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Wang YD, Wang X, Ngai SM, Wong YS. Comparative Proteomics Analysis of Selenium Responses in Selenium-Enriched Rice Grains. J Proteome Res 2013; 12:808-20. [DOI: 10.1021/pr300878y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Yu-Dong Wang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Xu Wang
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Sai-ming Ngai
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Yum-shing Wong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
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Rodríguez-Suárez E, Whetton AD. The application of quantification techniques in proteomics for biomedical research. MASS SPECTROMETRY REVIEWS 2013; 32:1-26. [PMID: 22847841 DOI: 10.1002/mas.21347] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Revised: 02/09/2012] [Accepted: 02/10/2012] [Indexed: 06/01/2023]
Abstract
The systematic analysis of biological processes requires an understanding of the quantitative expression patterns of proteins, their interacting partners and their subcellular localization. This information was formerly difficult to accrue as the relative quantification of proteins relied on antibody-based methods and other approaches with low throughput. The advent of soft ionization techniques in mass spectrometry plus advances in separation technologies has aligned protein systems biology with messenger RNA, DNA, and microarray technologies to provide data on systems as opposed to singular protein entities. Another aspect of quantitative proteomics that increases its importance for the coming few years is the significant technical developments underway both for high pressure liquid chromatography and mass spectrum devices. Hence, robustness, reproducibility and mass accuracy are still improving with every new generation of instruments. Nonetheless, the methods employed require validation and comparison to design fit for purpose experiments in advanced protein analyses. This review considers the newly developed systematic protein investigation methods and their value from the standpoint that relative or absolute protein quantification is required de rigueur in biomedical research.
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53
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Brioschi M, Lento S, Tremoli E, Banfi C. Proteomic analysis of endothelial cell secretome: A means of studying the pleiotropic effects of Hmg-CoA reductase inhibitors. J Proteomics 2013; 78:346-61. [DOI: 10.1016/j.jprot.2012.10.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Revised: 09/07/2012] [Accepted: 10/06/2012] [Indexed: 01/03/2023]
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54
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Jaros JA, Martins-de-Souza D, Rahmoune H, Rothermundt M, Leweke FM, Guest PC, Bahn S. Protein phosphorylation patterns in serum from schizophrenia patients and healthy controls. J Proteomics 2012; 76 Spec No.:43-55. [DOI: 10.1016/j.jprot.2012.05.027] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/11/2012] [Accepted: 05/16/2012] [Indexed: 01/10/2023]
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55
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Thalassinos K, Vissers JPC, Tenzer S, Levin Y, Thompson JW, Daniel D, Mann D, DeLong MR, Moseley MA, America AH, Ottens AK, Cavey GS, Efstathiou G, Scrivens JH, Langridge JI, Geromanos SJ. Design and application of a data-independent precursor and product ion repository. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1808-1820. [PMID: 22847389 DOI: 10.1007/s13361-012-0416-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Revised: 05/09/2012] [Accepted: 05/13/2012] [Indexed: 06/01/2023]
Abstract
The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results of a broad range of discovery experiments investigating various tissue types of two closely related mammalian species. The relative high degree of similarity in protein complement, ion detection, and peptide and protein identification allows for the analysis of normalized precursor and product ion intensity values, as well as standardized retention times, creating a multidimensional/orthogonal queryable, qualitative, and quantitative space. Peptide ion map selection for identification and quantification is primarily based on replication and limited variation. The information is stored in a relational database and is used to create peptide- and protein-specific fragment ion maps that can be queried in a targeted fashion against the raw or time aligned ion detections. These queries can be conducted either individually or as groups, where the latter affords pathway and molecular machinery analysis of the protein complement. The presented results also suggest that peptide ionization and fragmentation efficiencies are highly conserved between experiments and practically independent of the analyzed biological sample when using similar instrumentation. Moreover, the data illustrate only minor variation in ionization efficiency with amino acid sequence substitutions occurring between species. Finally, the data and the presented results illustrate how LC-MS performance metrics can be extracted and utilized to ensure optimal performance of the employed analytical workflows.
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56
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Chen S, Lu FF, Seeman P, Liu F. Quantitative proteomic analysis of human substantia nigra in Alzheimer's disease, Huntington's disease and Multiple sclerosis. Neurochem Res 2012; 37:2805-13. [PMID: 22926577 DOI: 10.1007/s11064-012-0874-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 07/20/2012] [Accepted: 08/14/2012] [Indexed: 02/07/2023]
Abstract
The substantia nigra plays important roles in the brain function and is critical in the development of many diseases, particularly Parkinson's disease. Pathological changes of the substantia nigra have also been reported in other neurodegenerative diseases. Using a quantitative proteomic approach, we investigated protein expressions in the substantia nigra of Alzheimer's disease, Huntington's disease, and Multiple sclerosis. The expression level of one hundred and four proteins that were identified in at least three samples of each group were compared with the control group, with nineteen, twenty-two and thirteen proteins differentially expressed in Alzheimer's diseases, Huntington's disease and Multiple sclerosis respectively. The result indicates that the substantia nigra also undergoes functional adaption or damage in these diseases.
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Affiliation(s)
- Sheng Chen
- Department of Molecular Neuroscience, Centre for Addiction and Mental Health, 250 College Street, Toronto, ON M5T 1R8, Canada
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57
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Patel NA, Crombie A, Slade SE, Thalassinos K, Hughes C, Connolly JB, Langridge J, Murrell JC, Scrivens JH. Comparison of One- and Two-dimensional Liquid Chromatography Approaches in the Label-free Quantitative Analysis of Methylocella silvestris. J Proteome Res 2012; 11:4755-63. [DOI: 10.1021/pr300253s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Nisha A. Patel
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew Crombie
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Susan E. Slade
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | | | - Chris Hughes
- Waters Corporation, Atlas Park, Simonsway, Manchester, M22 5PP, United Kingdom
| | - Joanne B. Connolly
- Waters Corporation, Atlas Park, Simonsway, Manchester, M22 5PP, United Kingdom
| | - James Langridge
- Waters Corporation, Atlas Park, Simonsway, Manchester, M22 5PP, United Kingdom
| | - J. Colin Murrell
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - James H. Scrivens
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
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58
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Wegdam W, Moerland PD, Meijer D, de Jong SM, Hoefsloot HCJ, Kenter GG, Buist MR, Aerts JMG. A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass. Proteome Sci 2012; 10:45. [PMID: 22824475 PMCID: PMC3494530 DOI: 10.1186/1477-5956-10-45] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Accepted: 06/29/2012] [Indexed: 01/13/2023] Open
Abstract
Background Less than 25% of patients with a pelvic mass who are presented to a gynecologist will eventually be diagnosed with epithelial ovarian cancer. Since there is no reliable test to differentiate between different ovarian tumors, accurate classification could facilitate adequate referral to a gynecological oncologist, improving survival. The goal of our study was to assess the potential value of a SELDI-TOF-MS based classifier for discriminating between patients with a pelvic mass. Methods Our study design included a well-defined patient population, stringent protocols and an independent validation cohort. We compared serum samples of 53 ovarian cancer patients, 18 patients with tumors of low malignant potential, and 57 patients with a benign ovarian tumor on different ProteinChip arrays. In addition, from a subset of 84 patients, tumor tissues were collected and microdissection was used to isolate a pure and homogenous cell population. Results Diagonal Linear Discriminant Analysis (DLDA) and Support Vector Machine (SVM) classification on serum samples comparing cancer versus benign tumors, yielded models with a classification accuracy of 71-81% (cross-validation), and 73-81% on the independent validation set. Cancer and benign tissues could be classified with 95-99% accuracy using cross-validation. Tumors of low malignant potential showed protein expression patterns different from both benign and cancer tissues. Remarkably, none of the peaks differentially expressed in serum samples were found to be differentially expressed in the tissue lysates of those same groups. Conclusion Although SELDI-TOF-MS can produce reliable classification results in serum samples of ovarian cancer patients, it will not be applicable in routine patient care. On the other hand, protein profiling of microdissected tumor tissue may lead to a better understanding of oncogenesis and could still be a source of new serum biomarkers leading to novel methods for differentiating between different histological subtypes.
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Affiliation(s)
- Wouter Wegdam
- Department of Gynecology, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105, AZ, Amsterdam, the Netherlands.
