, Tao D, Sun L, Liang Z, Zhang L, Zhang Y. Single chain variable fragment displaying M13 phage library functionalized magnetic microsphere-based protein equalizer for human serum protein analysis. Anal Chem 2012; 84:7633-7. [PMID: 22909037 DOI: 10.1021/ac3017746] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Single chain variable fragment (scFv) displaying the M13 phage library was covalently immobilized on magnetic microspheres and used as a protein equalizer for the treatment of human serum. First, scFv displaying M13 phage library functionalized magnetic microspheres (scFv@M13@MM) was incubated with a human serum sample. Second, captured proteins on scFv@M13@MM were eluted with 2 M NaCl, 50 mM glycine-hydrochloric acid (Gly-HCl), and 20% (v/v) acetonitrile with 0.5% (v/v) trifluoroacetic acid in sequence. Finally, the tightly bonded proteins were released by the treatment with thrombin. The eluates were first analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) with silver staining. Results indicated that the difference of protein concentration was reduced obviously in NaCl and Gly-HCl fractions compared with untreated human serum sample. The eluates were also digested with trypsin, followed by online 2D-strong cation exchange (SCX)-RPLC-ESI-MS/MS analysis. Results demonstrated that the number of proteins identified from an scFv@M13@MM treated human serum sample was improved 100% compared with that from the untreated sample. In addition, the spectral count of 10 high abundance proteins (serum albumin, serotransferrin, α-2-macroglobulin, α-1-antitrypsin, apolipoprotein B-100, Ig γ-2 chain C region, haptoglobin, hemopexin, α-1-acid glycoprotein 1, and α-2-HS-glycoprotein) decreased evidently after scFv@M13@MM treatment. All these results demonstrate that scFv@M13@MM could efficiently remove high-abundance proteins, reduce the protein concentration difference of human serum, and result in more protein identification.
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Affiliation(s)
- Guijie Zhu
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. and A. Center, Dalian Institute of Chemical Physics, The Chinese Academy of Science, Dalian, China
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Righetti PG, Boschetti E, Candiano G. Mark Twain: How to fathom the depth of your pet proteome. J Proteomics 2012; 75:4783-91. [DOI: 10.1016/j.jprot.2012.05.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Revised: 05/28/2012] [Accepted: 05/30/2012] [Indexed: 02/06/2023]
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19
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DIGE enables the detection of a putative serum biomarker of fungal origin in a mouse model of invasive aspergillosis. J Proteomics 2012; 75:2536-49. [DOI: 10.1016/j.jprot.2012.01.040] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 01/27/2012] [Accepted: 01/30/2012] [Indexed: 11/20/2022]
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20
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Guo X, Abliz G, Reyimu H, Zhao F, Kadeer N, Matsidik R, Wu G, Abudula A. The association of a distinct plasma proteomic profile with the cervical high-grade squamous intraepithelial lesion of Uyghur women: a 2D liquid-phase chromatography/mass spectrometry study. Biomarkers 2012; 17:352-61. [PMID: 22458349 DOI: 10.3109/1354750x.2012.673133] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To identify plasma protein biomarkers of cervical high-grade squamous intraepithelial lesion (HSIL) of Uyghur women by proteomics approach. METHODS Plasma protein samples of Uyghur women with HSIL and chronic cervicitis were analyzed with 2D HPLC followed by detection of target proteins with Linear Trap Quadrupole Mass Spectrometer (LTQ MS/MS). RESULTS We detected three upregulated and one downregulated protein peaks representing protein constituents distinguishing HSIL from controls by 2D HPLC, identified 31 target proteins by LTQ MS/MS. Further confirmed analysis with online software IPA® 8.7 and ELISA assay showed APOA1 and mTOR as potential biomarkers. CONCLUSIONS A distinct plasma proteomic profile may be associated with HSIL of Uyghur women.
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Affiliation(s)
- Xia Guo
- Xinjiang Key Laboratory of Molecular Biology and Endemic Diseases, Xinjiang Medical University, Urumqi, PR China
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21
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Malaud E, Piquer D, Merle D, Molina L, Guerrier L, Boschetti E, Saussine M, Marty-Ané C, Albat B, Fareh J. Carotid atherosclerotic plaques: Proteomics study after a low-abundance protein enrichment step. Electrophoresis 2012; 33:470-82. [DOI: 10.1002/elps.201100395] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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22
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Selvaraju S, Rassi ZE. Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis--an update covering the period 2008-2011. Electrophoresis 2012; 33:74-88. [PMID: 22125262 PMCID: PMC3516880 DOI: 10.1002/elps.201100431] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Revised: 09/05/2011] [Accepted: 09/06/2011] [Indexed: 11/08/2022]
Abstract
This review article expands on the previous one (Jmeian, Y. and El Rassi, Z. Electrophoresis 2009, 30, 249-261) by reviewing pertinent literature in the period extending from early 2008 to the present. Similar to the previous review article, the present one is concerned with proteomic sample preparation (e.g. depletion of high-abundance proteins, reduction of the protein dynamic concentration range, enrichment of a particular subproteome), and the subsequent chromatographic and/or electrophoretic prefractionation prior to peptide separation and identification by LC-MS/MS. This review article differs from the first version published in Electrophoresis 2009, 30, 249-261 by expanding on capturing/enriching subglycoproteomics by lectin affinity chromatography. Ninety-eight articles published in the period extending from early 2008 to the present have been reviewed. By no means is this review article exhaustive: its aim is to give a concise report on the latest developments in the field.
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Affiliation(s)
| | - Ziad El Rassi
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078-3071
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23
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Bulman AL, Dalmasso EA. Purification and identification of candidate biomarkers discovered using SELDI-TOF MS. Methods Mol Biol 2012; 818:49-66. [PMID: 22083815 DOI: 10.1007/978-1-61779-418-6_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Purification and identification of candidate biomarkers is a critical step in the biomarker development process, since it provides insight into the disease biology and facilitates the development of analyte-specific assays. Top-down biomarker discovery workflows like SELDI-TOF MS yield candidate markers that are identified based on native mass. Positive identification of these candidate biomarkers requires further enrichment and/or purification. While purification methods must be optimized for each protein target, there are two general workflows. Native peptides under approximately 4 kDa can be subjected to direct sequence analysis using a tandem mass spectrometer whereas proteins over approximately 4 kDa usually require proteolytic digestion prior to MS/MS analysis. In both cases, partial purification is usually necessary to enrich the candidate biomarker relative to other proteins in a complex biological mixture. This chapter provides detailed protocols for protein purification (including anion exchange, metal affinity, and reverse phase chromatography as well as SDS-PAGE) and identification (including protein processing, digestion, and database searching).
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Boschetti E, Chung MCM, Righetti PG. "The quest for biomarkers": are we on the right technical track? Proteomics Clin Appl 2011; 6:22-41. [PMID: 22213582 DOI: 10.1002/prca.201100039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 10/01/2011] [Accepted: 11/15/2011] [Indexed: 12/19/2022]
Abstract
The discovery phase of biomarkers of diagnostic or therapeutic interest started a decade ago with the very rapid development of proteomic investigations. In spite of the development of innovative technologies and multiple approaches, the "harvest" is still modest. Various reasons justified the encountered difficulties and most of them have been circumvented by specific sample treatments or dedicated analytical approaches. Nevertheless, the situation of very modest biomarker discovery level did not change much. This review intends to specifically analyze the main approaches used for biomarker discovery phase and evaluate related advantages and disadvantages. Thus, preliminary sample treatments such as fractionation, depletion and reduction of dynamic concentration range will critically be discussed and then the main differential expression investigation methods analyzed. Combinations of technologies are also discussed along with possible proposals to federate associations of complementary technologies for better chances of success.
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Affiliation(s)
- Egisto Boschetti
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milano, Italy.
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25
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Gil-Dones F, Darde VM, Alonso-Orgaz S, Lopez-Almodovar LF, Mourino-Alvarez L, Padial LR, Vivanco F, Barderas MG. Inside human aortic stenosis: a proteomic analysis of plasma. J Proteomics 2011; 75:1639-53. [PMID: 22178735 DOI: 10.1016/j.jprot.2011.11.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 11/28/2011] [Accepted: 11/29/2011] [Indexed: 11/20/2022]
Abstract
Valvular aortic stenosis (AS) produces a slowly progressive obstruction in left ventricular outflow track. For this reason, aortic valve replacement is warranted when the valvular stenosis is hemodinamically significant, becoming the most common worldwide cause of aortic valve surgery. Recent epidemiologic studies have revealed an association between degenerative AS and cardiovascular risk factors for atherosclerosis, althought reducing the exposure to such factors and statin therapies both fail to delay or reverse the pathology. Hence, a deeper understanding of the pathophysiology of this disease is required to identify appropriate preventive measures. A proteomic analysis of plasma will permit to know and identify the changes in protein expression induced by AS in this tissue. Using two-dimensional difference gel electrophoresis (2D-DIGE) followed by mass spectrometry (MS), we compared the crude (not pre-fractioned) and pre-fractioned plasma from AS patients and control subjects. We sought to identify plasma proteins whose expression is modified in AS. In addition we investigated if crude plasma presented some alterations in the more abundant proteins since to date, has never been studied before. We also further investigated the link between this disease and atherosclerosis with a view to identifying new potential markers and therapeutic targets.