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59
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Haçarız O, Sayers G, Baykal AT. A Proteomic Approach To Investigate the Distribution and Abundance of Surface and Internal Fasciola hepatica Proteins during the Chronic Stage of Natural Liver Fluke Infection in Cattle. J Proteome Res 2012; 11:3592-604. [DOI: 10.1021/pr300015p] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Orçun Haçarız
- TÜBİTAK
Marmara
Research Center, Genetic Engineering and Biotechnology Institute, P.O. Box 21, 41470, Gebze, Kocaeli, Turkey
| | - Gearóid Sayers
- Veterinary Sciences Centre,
School of Agriculture, Food Science and Veterinary Medicine, College
of Life Sciences, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ahmet Tarık Baykal
- TÜBİTAK
Marmara
Research Center, Genetic Engineering and Biotechnology Institute, P.O. Box 21, 41470, Gebze, Kocaeli, Turkey
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60
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Creskey MC, Li C, Wang J, Girard M, Lorbetskie B, Gravel C, Farnsworth A, Li X, Smith DGS, Cyr TD. Simultaneous quantification of the viral antigens hemagglutinin and neuraminidase in influenza vaccines by LC-MSE. Vaccine 2012; 30:4762-70. [PMID: 22643214 DOI: 10.1016/j.vaccine.2012.05.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 05/14/2012] [Accepted: 05/16/2012] [Indexed: 11/17/2022]
Abstract
Current methods for quality control of inactivated influenza vaccines prior to regulatory approval include determining the hemagglutinin (HA) content by single radial immunodiffusion (SRID), verifying neuraminidase (NA) enzymatic activity, and demonstrating that the levels of the contaminant protein ovalbumin are below a set threshold of 1 μg/dose. The SRID assays require the availability of strain-specific reference HA antigens and antibodies, the production of which is a potential rate-limiting step in vaccine development and release, particularly during a pandemic. Immune responses induced by neuraminidase also contribute to protection from infection; however, the amounts of NA antigen in influenza vaccines are currently not quantified or standardized. Here, we report a method for vaccine analysis that yields simultaneous quantification of HA and NA levels much more rapidly than conventional HA quantification techniques, while providing additional valuable information on the total protein content. Enzymatically digested vaccine proteins were analyzed by LC-MS(E), a mass spectrometric technology that allows absolute quantification of analytes, including the HA and NA antigens, other structural influenza proteins and chicken egg proteins associated with the manufacturing process. This method has potential application for increasing the accuracy of reference antigen standards and for validating label claims for HA content in formulated vaccines. It can also be used to monitor NA and chicken egg protein content in order to monitor manufacturing consistency. While this is a useful methodology with potential for broad application, we also discuss herein some of the inherent limitations of this approach and the care and caution that must be taken in its use as a tool for absolute protein quantification. The variations in HA, NA and chicken egg protein concentrations in the vaccines analyzed in this study are indicative of the challenges associated with the current manufacturing and quality control testing procedures.
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Affiliation(s)
- Marybeth C Creskey
- Centre for Vaccine Evaluation, Health Canada, 251 Sir Frederick Banting Driveway, Locator 2201E, Tunney's Pasture, Ottawa, ON K1A 0L2, Canada
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61
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Marzano V, Santini S, Rossi C, Zucchelli M, D'Alessandro A, Marchetti C, Mingardi M, Stagni V, Barilà D, Urbani A. Proteomic profiling of ATM kinase proficient and deficient cell lines upon blockage of proteasome activity. J Proteomics 2012; 75:4632-46. [PMID: 22641158 PMCID: PMC3426930 DOI: 10.1016/j.jprot.2012.05.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Revised: 04/27/2012] [Accepted: 05/16/2012] [Indexed: 11/24/2022]
Abstract
Ataxia Telangiectasia Mutated (ATM) protein kinase is a key effector in the modulation of the functionality of some important stress responses, including DNA damage and oxidative stress response, and its deficiency is the hallmark of Ataxia Telangiectasia (A-T), a rare genetic disorder. ATM modulates the activity of hundreds of target proteins, essential for the correct balance between proliferation and cell death. The aim of this study is to evaluate the phenotypic adaptation at the protein level both in basal condition and in presence of proteasome blockage in order to identify the molecules whose level and stability are modulated through ATM expression. We pursued a comparative analysis of ATM deficient and proficient lymphoblastoid cells by label-free shotgun proteomic experiments comparing the panel of proteins differentially expressed. Through a non-supervised comparative bioinformatic analysis these data provided an insight on the functional role of ATM deficiency in cellular carbohydrate metabolism's regulation. This hypothesis has been demonstrated by targeted metabolic fingerprint analysis SRM (Selected Reaction Monitoring) on specific thermodynamic checkpoints of glycolysis. This article is part of a Special Issue entitled: Translational Proteomics.
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Affiliation(s)
- Valeria Marzano
- Proteomic and Metabonomic Laboratory, Fondazione Santa Lucia, 00143 Rome, Italy
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62
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D'Aguanno S, D'Agnano I, De Canio M, Rossi C, Bernardini S, Federici G, Urbani A. Shotgun proteomics and network analysis of neuroblastoma cell lines treated with curcumin. MOLECULAR BIOSYSTEMS 2012; 8:1068-77. [DOI: 10.1039/c2mb05498a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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63
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Sau A, Filomeni G, Pezzola S, D'Aguanno S, Tregno FP, Urbani A, Serra M, Pasello M, Picci P, Federici G, Caccuri AM. Targeting GSTP1-1 induces JNK activation and leads to apoptosis in cisplatin-sensitive and -resistant human osteosarcoma cell lines. ACTA ACUST UNITED AC 2012; 8:994-1006. [DOI: 10.1039/c1mb05295k] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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64
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Pieragostino D, Bucci S, Agnifili L, Fasanella V, D'Aguanno S, Mastropasqua A, Ciancaglini M, Mastropasqua L, Ilio CD, Sacchetta P, Urbani A, Boccio PD. Differential protein expression in tears of patients with primary open angle and pseudoexfoliative glaucoma. ACTA ACUST UNITED AC 2012; 8:1017-28. [DOI: 10.1039/c1mb05357d] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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65
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D'Alessandro A, D'Aguanno S, Cencioni MT, Pieroni L, Diamantini A, Battistini L, Longone P, Spalloni A, De Laurenzi V, Bernardini S, Federici G, Urbani A. Protein repertoire impact of Ubiquitin-Proteasome System impairment: insight into the protective role of beta-estradiol. J Proteomics 2011; 75:1440-53. [PMID: 22146475 DOI: 10.1016/j.jprot.2011.11.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 10/18/2011] [Accepted: 11/14/2011] [Indexed: 01/01/2023]
Abstract
The Ubiquitin-Proteasome System (UPS) and the Autophagy-Lysosome Pathways (ALP) are key mechanisms for cellular homeostasis sustenance and protein clearance. A wide number of Neurodegenerative Diseases (NDs) are tied with UPS impairment and have been also described as proteinopathies caused by aggregate-prone proteins, not efficiently removed by proteasome. Despite the large knowledge on proteasome biological role, molecular mechanisms associated with its impairment are still blur. We have pursued a comprehensive proteomic investigation to evaluate the phenotypic rearrangements in protein repertoires associated with a UPS blockage. Different functional proteomic approaches have been employed to tackle UPS impairment impact on human NeuroBlastoma (NB) cell lines responsive to proteasome inhibition by Epoxomicin. 2-Dimensional Electrophoresis (2-DE) separation combined with Mass Spectrometry and Shotgun Proteomics experiments have been employed to design a thorough picture of protein profile. Unsupervised meta-analysis of the collected proteomic data revealed that all the identified proteins relate each other in a functional network centered on beta-estradiol. Moreover we showed that treatment of cells with beta-estradiol resulted in aggregate removal and increased cell survival due to activation of the autophagic pathway. Our data may provide the molecular basis for the use of beta-estradiol in neurodegenerative disorders by induction of protein aggregate removal.
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Affiliation(s)
- Annamaria D'Alessandro
- Department of Internal Medicine, University of Rome Tor Vergata, Faculty of Medicine and Surgery, Via Montpellier, 1, 00133-Rome, Italy
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66
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Evidence for disease and antipsychotic medication effects in post-mortem brain from schizophrenia patients. Mol Psychiatry 2011; 16:1189-202. [PMID: 20921955 DOI: 10.1038/mp.2010.100] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Extensive research has been conducted on post-mortem brain tissue in schizophrenia (SCZ), particularly the dorsolateral prefrontal cortex (DLPFC). However, to what extent the reported changes are due to the disorder itself, and which are the cumulative effects of lifetime medication remains to be determined. In this study, we employed label-free liquid chromatography-mass spectrometry-based proteomic and proton nuclear magnetic resonance-based metabonomic profiling approaches to investigate DLPFC tissue from two cohorts of SCZ patients grouped according to their lifetime antipsychotic dose, together with tissue from bipolar disorder (BPD) subjects, and normal controls (n=10 per group). Both techniques showed profound changes in tissue from low-cumulative-medication SCZ subjects, but few changes in tissue from medium-cumulative-medication subjects. Protein expression changes were validated by Western blot and investigated further in a third group of subjects who were subjected to high-cumulative-medication over the course of their lifetime. Furthermore, key protein expression and metabolite level changes correlated significantly with lifetime antipsychotic dose. This suggests that the detected changes are present before antipsychotic therapy and, moreover, may be normalized with treatment. Overall, our analyses revealed novel protein and metabolite changes in low-cumulative-medication subjects associated with synaptogenesis, neuritic dynamics, presynaptic vesicle cycling, amino acid and glutamine metabolism, and energy buffering systems. Most of these markers were altered specifically in SCZ as determined by analysis of the same brain region from BPD patients.