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Affiliation(s)
- Félix Gil-Dones
- Department of Vascular Physiopathology, Hospital Nacional de Parapléjicos, SESCAM, Toledo, Spain
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26
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Low abundance protein enrichment for discovery of candidate plasma protein biomarkers for early detection of breast cancer. J Proteomics 2011; 75:366-74. [DOI: 10.1016/j.jprot.2011.07.030] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 07/26/2011] [Accepted: 07/29/2011] [Indexed: 11/23/2022]
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27
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Monari E, Casali C, Cuoghi A, Nesci J, Bellei E, Bergamini S, Fantoni LI, Natali P, Morandi U, Tomasi A. Enriched sera protein profiling for detection of non-small cell lung cancer biomarkers. Proteome Sci 2011; 9:55. [PMID: 21929752 PMCID: PMC3184051 DOI: 10.1186/1477-5956-9-55] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 09/19/2011] [Indexed: 11/15/2022] Open
Abstract
Background Non Small Cell Lung Cancer (NSCLC) is the major cause of cancer related-death. Many patients receive diagnosis at advanced stage leading to a poor prognosis. At present, no satisfactory screening tests are available in clinical practice and the discovery and validation of new biomarkers is mandatory. Surface Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (SELDI-ToF-MS) is a recent high-throughput technique used to detect new tumour markers. In this study we performed SELDI-ToF-MS analysis on serum samples treated with the ProteoMiner™ kit, a combinatorial library of hexapeptide ligands coupled to beads, to reduce the wide dynamic range of protein concentration in the sample. Serum from 44 NSCLC patients and 19 healthy controls were analyzed with IMAC30-Cu and H50 ProteinChip Arrays. Results Comparing SELDI-ToF-MS protein profiles of NSCLC patients and healthy controls, 28 protein peaks were found significantly different (p < 0.05), and were used as predictors to build decision classification trees. This statistical analysis selected 10 protein peaks in the low-mass range (2-24 kDa) and 6 in the high-mass range (40-80 kDa). The classification models for the low-mass range had a sensitivity and specificity of 70.45% (31/44) and 68.42% (13/19) for IMAC30-Cu, and 72.73% (32/44) and 73.68% (14/19) for H50 ProteinChip Arrays. Conclusions These preliminary results suggest that SELDI-ToF-MS protein profiling of serum samples pretreated with ProteoMiner™ can improve the discovery of protein peaks differentially expressed between NSCLC patients and healthy subjects, useful to build classification algorithms with high sensitivity and specificity. However, identification of the significantly different protein peaks needs further study in order to provide a better understanding of the biological nature of these potential biomarkers and their role in the underlying disease process.
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Affiliation(s)
- Emanuela Monari
- Department of Laboratory Medicine, Medical Faculty, University of Modena and Reggio Emilia, Via del Pozzo 71, 41100, Modena, Italy.
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Combined use of a solid-phase hexapeptide ligand library with liquid chromatography and two-dimensional difference gel electrophoresis for intact plasma proteomics. INTERNATIONAL JOURNAL OF PROTEOMICS 2011; 2011:739615. [PMID: 22389768 PMCID: PMC3282153 DOI: 10.1155/2011/739615] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2011] [Accepted: 06/09/2011] [Indexed: 02/06/2023]
Abstract
The intact plasma proteome is of great interest in biomarker studies because intact proteins reflect posttranslational protein processing such as phosphorylation that may correspond to disease status. We examined the utility of a solid-phase hexapeptide ligand library in combination with conventional plasma proteomics modalities for comprehensive profiling of intact plasma proteins. Plasma proteins were sequentially fractionated using depletion columns for albumin and immunoglobulin, and separated using an anion-exchange column. Proteins in each fraction were treated with a solid-phase hexapeptide ligand library and compared to those without treatment. Two-dimensional difference gel electrophoresis demonstrated an increased number of protein spots in the treated samples. Mass spectrometric studies of these protein spots with unique intensity in the treated samples resulted in the identification of high- and medium-abundance proteins. Our results demonstrated the possible utility of a solid-phase hexapeptide ligand library to reveal greater number of intact plasma proteins. The characteristics of proteins with unique affinity to the library remain to be clarified by more extensive mass spectrometric protein identification, and optimized protocols should be established for large-scale plasma biomarker studies.
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29
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Zhi W, Sharma A, Purohit S, Miller E, Bode B, Anderson SW, Reed JC, Steed RD, Steed L, Hopkins D, She JX. Discovery and validation of serum protein changes in type 1 diabetes patients using high throughput two dimensional liquid chromatography-mass spectrometry and immunoassays. Mol Cell Proteomics 2011; 10:M111.012203. [PMID: 21900154 DOI: 10.1074/mcp.m111.012203] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Type 1 diabetes (T1D) is expected to cause significant changes in the serum proteome; however, few studies have systematically assessed the proteomic profile change associated with the disease. In this study, a semiquantitative spectral counting-based two dimensional liquid chromatography mass spectrometry platform was used to analyze serum samples from T1D patients and controls. In this discovery phase, significant differences were found for 21 serum proteins implicated in inflammation, oxidation, metabolic regulation, and autoimmunity. To assess the validity of these findings, six candidate proteins including adiponectin, insulin-like growth factor binding protein 2, serum amyloid protein A, C-reactive protein, myeloperoxidase, and transforming growth factor beta induced were selected for subsequent immune assays for 1139 T1D patients and 848 controls. A series of statistical analyses using cases and controls matched for age, sex, and genetic risk confirmed that T1D patients have significantly higher serum levels for four of the six proteins: adiponectin (odds ratio (OR) = 1.95, p = 10(-27)), insulin-like growth factor binding protein 2 (OR = 2.02, p < 10(-20)), C-reactive protein (OR = 1.13, p = 0.007), serum amyloid protein A (OR = 1.51, p < 10(-16)); whereas the serum levels were significantly lower in patients than controls for the two other proteins: transforming growth factor beta induced (OR = 0.74, p < 10(-5)) and myeloperoxidase (OR = 0.51, p < 10(-41)). Compared with subjects in the bottom quartile, subjects in the top quartile for adiponectin (OR = 6.29, p < 10(-37)), insulin-like growth factor binding protein 2 (OR = 7.95, p < 10(-46)), C-reactive protein (OR = 1.38, p = 0.025), serum amyloid protein A (OR = 3.36, p < 10(-16)) had the highest risk of T1D, whereas subjects in the top quartile of transforming growth factor beta induced (OR = 0.41, p < 10(-11)) and myeloperoxidase (OR = 0.10, p < 10(-43)) had the lowest risk of T1D. These findings provided valuable information on the proteomic changes in the sera of T1D patients.
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Affiliation(s)
- Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Georgia Health Sciences University, Augusta, GA 30912, USA
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30
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Zhu P, Bowden P, Zhang D, Marshall JG. Mass spectrometry of peptides and proteins from human blood. MASS SPECTROMETRY REVIEWS 2011; 30:685-732. [PMID: 24737629 DOI: 10.1002/mas.20291] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 12/09/2009] [Accepted: 01/19/2010] [Indexed: 06/03/2023]
Abstract
It is difficult to convey the accelerating rate and growing importance of mass spectrometry applications to human blood proteins and peptides. Mass spectrometry can rapidly detect and identify the ionizable peptides from the proteins in a simple mixture and reveal many of their post-translational modifications. However, blood is a complex mixture that may contain many proteins first expressed in cells and tissues. The complete analysis of blood proteins is a daunting task that will rely on a wide range of disciplines from physics, chemistry, biochemistry, genetics, electromagnetic instrumentation, mathematics and computation. Therefore the comprehensive discovery and analysis of blood proteins will rank among the great technical challenges and require the cumulative sum of many of mankind's scientific achievements together. A variety of methods have been used to fractionate, analyze and identify proteins from blood, each yielding a small piece of the whole and throwing the great size of the task into sharp relief. The approaches attempted to date clearly indicate that enumerating the proteins and peptides of blood can be accomplished. There is no doubt that the mass spectrometry of blood will be crucial to the discovery and analysis of proteins, enzyme activities, and post-translational processes that underlay the mechanisms of disease. At present both discovery and quantification of proteins from blood are commonly reaching sensitivities of ∼1 ng/mL.