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67
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Meng Y, Liu F, Pang C, Fan S, Song M, Wang D, Li W, Yu S. Label-Free Quantitative Proteomics Analysis of Cotton Leaf Response to Nitric Oxide. J Proteome Res 2011; 10:5416-32. [DOI: 10.1021/pr200671d] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yanyan Meng
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China
| | - Feng Liu
- National Center of Biomedical Analysis, Beijing, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China
| | - Dan Wang
- College of Agronomy, Northwest Sci-Tech University of Agriculture and Forest, Yangling, P. R. China
| | - Weihua Li
- National Center of Biomedical Analysis, Beijing, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang 455000, Henan Province, China
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68
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Calabrese C, Marzano V, Urbani A, Lazzarini G, Valerii MC, Liguori G, Di Molfetta S, Rizzello F, Gionchetti P, Campieri M, Spisni E. Distinct proteomic profiles characterise non-erosive from erosive reflux disease. Aliment Pharmacol Ther 2011; 34:982-93. [PMID: 21848794 DOI: 10.1111/j.1365-2036.2011.04801.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Erosive reflux disease (ERD) and non-erosive reflux disease (NERD) are often regarded as part of the spectrum of the same disease. AIM To elucidate molecular features that characterise NERD and ERD at the protein level. METHODS A total of 56 consecutive subjects were enrolled: 10 healthy subjects, 24 with NERD and 22 with ERD. Eight specimens were taken from macroscopically normal mucosa at 5 cm of gastro-oesophageal junction. Four were processed for the proteins extraction and four for evaluation using haematoxylin-eosin and immunohistochemistry. We used shotgun proteomics to identify tentative disease molecular features for ERD or NERD. Candidate distinctive proteins were verified using immunohistochemistry. RESULTS Shotgun proteomics analysis revealed 33 differentially expressed proteins in NERD vs. ERD samples, involved in cellular proliferation, keratinisation, stress responses and sugar metabolism. Based on a gene ontology meta-analysis, seven of them were further analysed using Western blotting (WB) and four also using immunohistochemistry. We identified novel candidate disease molecular features for GERD and few distinctive proteins to discriminate NERD and ERD. In particular, Transitional Endoplasmic Reticulum ATPase (TER ATPase), GAPDH, Alpha 1 Acid Glycoprotein 1, Annexin A1, Calmodulin and 14-3-3 proteins were confirmed at WB analysis. CONCLUSIONS Non-erosive reflux disease and ERD are distinct disease entities at the protein level. This study proposes an array of candidate biomarkers possibly useful to discriminate between NERD and ERD.
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Affiliation(s)
- C Calabrese
- Department of Clinical Medicine, University of Bologna, Bologna, Italy.
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69
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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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70
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Levin Y, Hradetzky E, Bahn S. Quantification of proteins using data-independent analysis (MSE) in simple andcomplex samples: a systematic evaluation. Proteomics 2011; 11:3273-87. [PMID: 21751355 DOI: 10.1002/pmic.201000661] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2010] [Revised: 03/23/2011] [Accepted: 05/03/2011] [Indexed: 01/25/2023]
Abstract
A MS-based method for the quantification of proteins termed data-independent analysis (or MS(E)) has been introduced recently. Although this method has been applied to the analysis of various types of biological samples, a thorough evaluation to assess the performance of this approach has yet to be conducted. Presented here is the first systematic and comprehensive study investigating the MS(E) approach for quantitative analysis of low-, medium-, and high-complexity samples. We demonstrate that this method has a linear dynamic range spanning three orders of magnitude with a limit of quantification of 61 amol/uL in low-complexity samples and 488 amol/uL in high-complexity samples. In addition, comprehensive sequence coverage was obtained and accurate quantification achieved for expression ratios ranging from 1:1.5 to 1:6. However, underestimation of ratios was detected independent of sample type, consistent with other quantitative proteomic methods. The present study provides validation of the MS(E) approach for accurate quantitative proteomic analysis of biological samples while, at the same time, proving high sequence coverage of target proteins.
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Affiliation(s)
- Yishai Levin
- Biological Services, Weizmann Institute of Science, Rehovot, Israel.
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71
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Sedic M, Kraljevic Pavelic S, Cindric M, Vissers JPC, Peronja M, Josic D, Cuk M, Fumic K, Pavelic K, Baric I. Plasma biomarker identification in S-adenosylhomocysteine hydrolase deficiency. Electrophoresis 2011; 32:1970-5. [PMID: 21732553 DOI: 10.1002/elps.201000556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Revised: 02/07/2011] [Accepted: 02/07/2011] [Indexed: 11/09/2022]
Abstract
S-Adenosylhomocysteine hydrolase (AHCY) deficiency is a rare congenital disorder in methionine metabolism clinically characterized by white matter atrophy, delayed myelination, slowly progressive myopathy, retarded psychomotor development and mildly active chronic hepatitis. In the present study, we utilized a comparative proteomics strategy based on 2-DE/MALDI-MS and LC/ESI-MS to analyze plasma proteins from three AHCY-deficient patients prior to and after receiving dietary treatment designed to alleviate disease symptoms. Obtained results revealed candidate biomarkers for the detection of myopathy specifically associated with AHCY deficiency, such as carbonic anhydrase 3, creatine kinase, and thrombospondin 4. Several proteins mediating T-cell activation and function were identified as well, including attractin and diacylglycerol kinase α. Further validation and functional analysis of identified proteins with clinical value would ensure that these biomarkers make their way into routine diagnosis and management of AHCY deficiency.
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Affiliation(s)
- Mirela Sedic
- Department of Biotechnology, University of Rijeka, Rijeka, Croatia
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72
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Kota U, Goshe MB. Advances in qualitative and quantitative plant membrane proteomics. PHYTOCHEMISTRY 2011; 72:1040-60. [PMID: 21367437 DOI: 10.1016/j.phytochem.2011.01.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/13/2011] [Accepted: 01/19/2011] [Indexed: 05/08/2023]
Abstract
The membrane proteome consists of integral and membrane-associated proteins that are involved in various physiological and biochemical functions critical for cellular function. It is also dynamic in nature, where many proteins are only expressed during certain developmental stages or in response to environmental stress. These proteins can undergo post-translational modifications in response to these different conditions, allowing them to transiently associate with the membrane or other membrane proteins. Along with their increased size, hydrophobicity, and the additional organelle and cellular features of plant cells relative to mammalian systems, the characterization of the plant membrane proteome presents unique challenges for effective qualitative and quantitative analysis using mass spectrometry (MS) analysis. Here, we present the latest advancements developed for the isolation and fractionation of plant organelles and their membrane components amenable to MS analysis. Separations of membrane proteins from these enriched preparations that have proven effective are discussed for both gel- and liquid chromatography-based MS analysis. In this context, quantitative membrane proteomic analyses using both isotope-coded and label-free approaches are presented and reveal the potential to establish a wider-biological interpretation of the function of plant membrane proteins that will ultimately lead to a more comprehensive understanding of plant physiology and their response mechanisms.
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Affiliation(s)
- Uma Kota
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695-7622, USA
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73
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Aerts JMFG, Kallemeijn WW, Wegdam W, Joao Ferraz M, van Breemen MJ, Dekker N, Kramer G, Poorthuis BJ, Groener JEM, Cox-Brinkman J, Rombach SM, Hollak CEM, Linthorst GE, Witte MD, Gold H, van der Marel GA, Overkleeft HS, Boot RG. Biomarkers in the diagnosis of lysosomal storage disorders: proteins, lipids, and inhibodies. J Inherit Metab Dis 2011; 34:605-19. [PMID: 21445610 PMCID: PMC3109260 DOI: 10.1007/s10545-011-9308-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 01/21/2011] [Accepted: 02/17/2011] [Indexed: 12/23/2022]
Abstract
A biomarker is an analyte indicating the presence of a biological process linked to the clinical manifestations and outcome of a particular disease. In the case of lysosomal storage disorders (LSDs), primary and secondary accumulating metabolites or proteins specifically secreted by storage cells are good candidates for biomarkers. Clinical applications of biomarkers are found in improved diagnosis, monitoring disease progression, and assessing therapeutic correction. These are illustrated by reviewing the discovery and use of biomarkers for Gaucher disease and Fabry disease. In addition, recently developed chemical tools allowing specific visualization of enzymatically active lysosomal glucocerebrosidase are described. Such probes, coined inhibodies, offer entirely new possibilities for more sophisticated molecular diagnosis, enzyme replacement therapy monitoring, and fundamental research.