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Affiliation(s)
- Peihong Zhu
- Department of Chemistry and Biology, Ryerson University, 350 Victoria Street, Toronto, Ontario, Canada M5B 2K3
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31
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Bellei E, Monari E, Bergamini S, Ozben T, Tomasi A. Optimizing protein recovery yield from serum samples treated with beads technology. Electrophoresis 2011; 32:1414-21. [DOI: 10.1002/elps.201000699] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 02/04/2011] [Accepted: 02/13/2011] [Indexed: 11/10/2022]
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32
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Faulkner S, Elia G, Hillard M, O'Boyle P, Dunn M, Morris D. Immunodepletion of albumin and immunoglobulin G from bovine plasma. Proteomics 2011; 11:2329-35. [DOI: 10.1002/pmic.201000364] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Revised: 03/04/2011] [Accepted: 03/08/2011] [Indexed: 11/11/2022]
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Tsai IY, Tomczyk N, Eckmann JI, Composto RJ, Eckmann DM. Human plasma protein adsorption onto dextranized surfaces: a two-dimensional electrophoresis and mass spectrometry study. Colloids Surf B Biointerfaces 2011; 84:241-52. [PMID: 21277175 PMCID: PMC3079350 DOI: 10.1016/j.colsurfb.2011.01.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 12/29/2010] [Accepted: 01/06/2011] [Indexed: 11/19/2022]
Abstract
Protein adsorption is fundamental to thrombosis and to the design of biocompatible materials. We report a two-dimensional electrophoresis and mass spectrometry study to characterize multiple human plasma proteins adsorbed onto four different types of model surfaces: silicon oxide, dextranized silicon, polyurethane and dextranized polyurethane. Dextran was grafted onto the surfaces of silicon and polyurethane to mimic the blood-contacting endothelial cell glycocalyx surface. Surface topography and hydrophobicity/hydrophilicity were determined and analyzed using atomic force microscopy and water contact angle measurements, respectively. Using two-dimensional electrophoresis, we show that, relative to the unmodified surfaces, dextranization significantly inhibits the adsorption of several human plasma proteins including IGHG1 protein, fibrinogen, haptoglobin, Apo A-IV, Apo A-I, immunoglobulin, serum retinal-binding protein and truncated serum albumin. We further demonstrate the selectivity of plasma protein adsorbed onto the different functionalized surfaces and the potential to control and manipulate proteins adsorption on the surfaces of medical devices, implants and microfluidic devices. This result shows that adsorption experiments using a single protein or a binary mixture of proteins are consistent with competitive protein adsorption studies. In summary, these studies indicate that coating blood-contacting biomedical applications with dextran is an effective route to reduce thrombo-inflammatory responses and to surface-direct biological activities.
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Affiliation(s)
- Irene Y. Tsai
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nancy Tomczyk
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua I. Eckmann
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Russell J. Composto
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - David M. Eckmann
- Department of Anesthesiology and Critical Care, University of Pennsylvania, Philadelphia, PA 19104, USA
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“Proteomineering” or not? The debate on biomarker discovery in sera continues. J Proteomics 2011; 74:589-94. [DOI: 10.1016/j.jprot.2011.01.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 01/03/2011] [Accepted: 01/21/2011] [Indexed: 11/20/2022]
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35
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Léger T, Lavigne D, Le Caër JP, Guerrier L, Boschetti E, Fareh J, Feldman L, Laprévote O, Meilhac O. Solid-phase hexapeptide ligand libraries open up new perspectives in the discovery of biomarkers in human plasma. Clin Chim Acta 2011; 412:740-7. [DOI: 10.1016/j.cca.2010.12.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Revised: 12/27/2010] [Accepted: 12/27/2010] [Indexed: 10/18/2022]
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36
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Righetti PG, Fasoli E, Boschetti E. Combinatorial peptide ligand libraries: The conquest of the ‘hidden proteome’ advances at great strides. Electrophoresis 2011; 32:960-6. [DOI: 10.1002/elps.201000589] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 11/21/2010] [Accepted: 11/21/2010] [Indexed: 12/27/2022]
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37
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Di Girolamo F, Bala K, Chung MCM, Righetti PG. “Proteomineering” serum biomarkers. A Study in Scarlet. Electrophoresis 2011; 32:976-80. [DOI: 10.1002/elps.201000695] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2010] [Revised: 01/16/2011] [Accepted: 01/16/2011] [Indexed: 11/11/2022]