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Affiliation(s)
- Johannes M F G Aerts
- Sphinx-Amsterdam Lysosome Center, Departments of Medical Biochemistry and Internal Medicine, Academic Medical Centre, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands.
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74
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Moon PG, Lee JE, You S, Kim TK, Cho JH, Kim IS, Kwon TH, Kim CD, Park SH, Hwang D, Kim YL, Baek MC. Proteomic analysis of urinary exosomes from patients of early IgA nephropathy and thin basement membrane nephropathy. Proteomics 2011; 11:2459-75. [PMID: 21595033 DOI: 10.1002/pmic.201000443] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 03/01/2011] [Accepted: 03/08/2011] [Indexed: 12/12/2022]
Abstract
To identify biomarker candidates associated with early IgA nephropathy (IgAN) and thin basement membrane nephropathy (TBMN), the most common causes presenting isolated hematuria in childhood, a proteomic approach of urinary exosomes from early IgAN and TBMN patients was introduced. The proteomic results from the patients were compared with a normal group to understand the pathophysiological processes associated with these diseases at the protein level. The urinary exosomes, which reflect pathophysiological processes, collected from three groups of young adults (early IgAN, TBMN, and normal) were trypsin-digested using a gel-assisted protocol, and quantified by label-free LC-MS/MS, using an MS(E) mode. A total of 1877 urinary exosome proteins, including cytoplasmic, membrane, and vesicle trafficking proteins, were identified. Among the differentially expressed proteins, four proteins (aminopeptidase N, vasorin precursor, α-1-antitrypsin, and ceruloplasmin) were selected as biomarker candidates to differentiate early IgAN from TBMN. We confirmed the protein levels of the four biomarker candidates by semi-quantitative immunoblot analysis in urinary exosomes independently prepared from other patients, including older adult groups. Further clinical studies are needed to investigate the diagnostic and prognostic value of these urinary markers for early IgAN and TBMN. Taken together, this study showed the possibility of identifying biomarker candidates for human urinary diseases using urinary exosomes and might help to understand the pathophysiology of early IgAN and TBMN at the protein level.
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Affiliation(s)
- Pyong-Gon Moon
- Department of Molecular Medicine, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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75
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Colucci-D'Amato L, Farina A, Vissers JPC, Chambery A. Quantitative neuroproteomics: classical and novel tools for studying neural differentiation and function. Stem Cell Rev Rep 2011; 7:77-93. [PMID: 20352529 DOI: 10.1007/s12015-010-9136-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mechanisms underlying neural stem cell proliferation, differentiation and maturation play a critical role in the formation and wiring of neuronal connections. This process involves the activation of multiple serial events, which guide the undifferentiated cells to different lineages via distinctive developmental programs, forming neuronal circuits and thus shaping the adult nervous system. Furthermore, alterations within these strictly regulated pathways can lead to severe neurological and psychiatric diseases. In this framework, the investigation of the high dynamic protein expression changes and other factors affecting protein functions, for example post-translational modifications, the alterations of protein interaction networks, is of pivotal importance for the understanding of the molecular mechanisms responsible for cell differentiation. More recently, proteomic studies in neuroscience ("neuroproteomics") are receiving increased interest for the primary understanding of the regulatory networks underlying neuronal differentiation processes. Besides the classical two-dimensional-based proteomic strategies, the emerging platforms for LC-MS shotgun proteomic analysis hold great promise in unraveling the molecular basis of neural stem cell differentiation. In this review, recent advancements in label-free LC-MS quantitative neuroproteomics are highlighted as a new tool for the study of neural differentiation and functions, in comparison to mass spectrometry-based labeling approaches. The more commonly used protein profiling strategies and model systems for the analysis of neural differentiation are also discussed, along with the challenging proteomic approaches aimed to analyze the nervous system-specific organelles, the neural cells secretome and the specific protein interaction networks.
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Affiliation(s)
- Luca Colucci-D'Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, Via Vivaldi 43, 81100 Caserta, Italy
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76
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Stein P, Yang R, Liu J, Pastores GM, Mistry PK. Evaluation of high density lipoprotein as a circulating biomarker of Gaucher disease activity. J Inherit Metab Dis 2011; 34:429-37. [PMID: 21290183 PMCID: PMC3186206 DOI: 10.1007/s10545-010-9271-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Revised: 12/14/2010] [Accepted: 12/23/2010] [Indexed: 01/10/2023]
Abstract
Circulating biomarkers are important surrogates for monitoring disease activity in type I Gaucher disease (GD1). We and others have reported low high-density lipoprotein (HDL) in GD1. We assessed HDL cholesterol as a biomarker of GD1, with respect to its correlation with indicators of disease severity and its response to imiglucerase enzyme replacement therapy (ERT). In 278 consecutively evaluated GD1 patients, we correlated HDL cholesterol, chitotriosidase, and angiotensin-converting enzyme (ACE) with indicators of disease severity. Additionally, we measured the response of these biomarkers to ERT. HDL cholesterol was negatively correlated with spleen volume, liver volume, and GD severity score index; the magnitude of this association of disease severity with HDL cholesterol was similar to that for ACE and for chitotriosidase. Within individual patients monitored over many years, there was a strikingly strong correlation of HDL with liver and spleen volumes; there was a similarly strong correlation of chitotriosidase and ACE with disease severity in individual patients monitored serially over many years (chitotriosidase r = 0.96 to 0.98, ACE r = 0.88 to 0.94, and HDL r = -0.84 to -0.94, p < 0.001). ERT for 3 years resulted in a striking increase of HDL while serum levels of chitotriosidase and ACE decreased. Our results reveal markedly low HDL cholesterol in untreated GD1, a correlation with indicators of disease severity in GD1, and a rise towards normal after ERT. These findings suggest HDL cholesterol merits inclusion within the "biomarker basket" for monitoring of patients with GD1.
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Affiliation(s)
- Philip Stein
- Department of Pediatrics, National Gaucher Disease Treatment Center, Yale University School of Medicine, New Haven, CT 06562, USA.
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77
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Hwang HH, Moon PG, Lee JE, Kim JG, Lee W, Ryu SH, Baek MC. Identification of the target proteins of rosiglitazone in 3T3-L1 adipocytes through proteomic analysis of cytosolic and secreted proteins. Mol Cells 2011; 31:239-46. [PMID: 21347706 PMCID: PMC3932691 DOI: 10.1007/s10059-011-0026-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 11/27/2010] [Accepted: 12/06/2010] [Indexed: 12/13/2022] Open
Abstract
Rosiglitazone, one of the thiazolidinedione (TZD), is an oral antidiabetic drug that activates a gamma isoform of peroxisome proliferator-activated receptor (PPARγ). To identify target proteins induced by rosiglitazone in adipocytes, we first performed simultaneous in-depth proteomic profiling of cytosolic proteins and secreted proteins (secretome) from 3T3-L1 adipocytes using a label-free quantification method with nano-UPLC MS/MS. In total, we identified 646 proteins from 3T3-L1 adipocytes, of which 172 and 162 proteins were upregulated and downregulated >1.5-fold, respectively, in rosiglitazone-treated cells, as compared to controls. Some differentially expressed proteins in particular, including fatty acid translocase (FAT)/CD36, fatty acid binding protein, lipoprotein lipase, acetyl CoA acyltransferase, carnitine O-palmitoyltransferase 2, sterol carrier protein, adiponectin, and phosphoenolpyruvate carboxykinase could explain the current action mechanism of TZDs. Furthermore, this study is the first to report on two potential target proteins of rosiglitazone, such as adenomatosis polyposis coli 2 (APC2), and eukaryotic translation initiation factor 5A-1 (eIF5A) related to apoptosis and cell division. Our data clearly suggest that in-depth proteomic approaches using cytosolic and secreted proteins are important and necessary for identification of drug targets at the protein level.
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Affiliation(s)
- Hyun-Ho Hwang
- Department of Molecular Medicine, Kyungpook National University, Daegu 700-422, Korea
- Cell and Matrix Biology Research Institute, Kyungpook National University, Daegu 700-422, Korea
| | - Pyong-Gon Moon
- Department of Molecular Medicine, Kyungpook National University, Daegu 700-422, Korea
- Cell and Matrix Biology Research Institute, Kyungpook National University, Daegu 700-422, Korea
| | - Jeong-Eun Lee
- Department of Molecular Medicine, Kyungpook National University, Daegu 700-422, Korea
- Cell and Matrix Biology Research Institute, Kyungpook National University, Daegu 700-422, Korea
| | - Jung-Guk Kim
- Department of Internal Medicine, Kyungpook National University Hospital, Daegu, 700-721, Korea
| | - Wan Lee
- College of Medicine, Dongguk University, Gyeongju 780-714, Korea
| | - Sung-Ho Ryu
- Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Moon-Chang Baek
- Department of Molecular Medicine, Kyungpook National University, Daegu 700-422, Korea
- Cell and Matrix Biology Research Institute, Kyungpook National University, Daegu 700-422, Korea
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78
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Guo D, Wong WS, Xu WZ, Sun FF, Qing DJ, Li N. Cis-cinnamic acid-enhanced 1 gene plays a role in regulation of Arabidopsis bolting. PLANT MOLECULAR BIOLOGY 2011; 75:481-95. [PMID: 21298397 DOI: 10.1007/s11103-011-9746-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Accepted: 01/22/2011] [Indexed: 05/22/2023]
Abstract
Cis-cinnamic acid (CA) is one of many cis-phenylpropanoids found in both monocots and dicots. It is produced in planta via sunlight-mediated isomerization of trans-cinnamic acid. This pair of isomers plays a differential role in regulation of plant growth. A functional proteomics approach has been adopted to identify genes of cis/trans-CA mixture-enhanced expression. Out of 1,241 proteins identified by mass spectrometry, 32 were CA-enhanced and 13 repressed. Further analysis with the molecular biology approach revealed 2 cis-CA (Z usammen-CA)-E nhanced genes, named ZCE1 and ZCE2, which encode members of the major latex protein-like (MLPL) gene family. The transcript accumulation of both genes is positively correlated with the amount of cis-CA applied externally, ranging from 1 to 100 μM. ZCE1 transcript accumulation is enhanced largely by cis-CA and slightly by other cis-phenylpropanoids. Treatment of several well-characterized plant growth regulator perception-deficient mutants with cis-CA is able to promote ZCE1 transcript accumulation, suggestive of distinct signaling pathways regulating cis-CA response. The zce1 loss-of-function mutant produced via the RNA-interference technique produces an earlier bolting phenotype in Arabidopsis, suggesting that ZCE1 plays a role in promoting vegetative growth and delay flowering.
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Affiliation(s)
- Di Guo
- Division of Life Science, The Hong Kong University of Science and Technology, Clear water bay, Hong Kong SAR, China
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79
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Ciavardelli D, Ammendola S, Ronci M, Consalvo A, Marzano V, Lipoma M, Sacchetta P, Federici G, Di Ilio C, Battistoni A, Urbani A. Phenotypic profile linked to inhibition of the major Zn influx system in Salmonella enterica: proteomics and ionomics investigations. ACTA ACUST UNITED AC 2011; 7:608-19. [DOI: 10.1039/c0mb00140f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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80
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D’Aguanno S, D’Alessandro A, Pieroni L, Roveri A, Zaccarin M, Marzano V, Canio MD, Bernardini S, Federici G, Urbani A. New Insights into Neuroblastoma Cisplatin Resistance: A Comparative Proteomic and Meta-Mining Investigation. J Proteome Res 2010; 10:416-28. [DOI: 10.1021/pr100457n] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Simona D’Aguanno
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Annamaria D’Alessandro
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Luisa Pieroni
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Antonella Roveri
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Mattia Zaccarin
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Valeria Marzano
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Michele De Canio
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Sergio Bernardini
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Giorgio Federici
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
| | - Andrea Urbani
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy, S. Lucia Foundation - IRCCS, Rome, Italy, and Departement of Biological Chemistry, University of Padova, Padova, Italy
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81
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Protein markers for insulin-producing beta cells with higher glucose sensitivity. PLoS One 2010; 5:e14214. [PMID: 21151894 PMCID: PMC2997773 DOI: 10.1371/journal.pone.0014214] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 10/16/2010] [Indexed: 01/02/2023] Open
Abstract
Background and Methodology Pancreatic beta cells show intercellular differences in their metabolic glucose sensitivity and associated activation of insulin production. To identify protein markers for these variations in functional glucose sensitivity, rat beta cell subpopulations were flow-sorted for their level of glucose-induced NAD(P)H and their proteomes were quantified by label-free data independent alternate scanning LC-MS. Beta cell-selective proteins were also identified through comparison with rat brain and liver tissue and with purified islet alpha cells, after geometrical normalization using 6 stably expressed reference proteins. Principal Findings All tissues combined, 943 proteins were reliably quantified. In beta cells, 93 out of 467 quantifiable proteins were uniquely detected in this cell type; several other proteins presented a high molar abundance in beta cells. The proteome of the beta cell subpopulation with high metabolic and biosynthetic responsiveness to 7.5 mM glucose was characterized by (i) an on average 50% higher expression of protein biosynthesis regulators such as 40S and 60S ribosomal constituents, NADPH-dependent protein folding factors and translation elongation factors; (ii) 50% higher levels of enzymes involved in glycolysis and in the cytosolic arm of the malate/aspartate-NADH-shuttle. No differences were noticed in mitochondrial enzymes of the Krebs cycle, beta-oxidation or respiratory chain. Conclusions Quantification of subtle variations in the proteome using alternate scanning LC-MS shows that beta cell metabolic glucose responsiveness is mostly associated with higher levels of glycolytic but not of mitochondrial enzymes.
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82
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Abstract
Schizophrenia is one of the most severe psychiatric disorders affecting 1% of the world population. There is yet no empirical method to validate the diagnosis of the disease. The identification of an underlying molecular alteration could lead to an improved disease understanding and may yield an objective panel of biomarkers to aid in the diagnosis of this devastating disease. Presented is the largest reported liquid chromatography-mass spectrometry-based proteomic profiling study investigating serum samples taken from first-onset drug-naive patients compared with samples collected from healthy volunteers. The results of this large-scale study are presented along with enzyme-linked immunosorbent assay-based validation data.
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83
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A strategy with label-free quantification of the targeted peptides for quantitative peptidome analysis of human serum. Sci China Chem 2010. [DOI: 10.1007/s11426-010-0127-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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84
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Létuvé S, Kozhich A, Humbles A, Brewah Y, Dombret MC, Grandsaigne M, Adle H, Kolbeck R, Aubier M, Coyle AJ, Pretolani M. Lung chitinolytic activity and chitotriosidase are elevated in chronic obstructive pulmonary disease and contribute to lung inflammation. THE AMERICAN JOURNAL OF PATHOLOGY 2010; 176:638-49. [PMID: 20042671 PMCID: PMC2808072 DOI: 10.2353/ajpath.2010.090455] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/06/2009] [Indexed: 11/20/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by chronic airway inflammation and emphysematous alveolar destruction. In this study, we have investigated whether chitotriosidase (ChTRase) and acidic mammalian chitinase, two chitinases with chitinolytic activity, are selectively augmented in COPD and contribute to its pathogenesis. We found that smokers with COPD, but not asthmatics, had higher chitinolytic activity and increased levels of ChTRase in bronchoalveolar lavage, more ChTRase-positive cells in bronchial biopsies, and an elevated proportion of alveolar macrophages expressing ChTRase than smokers without COPD or never-smokers. ChTRase accounted for approximately 80% of bronchoalveolar lavage chitinolytic activity, while acidic mammalian chitinase was undetectable. Bronchoalveolar lavage chitinolytic activity and ChTRase were associated with airflow obstruction and emphysema and with the levels of interleukin (IL)-1beta, IL-8, tumor-necrosis factor (TNF)-alpha, and its type II soluble receptor. Tumor necrosis factor-alpha stimulated ChTRase release only from alveolar macrophages from smokers with COPD, and exposure of these cells to ChTRase promoted the release of IL-8, monocyte-chemoattractant protein-1, and metalloproteinase-9. Finally, ChTRase overexpression in the lung of normal mice promoted macrophage recruitment and the synthesis of the murine homologue of IL-8, keratinocyte-derived cytokine, and of monocyte-chemoattractant protein-1. We conclude that pulmonary ChTRase overexpression may represent a novel important mechanism involved in COPD onset and progression.