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38
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Selvaraju S, El Rassi Z. Reduction of protein concentration range difference followed by multicolumn fractionation prior to 2-DE and LC-MS/MS profiling of serum proteins. Electrophoresis 2011; 32:674-85. [PMID: 21365658 DOI: 10.1002/elps.201000606] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 12/20/2010] [Accepted: 12/21/2010] [Indexed: 11/11/2022]
Abstract
This article is concerned with the reduction of protein concentration range differences by the peptide beads library technology (ProteoMiner™ or "equalizer" technology), which in principle allows the enrichment of proteins to the same concentration level (i.e. protein equalizer) regardless of the original protein abundance in a given biological fluid such as human serum, which is the subject of our investigation. After the equalization step, the captured proteins from human serum were fractionated on a series of tandem monolithic columns with surface-bound iminodiacetic acid ligands to which three different metal ions, namely, Zn²+, Ni²+ and Cu²+ were immobilized to yield the so-called immobilized metal affinity chromatography columns. These three monolithic columns were connected to a reversed-phase column packed with polystyrene divinyl benzene beads. Aliquots taken from the four collected fractions from the four tandem columns were subsequently fractionated by 2-DE. Also, aliquots from the four collected fractions were tryptically digested and analyzed by LC-MS/MS. The strategy of subsequent fractionation on the four tandem columns after equalization allowed the identification of more proteins than simply using the equalization by ProteoMiner™ . The equalizer technology was compared to the immuno-subtraction approach. While the ProteoMiner™ technology is superior in terms of the overall number of captured proteins, it only complements the immuno-subtraction approach since the latter can capture the proteins that were not captured by the former.
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Deep insights into the plant proteome by pretreatment with combinatorial hexapeptide ligand libraries. J Proteomics 2011; 74:1182-9. [PMID: 21354349 DOI: 10.1016/j.jprot.2011.02.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/11/2011] [Accepted: 02/16/2011] [Indexed: 01/21/2023]
Abstract
Proteome analyses suffer from the large complexity of even small proteomes. Additionally, in many protein samples a few highly abundant proteins are hindering detailed proteomic studies, since they mask low abundant proteins. Recently, a new technology has emerged, which reduces dynamic range of protein concentrations within a given sample using combinatorial hexapeptide ligand libraries (CPLLs). This technique has been widely used in the microbial, animal and human fields and is now going to enter plant research. It can be a useful tool for fractionation of protein samples and might help to get a deeper insight into specific plant proteomes. In this review we describe the CPLL protein fractionation, summarize its possible applications in the plant field and discuss the limitations of this method.
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40
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Beseme O, Fertin M, Drobecq H, Amouyel P, Pinet F. Combinatorial peptide ligand library plasma treatment: Advantages for accessing low-abundance proteins. Electrophoresis 2010; 31:2697-704. [PMID: 20665525 DOI: 10.1002/elps.201000188] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Depletion of major blood proteins is one of the most promising approaches to accessing low-abundance biomarkers. This study compared the use of combinatorial peptide ligand library (CPLL) and albumin and immunoglobulins (IgGs) depletion technology for accessing these low-abundance proteins in plasma using 2-DE in an acidic restricted pH range (4-7). Compared with native plasma, both techniques enlarge the visibility of other proteins than albumin and IgG, but there were marked differences in their composition. An increase of the number of spots was detected compared with native plasma (157 spots) with 427 and 557 spots, respectively, detected with albumin and IgG depletion, and CPLL treatment. We selected 70 spots to be identified by MALDI-TOF related to their absence in the 2-D gels from native or albumin and IgG-depleted plasma. The 42 spots identified corresponded to 24 different proteins, with more than half of the proteins which did not belong to the major plasma proteins. CPLL treatment allowed the accessibility to proteolytic fragments obtained from major plasma proteins. We found a large superiority of the CPLL approach over the albumin and IgG depletion process. These findings show the utility of depleting major blood proteins to be able to access low-abundance proteins and the potential of CPLL to select and identify candidate biomarkers in clinical studies.
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41
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Olson FJ, Sihlbom C, Davidsson P, Hulthe J, Fagerberg B, Bergström G. Consistent differences in protein distribution along the longitudinal axis in symptomatic carotid atherosclerotic plaques. Biochem Biophys Res Commun 2010; 401:574-80. [DOI: 10.1016/j.bbrc.2010.09.103] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 09/26/2010] [Indexed: 10/19/2022]
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Righetti PG, Boschetti E, Kravchuk AV, Fasoli E. The proteome buccaneers: how to unearth your treasure chest via combinatorial peptide ligand libraries. Expert Rev Proteomics 2010; 7:373-85. [PMID: 20536309 DOI: 10.1586/epr.10.25] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The latest advances in combinatorial peptide ligand libraries, with their unique performance in discovering low-abundance species in proteomes, are reviewed here. Explanations of mechanism, potential applications, capture of proteomes at different pH values to enhance the total catch and quantitative elutions, such as boiling in the presence of 5% sodium dodecyl sulfate and 3% dithiothreitol are included. The reproducibility of protein capture among different experiments with the same batch of beads or with different batches is also reported to be very high, with coefficient of variations in the order of 10-20%. Miniaturized operations, consisting of capture with as little as 20 or even 5 microl of peptide beads are reported, thus demonstrating that the described technology could be exploited for routine biomarker discovery in a biomedical environment. Finally, it is shown that the signal of captured proteins is linear over approximately three orders of magnitude, ranging from nM to microM, thus ensuring that differential quantitative proteomics for biomarker discovery can be fully implemented, providing species do not saturate their ligands.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering Giulio Natta, Via Mancinelli 7, Politecnico di Milano, Milano, Italy.
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Proteomics of wine additives: Mining for the invisible via combinatorial peptide ligand libraries. J Proteomics 2010; 73:1732-9. [DOI: 10.1016/j.jprot.2010.05.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Revised: 05/05/2010] [Accepted: 05/18/2010] [Indexed: 10/19/2022]
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Abstract
In this review, we discuss several important issues concerning the discovery of protein biomarkers for complex human diseases, with a focus on type 1 diabetes. Serum or plasma is the first choice of specimen due to its richness in biological information and relatively easy availability. It is a challenging task to comprehensively characterize the serum/plasma proteome because of the large dynamic range of protein concentration. Therefore, sample pretreatment is required in order to explore the low- to medium-abundance proteins contained in serum/plasma. In this regard, enrichment of low-abundance proteins using random hexapeptide library beads has distinct advantages over the traditional immune-depletion methods, including higher efficiency, higher binding capacity, and lower cost. In-depth mining of serum/plasma proteome using different separation techniques have also been evaluated and are discussed in this review. Overall, the shotgun proteomics-multidimensional separation of digested peptides followed by mass spectrometry analysis--is highly efficient and therefore has become a preferred method for protein biomarker discovery.
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Affiliation(s)
- Wenbo Zhi
- Center for Biotechnology and Genomic Medicine, Medical College of Georgia, Augusta, Georgia 30912, USA
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A proteomic approach for plasma biomarker discovery with 8-plex iTRAQ labeling and SCX-LC-MS/MS. Mol Cell Biochem 2010; 343:91-9. [PMID: 20526653 DOI: 10.1007/s11010-010-0502-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 05/12/2010] [Indexed: 10/19/2022]
Abstract
Plasma is recognized as a promising source of disease-related biomarkers, and proteomic approaches for identifying novel plasma biomarkers are in great demand. However, the complexity and dynamic protein concentration range of plasma remain the main obstacles for current research in this field. In this study, plasma proteins were prefractioned by immunodepletion and Protein Equalizer Technology to remove high abundant proteins, then labeled with an 8-plex isobaric tags for relative and absolute quantitation (iTRAQ) to improve the peptide ionization, and analyzed by strong-cation-exchange(SCX) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our results showed that both prefraction methods were complementary, with regard to the number of identified proteins. Good chromatographic technique is important to further fractionate the iTRAQ labeling peptides, which allowed 320 and 248 different proteins to be characterized from two prefraction methods, respectively, encompassing a wide array of biological functions and a broad dynamic range of 10(7). Furthermore, the accuracy of iTRAQ relative quantitation for differentially expressed proteins is associated with the number of peptides hits per protein.