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Affiliation(s)
- Séverine Létuvé
- Institut National de la Sante et de la RechercheMedicale (Inserm) U700, 75018 Paris, France
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85
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Hůlková H, Poupětová H, Harzer K, Mistry P, Aerts JMFG, Elleder M. Abnormal nonstoring capillary endothelium: a novel feature of Gaucher disease. Ultrastructural study of dermal capillaries. J Inherit Metab Dis 2010; 33:69-78. [PMID: 20049530 PMCID: PMC2828558 DOI: 10.1007/s10545-009-9018-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 10/30/2009] [Accepted: 11/10/2009] [Indexed: 01/05/2023]
Abstract
Ultrastructural study of skin biopsies in two cases of Gaucher disease (GD) patients (types II and III) revealed hitherto unknown alteration of the blood capillary endothelial cells (ECs) featured by hypertrophy and numerous subplasmalemmal microvesicles underneath both the apical and basal membranes. There was also prominent apical membrane folding with formation of filiform and large cytoplasmic projections, with occasional transcapillary cytoplasmic bridges. Similar, though less frequently expressed, changes were manifested at the basal membrane by numerous cytoplasmic projections into the subendothelial space. Regressive changes with EC breakdown were rare. Lysosomal storage was always absent. Besides EC hypertrophy, there was also increased EC density in the capillary lumen, leading to pronounced changes in capillary architecture with loose or incomplete EC anchoring. There were also signs of EC sprouting. Some pericytes displayed an increase in size and number of cytoplasmic processes, which often extended into distant pericapillary regions. The spectrum of changes suggests that a significant positive growth effect on EC occurs in GD. The putative mechanisms triggered by GBA1 deficiency leading to EC involvement are discussed. The authors are well aware of the fact the results, based on a nontraditional type of bioptic samples, are preliminary, but they are worth following, as further ultrastructural and functional studies of blood endothelium in GD may open a novel field in molecular cell pathophysiology of the disorder: endothelial dysfunction.
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Affiliation(s)
- Helena Hůlková
- 1st Faculty of Medicine and General Teaching Hospital, Institute of Inherited Metabolic Disorders, Charles University in Prague, Ke Karlovu 2, Bldg. D, 12000 Praha 2, Czech Republic
| | - Helena Poupětová
- 1st Faculty of Medicine and General Teaching Hospital, Institute of Inherited Metabolic Disorders, Charles University in Prague, Ke Karlovu 2, Bldg. D, 12000 Praha 2, Czech Republic
| | - Klaus Harzer
- Department of Pediatrics and Child Development, Universitäts-Kinderklinik, Tübingen, Germany
| | - Pramod Mistry
- Section of Pediatric Hepatology and Gastroenterology, Department of Pediatrics and Medicine, Yale School of Medicine, New Haven, CT USA
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Milan Elleder
- 1st Faculty of Medicine and General Teaching Hospital, Institute of Inherited Metabolic Disorders, Charles University in Prague, Ke Karlovu 2, Bldg. D, 12000 Praha 2, Czech Republic
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86
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Lanucara F, Brownridge P, Young IS, Whitfield PD, Doherty MK. Degradative proteomics and disease mechanisms. Proteomics Clin Appl 2010; 4:133-42. [PMID: 21137039 DOI: 10.1002/prca.200900159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 09/22/2009] [Accepted: 10/08/2009] [Indexed: 02/01/2023]
Abstract
Protein degradation is a fundamental biological process, which is essential for the maintenance and regulation of normal cellular function. In humans and animals, proteins can be degraded by a number of mechanisms: the ubiquitin-proteasome system, autophagy and intracellular proteases. The advances in contemporary protein analysis means that proteomics is increasingly being used to explore these key pathways and as a means of monitoring protein degradation. The dysfunction of protein degradative pathways has been associated with the development of a number of important diseases including cancer, muscle wasting disorders and neurodegenerative diseases. This review will focus on the role of proteomics to study cellular degradative processes and how these strategies are being applied to understand the molecular basis of diseases arising from disturbances in protein degradation.
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Affiliation(s)
- Francesco Lanucara
- The Physiological Laboratory, School of Biomedical Sciences, University of Liverpool, UK
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87
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Fiorentino L, Vivanti A, Cavalera M, Marzano V, Ronci M, Fabrizi M, Menini S, Pugliese G, Menghini R, Khokha R, Lauro R, Urbani A, Federici M. Increased tumor necrosis factor alpha-converting enzyme activity induces insulin resistance and hepatosteatosis in mice. Hepatology 2010; 51:103-10. [PMID: 19877183 DOI: 10.1002/hep.23250] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
UNLABELLED Tumor necrosis factor alpha-converting enzyme (TACE, also known as ADAM17) was recently involved in the pathogenesis of insulin resistance. We observed that TACE activity was significantly higher in livers of mice fed a high-fat diet (HFD) for 1 month, and this activity was increased in liver > white adipose tissue > muscle after 5 months compared with chow control. In mouse hepatocytes, C(2)C(12) myocytes, and 3T3F442A adipocytes, TACE activity was triggered by palmitic acid, lipolysaccharide, high glucose, and high insulin. TACE overexpression significantly impaired insulin-dependent phosphorylation of AKT, GSK3, and FoxO1 in mouse hepatocytes. To test the role of TACE activation in vivo, we used tissue inhibitor of metalloproteinase 3 (Timp3) null mice, because Timp3 is the specific inhibitor of TACE and Timp3(-/-) mice have higher TACE activity compared with wild-type (WT) mice. Timp3(-/-) mice fed a HFD for 5 months are glucose-intolerant and insulin-resistant; they showed macrovesicular steatosis and ballooning degeneration compared with WT mice, which presented only microvesicular steatosis. Shotgun proteomics analysis revealed that Timp3(-/-) liver showed a significant differential expression of 38 proteins, including lower levels of adenosine kinase, methionine adenosysltransferase I/III, and glycine N-methyltransferase and higher levels of liver fatty acid-binding protein 1. These changes in protein levels were also observed in hepatocytes infected with adenovirus encoding TACE. All these proteins play a role in fatty acid uptake, triglyceride synthesis, and methionine metabolism, providing a molecular explanation for the increased hepatosteatosis observed in Timp3(-/-) compared with WT mice. CONCLUSION We have identified novel mechanisms, governed by the TACE-Timp3 interaction, involved in the determination of insulin resistance and liver steatosis during overfeeding in mice.
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Affiliation(s)
- Loredana Fiorentino
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy
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88
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De Canio M, D'Aguanno S, Sacchetti C, Petrucci F, Cavagni G, Nuccetelli M, Federici G, Urbani A, Bernardini S. Novel IgE recognized components of Lolium perenne pollen extract: comparative proteomics evaluation of allergic patients sensitization profiles. J Proteome Res 2009; 8:4383-91. [PMID: 19585971 DOI: 10.1021/pr900315a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the last years, proteomic investigation provided a powerful tool in molecular characterization of complex allergen sources with relevant implications in both diagnosis and immunotherapic treatment of allergies. We followed a proteomic approach to characterize ryegrass (Lolium perenne) pollen, a common cause of seasonal allergic diseases affecting an increasing part of world population. Peptide shotgun experiments performed on nanoLiquid Ultra Pressure Chromatography coupled with fast Q-TOF MS-MS/MS acquisition protocols (MS(E)) and 2-DE immunoblot combined with MALDI-TOF-TOF analysis allowed the detection of all previously identified ryegrass allergens. Comparative analysis of immunoblot highlighted a class of patients characterized by a more complex 2-DE pattern associated with increased levels of IgE antibodies and by higher susceptibility to multiple sensitization toward different allergen sources. Cluster analysis revealed that all these patients recognized profilin, considered the main cross-reactive allergen in grass pollen. Furthermore, mass spectrometry analysis revealed the presence of other IgE reactive components in ryegrass pollen that might be involved in polysensitization, such as cyclophilin, fructosyltransferase and legumin-like protein.
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Affiliation(s)
- Michele De Canio
- Department of Internal Medicine, University of Rome Tor Vergata, Rome, Italy
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89
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Williams D, Ackloo S, Zhu P, Bowden P, Evans KR, Addison CL, Lock C, Marshall JG. Precipitation and selective extraction of human serum endogenous peptides with analysis by quadrupole time-of-flight mass spectrometry reveals posttranslational modifications and low-abundance peptides. Anal Bioanal Chem 2009; 396:1223-47. [PMID: 20033139 DOI: 10.1007/s00216-009-3345-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2009] [Revised: 11/23/2009] [Accepted: 11/24/2009] [Indexed: 11/30/2022]
Abstract
The endogenous peptides of human serum may have regulatory functions, have been associated with physiological states, and their modifications may reveal some mechanisms of disease. In order to correlate levels of specific peptides with disease alongside internal standards, the polypeptides must first be reliably extracted and identified. Endogenous blood peptides can be effectively enriched by precipitation of the serum with organic solvents followed by selective extraction of peptides using aqueous solutions modified with organic solvents. Polypeptides on filter paper were assayed with Coomasie brilliant blue binding. The polypeptides were resolved by detergent tricine polyacrylamide electrophoresis and visualized by diamine silver staining. Peptides in the extracts were collected by C18 and analyzed by matrix-assisted laser desorption/ionization and liquid chromatography-electrospray ionization-tandem mass spectrometry (MS/MS) quadrupole time-of-flight MS/MS. Peptides were resolved as multiple isotopic peaks in MS mode with mass deviation of 0.1 Da or less and similar accuracy for fragments. The sensitivity of MS and MS/MS analysis was estimated to be in the picomolar range or less. The peptide composition of the extracts was dependent on solvent formulation. Multiple peptides from apolipoproteins, complement proteins, coagulation factors, and many others were identified by X!Tandem with high mass accuracy of peptide ions and fragments from collision-induced dissociation. Many previously unreported posttranslational modifications of peptides including phosphorylations, oxidations, glycosylations, and others were detected with high mass accuracy and may be of clinical importance. About 4,630 redundant peptides were identified with 99% confidence separately, and together some 1,251 distinct proteins were identified with 99% confidence or greater using the Paragon algorithm.
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Affiliation(s)
- Declan Williams
- Department of Chemistry and Biology, Faculty of Engineering and Applied Science, Ryerson University, 350 Victoria Street, Toronto, ON, M5B 2K3, Canada
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90
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Mass spectrometry-based label-free quantitative proteomics. J Biomed Biotechnol 2009; 2010:840518. [PMID: 19911078 PMCID: PMC2775274 DOI: 10.1155/2010/840518] [Citation(s) in RCA: 342] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 09/01/2009] [Indexed: 01/22/2023] Open
Abstract
In order to study the differential protein expression in complex biological samples, strategies for rapid, highly reproducible and accurate quantification are necessary. Isotope labeling and fluorescent labeling techniques have been widely used in quantitative proteomics research. However, researchers are increasingly turning to label-free shotgun proteomics techniques for faster, cleaner, and simpler results. Mass spectrometry-based label-free quantitative proteomics falls into two general categories. In the first are the measurements of changes in chromatographic ion intensity such as peptide peak areas or peak heights. The second is based on the spectral counting of identified proteins. In this paper, we will discuss the technologies of these label-free quantitative methods, statistics, available computational software, and their applications in complex proteomics studies.
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91
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Röwer C, Vissers JPC, Koy C, Kipping M, Hecker M, Reimer T, Gerber B, Thiesen HJ, Glocker MO. Towards a proteome signature for invasive ductal breast carcinoma derived from label-free nanoscale LC-MS protein expression profiling of tumorous and glandular tissue. Anal Bioanal Chem 2009; 395:2443-56. [PMID: 19876624 DOI: 10.1007/s00216-009-3187-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2009] [Revised: 09/18/2009] [Accepted: 09/23/2009] [Indexed: 11/26/2022]
Abstract
As more and more alternative treatments become available for breast carcinoma, there is a need to stratify patients and individual molecular information seems to be suitable for this purpose. In this study, we applied label-free protein quantitation by nanoscale LC-MS and investigated whether this approach could be used for defining a proteome signature for invasive ductal breast carcinoma. Tissue samples from healthy breast and tumor were collected from three patients. Protein identifications were based on LC-MS peptide fragmentation data which were obtained simultaneously to the quantitative information. Hereby, an invasive ductal breast carcinoma proteome signature was generated which contains 60 protein entries. The on-column concentrations for osteoinductive factor, vimentin, GAP-DH, and NDKA are provided as examples. These proteins represent distinctive gene ontology groups of differentially expressed proteins and are discussed as risk markers for primary tumor pathogenesis. The developed methodology has been found well applicable in a clinical environment in which standard operating procedures can be kept; a prerequisite for the definition of molecular parameter sets that shall be capable for stratification of patients.
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MESH Headings
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/metabolism
- Blotting, Western
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Chromatography, Liquid/methods
- Computational Biology
- Female
- Humans
- Immunoenzyme Techniques
- Nanotechnology
- Proteome/analysis
- Proteomics/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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Affiliation(s)
- Claudia Röwer
- Proteome Center Rostock, University of Rostock, 18055, Rostock, Germany
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92
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Bussink AP, Verhoek M, Vreede J, Ghauharali-van der Vlugt K, Donker-Koopman WE, Sprenger RR, Hollak CE, Aerts JMFG, Boot RG. Common G102S polymorphism in chitotriosidase differentially affects activity towards 4-methylumbelliferyl substrates. FEBS J 2009; 276:5678-88. [PMID: 19725875 DOI: 10.1111/j.1742-4658.2009.07259.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chitotriosidase (CHIT1) is a chitinase that is secreted by activated macrophages. Plasma chitotriosidase activity reflects the presence of lipid-laden macrophages in patients with Gaucher disease. CHIT1 activity can be conveniently measured using fluorogenic 4-methylumbelliferyl (4MU)-chitotrioside or 4MU-chitobioside as the substrate, however, nonsaturating concentrations have to be used because of apparent substrate inhibition. Saturating substrate concentrations can, however, be used with the newly designed substrate 4MU-deoxychitobioside. We studied the impact of a known polymorphism, G102S, on the catalytic properties of CHIT1. The G102S allele was found to be common in type I Gaucher disease patients in the Netherlands ( approximately 24% of alleles). The catalytic efficiency of recombinant Ser102 CHIT1 was approximately 70% that of wild-type Gly102 CHIT1 when measured with 4MU-chitotrioside at a nonsaturating concentration. However, the activity was normal with 4MU-deoxychitobioside as the substrate at saturating concentrations, consistent with predictions from molecular dynamics simulations. In conclusion, interpretation of CHIT1 activity measurements with 4MU-chitotrioside with respect to CHIT1 protein concentrations depends on the presence of Ser102 CHIT1 in an individual, complicating estimation of the body burden of storage macrophages. Use of the superior 4MU-deoxychitobioside substrate avoids such complications because activity towards this substrate under saturating conditions is not affected by the G102S substitution.
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Affiliation(s)
- Anton P Bussink
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, The Netherlands
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93
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Shen Z, Li P, Ni RJ, Ritchie M, Yang CP, Liu GF, Ma W, Liu GJ, Ma L, Li SJ, Wei ZG, Wang HX, Wang BC. Label-free quantitative proteomics analysis of etiolated maize seedling leaves during greening. Mol Cell Proteomics 2009; 8:2443-60. [PMID: 19666873 DOI: 10.1074/mcp.m900187-mcp200] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To better understand light regulation of C(4) plant maize development, we investigated dynamic proteomic differences between green seedlings (control), etiolated seedlings, and etiolated seedlings illuminated for 6 or 12 h using a label-free quantitative proteomics approach based on nanoscale ultraperformance liquid chromatography-ESI-MS(E). Among more than 400 proteins identified, 73 were significantly altered during etiolated maize seedling greening. Of these 73 proteins, 25 were identified as membrane proteins that seldom had been identified with two-dimensional electrophoresis methods, indicating the power of our label-free method for membrane protein identification; 31 were related to light reactions of chlorophyll biosynthesis, photosynthesis, and photosynthetic carbon assimilation. The expression of photosystem II subunits was highly sensitive to light; most of them were not identified in etiolated maize seedlings but drastically increased upon light exposure, indicating that the complex process of biogenesis of the photosynthetic apparatus correlates with the transition from a dark-grown to a light-grown morphology. However, transcriptional analysis indicated that most transcripts encoding these proteins were not regulated by light. In contrast, the levels of mRNAs and proteins for enzymes involved in carbon assimilation were tightly regulated by light. Additionally phosphoenolpyruvate carboxykinase, the key enzyme of the phosphoenolpyruvate carboxykinase C(4) pathway, was more tightly regulated by light than the key enzymes of the NADP-malic enzyme C(4) pathway. Furthermore phosphoenolpyruvate carboxylase 1C, which was originally reported to be specifically expressed in roots, was also identified in this study; expression of this enzyme was more sensitive to light than its isoforms. Taken together, these results represent a comprehensive dynamic protein profile and light-regulated network of C(4) plants for etiolated seedling greening and provide a basis for further study of the mechanism of gene function and regulation in light-induced development of C(4) plants.