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Ben Ameur R, Molina L, Bolvin C, Kifagi C, Jarraya F, Ayadi H, Molina F, Granier C. Proteomic approaches for discovering biomarkers of diabetic nephropathy. Nephrol Dial Transplant 2010; 25:2866-75. [PMID: 20472580 DOI: 10.1093/ndt/gfq258] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Keidel EM, Ribitsch D, Lottspeich F. Equalizer technology - Equal rights for disparate beads. Proteomics 2010; 10:2089-98. [DOI: 10.1002/pmic.200900767] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fertin M, Beseme O, Duban S, Amouyel P, Bauters C, Pinet F. Deep plasma proteomic analysis of patients with left ventricular remodeling after a first myocardial infarction. Proteomics Clin Appl 2010; 4:654-73. [PMID: 21137084 DOI: 10.1002/prca.200900178] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 02/10/2010] [Accepted: 02/27/2010] [Indexed: 11/10/2022]
Abstract
PURPOSE Depletion of major blood proteins is one of the most promising approaches to accessing low abundance biomarkers for proteomics studies. The use of combinatorial peptide ligand library (CPLL) for accessing these low abundance proteins in plasma from patients with a myocardial infarction (MI) was tested to identify candidate protein biomarkers of left ventricular remodeling (LVR). EXPERIMENTAL DESIGN Serial blood samples of MI patients followed for one year (at inclusion, 1 month, 3 months, and 1 year) were treated with CPLL and analyzed by SELDI-TOF-MS. RESULT The use of CPLL increased resolution, with loss of most abundant plasma proteins, reproducibly and improved the intensity of low-abundance proteins. Longitudinal information allowed us to reduce by 55% the final number of peaks identified as significantly modulated throughout the 1-year follow-up after MI. Interestingly, 19 of the 26 peaks finally selected were detected only in samples treated from CPLL. The 2777 m/z peak, found in less elevated level in high remodeling patients, was identified as being DAHKSEVAHR FKDLGEENFKALVL, the N-terminal peptide (24-48 aa) generated from albumin by pepsin cleavage. CONCLUSIONS AND CLINICAL RELEVANCE This finding shows the potential of CPLL in accessing low-abundance proteins to select and identify candidate biomarkers in patients with LVR.
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Application of "omics" to prion biomarker discovery. J Biomed Biotechnol 2010; 2010:613504. [PMID: 20224650 PMCID: PMC2833310 DOI: 10.1155/2010/613504] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 12/03/2009] [Accepted: 12/30/2009] [Indexed: 02/01/2023] Open
Abstract
The advent of genomics and proteomics has been a catalyst for the discovery of biomarkers able to discriminate biological processes such as the pathogenesis of complex diseases. Prompt detection of prion diseases is particularly desirable given their transmissibility, which is responsible for a number of human health risks stemming from exogenous sources of prion protein. Diagnosis relies on the ability to detect the biomarker PrPSc, a pathological isoform of the host protein PrPC, which is an essential component of the infectious prion. Immunochemical detection of PrPSc is specific and sensitive enough for antemortem testing of brain tissue, however, this is not the case in accessible biological fluids or for the detection of recently identified novel prions with unique biochemical properties. A complementary approach to the detection of PrPSc itself is to identify alternative, “surrogate” gene or protein biomarkers indicative of disease. Biomarkers are also useful to track the progress of disease, especially important in the assessment of therapies, or to identify individuals “at risk”. In this review we provide perspective on current progress and pitfalls in the use of “omics” technologies to screen body fluids and tissues for biomarker discovery in prion diseases.
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Challenges for biomarker discovery in body fluids using SELDI-TOF-MS. J Biomed Biotechnol 2009; 2010:906082. [PMID: 20029632 PMCID: PMC2793423 DOI: 10.1155/2010/906082] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2009] [Accepted: 09/01/2009] [Indexed: 01/17/2023] Open
Abstract
Protein profiling using SELDI-TOF-MS has gained over the past few years an increasing interest in the field of biomarker discovery. The technology presents great potential if some parameters, such as sample handling, SELDI settings, and data analysis, are strictly controlled. Practical considerations to set up a robust and sensitive strategy for biomarker discovery are presented. This paper also reviews biological fluids generally available including a description of their peculiar properties and the preanalytical challenges inherent to sample collection and storage. Finally, some new insights for biomarker identification and validation challenges are provided.
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