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Affiliation(s)
- Zhuo Shen
- Key Laboratory of Forest Tree Genetic Improvement and Biotechnology, Ministry of Education, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
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94
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Liu S, Bai S, Qin Z, Yang Y, Cui Y, Qin Y. Quantitative proteomic analysis of the cerebrospinal fluid of patients with multiple sclerosis. J Cell Mol Med 2009; 13:1586-603. [PMID: 19602050 PMCID: PMC3828869 DOI: 10.1111/j.1582-4934.2009.00850.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The diagnosis of multiple sclerosis (MS) is challenging for the lack of a specific diagnostic test. Recent researches in quantitative proteomics, however, offer new opportunities for biomarker discovery and the study of disease pathogenesis. To find more potential protein biomarkers, we used two technologies, 2-dimensional fluorescence difference in-gel electrophoresis (2D-DIGE), followed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and ultra-performance liquid chromato-graph coupled with quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS), to quantitatively analyse differential proteomic expression in the cerebrospinal fluid (CSF) between patients with MS (the experiment group) and patients with other neurological diseases (ONDs; the control group). Analysis by the former technology identified more than 43 different protein spots (39 proteins), of which 17 spots (13 proteins) showed more than 1.5-fold difference in abundance as analysed by DeCyder software (GE Healthcare, Piscataway. NJ, USA) between the MS and the ONDs groups. The expression of five protein spots was elevated and the expression of 12 protein spots was decreased in the MS group. Meanwhile, the latter method, UPLC/Q-TOF MS showed 68 different proteins. There were 45 proteins with a difference of more than 1.5 folds between the two groups, in which the expression of 20 proteins was elevated and the expression of 25 proteins was decreased in the MS group. Data provided by the two methods indicated that the proteins overlapped ratio was 27% in the 26 significant proteins that had the same regulation tendency. The differential CSF proteins were analysed further by biological network and it revealed interaction of them. The subsequent ELISA measuring the concentration of cystatin C (P < 0.01), which was one of the proteins discovered simultaneously with the two technologies, confirmed the results of the two quantitative proteomic analysis. The combination of the two quantitative proteomic technologies was helpful in discovering differentially expressed proteins that may have a connection with MS disease physiology and serve as useful biomarkers for diagnosis and treatment of MS diseases.
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Affiliation(s)
- Shilian Liu
- Institute of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong, China. :
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95
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Patel VJ, Thalassinos K, Slade SE, Connolly JB, Crombie A, Murrell JC, Scrivens JH. A Comparison of Labeling and Label-Free Mass Spectrometry-Based Proteomics Approaches. J Proteome Res 2009; 8:3752-9. [DOI: 10.1021/pr900080y] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Vibhuti J. Patel
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom, and Waters Corporation, Atlas Park, Simonsway, Manchester M22 5PP, United Kingdom
| | - Konstantinos Thalassinos
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom, and Waters Corporation, Atlas Park, Simonsway, Manchester M22 5PP, United Kingdom
| | - Susan E. Slade
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom, and Waters Corporation, Atlas Park, Simonsway, Manchester M22 5PP, United Kingdom
| | - Joanne B. Connolly
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom, and Waters Corporation, Atlas Park, Simonsway, Manchester M22 5PP, United Kingdom
| | - Andrew Crombie
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom, and Waters Corporation, Atlas Park, Simonsway, Manchester M22 5PP, United Kingdom
| | - J. Colin Murrell
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom, and Waters Corporation, Atlas Park, Simonsway, Manchester M22 5PP, United Kingdom
| | - James H. Scrivens
- Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom, and Waters Corporation, Atlas Park, Simonsway, Manchester M22 5PP, United Kingdom
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96
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Ma D, Chan MK, Lockstone HE, Pietsch SR, Jones DNC, Cilia J, Hill MD, Robbins MJ, Benzel IM, Umrania Y, Guest PC, Levin Y, Maycox PR, Bahn S. Antipsychotic Treatment Alters Protein Expression Associated with Presynaptic Function and Nervous System Development in Rat Frontal Cortex. J Proteome Res 2009; 8:3284-97. [DOI: 10.1021/pr800983p] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Dan Ma
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Man K. Chan
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Helen E. Lockstone
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Sandra R. Pietsch
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Declan N. C. Jones
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Jackie Cilia
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Mark D. Hill
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Melanie J. Robbins
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Isabel M. Benzel
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Yagnesh Umrania
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Paul C. Guest
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Yishai Levin
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Peter R. Maycox
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
| | - Sabine Bahn
- Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QT, U.K., and Psychiatry CEDD, New Frontiers Science Park, GlaxoSmithKline, Third Avenue, Harlow, CM19 5AW, U.K
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97
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Geromanos SJ, Vissers JPC, Silva JC, Dorschel CA, Li GZ, Gorenstein MV, Bateman RH, Langridge JI. The detection, correlation, and comparison of peptide precursor and product ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics 2009; 9:1683-95. [PMID: 19294628 DOI: 10.1002/pmic.200800562] [Citation(s) in RCA: 390] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The detection, correlation, and comparison of peptide and product ions from a data independent LC-MS acquisition strategy with data dependent LC-MS/MS is described. The data independent mode of acquisition differs from an LC-MS/MS data acquisition since no ion transmission window is applied with the first mass analyzer prior to collision induced disassociation. Alternating the energy applied to the collision cell, between low and elevated energy, on a scan-to-scan basis, provides accurate mass precursor and associated product ion spectra from every ion above the LOD of the mass spectrometer. The method therefore provides a near 100% duty cycle, with an inherent increase in signal intensity due to the fact that both precursor and product ion data are collected on all isotopes of every charge-state across the entire chromatographic peak width. The correlation of product to precursor ions, after deconvolution, is achieved by using reconstructed retention time apices and chromatographic peak shapes. Presented are the results from the comparison of a simple four protein mixture, in the presence and absence of an enzymatically digested protein extract from Escherichia coli. The samples were run in triplicate by both data dependant analysis (DDA) LC-MS/MS and data-independent, alternate scanning LC-MS. The detection and identification of precursor and product ions from the combined DDA search results of the four protein mixture were used for comparison to all other data. Each individual set of data-independent LC-MS data provides a more comprehensive set of detected ions than the combined peptide identifications from the DDA LC-MS/MS experiments. In the presence of the complex E. coli background, over 90% of the monoisotopic masses from the combined LC-MS/MS identifications were detected at the appropriate retention time. Moreover, the fragmentation pattern and number of associated elevated energy product ions in each replicate experiment was found to be very similar to the DDA identifications. In the case of the corresponding individual DDA LC-MS/MS experiment, 43% of the possible detectable peptides of interest were identified. The presented data illustrates that the time-aligned data from data-independent alternate scanning LC-MS experiments is highly comparable to the data obtained via DDA. The obtained information can therefore be effectively and correctly deconvolved to correlate product ions with parent precursor ions. The ability to generate precursor-product ion tables from this information and subsequently identify the correct parent precursor peptide will be illustrated in a companion manuscript.
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98
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Li GZ, Vissers JPC, Silva JC, Golick D, Gorenstein MV, Geromanos SJ. Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics 2009; 9:1696-719. [DOI: 10.1002/pmic.200800564] [Citation(s) in RCA: 444] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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99
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Chambery A, Vissers JPC, Langridge JI, Lonardo E, Minchiotti G, Ruvo M, Parente A. Qualitative and Quantitative Proteomic Profiling of Cripto−/− Embryonic Stem Cells by Means of Accurate Mass LC−MS Analysis. J Proteome Res 2009; 8:1047-58. [DOI: 10.1021/pr800485c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Angela Chambery
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Johannes P. C. Vissers
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - James I. Langridge
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Enza Lonardo
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Gabriella Minchiotti
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Menotti Ruvo
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
| | - Augusto Parente
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom, Istituto di Genetica e Biofisica “A Buzzati-Traverso”, CNR, I-80131 Napoli, Italy, and Istituto di Biostrutture e Bioimmagini, CNR, I-80134, Napoli, Italy
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Chambery A, Colucci-D’Amato L, Vissers JPC, Scarpella S, Langridge JI, Parente A. Proteomic Profiling of Proliferating and Differentiated Neural mes-c-myc A1 Cell Line from Mouse Embryonic Mesencephalon by LC−MS. J Proteome Res 2008; 8:227-38. [DOI: 10.1021/pr800454n] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Angela Chambery
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Luca Colucci-D’Amato
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Johannes P. C. Vissers
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Simona Scarpella
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - James I. Langridge
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
| | - Augusto Parente
- Dipartimento di Scienze della Vita, Seconda Università di Napoli, I-81100 Caserta, Italy, Istituto di Genetica e Biofisica “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, 80131-Napoli, Italy, and Waters Corporation, MS Technologies Center, M22 5PP Manchester, United Kingdom
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