Towards clinical proteomics analysis

Imai, Kazuhiro; Koshiyama, Akiyo; Nakata, Katsunori

doi:10.1002/bmc.1541

Cited by 26 publications

(18 citation statements)

References 27 publications

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“…However, 2D-GE has many drawbacks, including a narrow dynamic range that requires the multistep removal of abundant proteins before low abundance serum proteins or biomarkers can be detected, problematic solubilization and separation of hydrophobic proteins, and a restricted ability to load limited sample amounts on a gel (ϳ250 g) (18). Poor reproducibility of gel images between experiments, imprecise quantitation, and intensive labor requirements are additional limitations in applying the 2D-GE approach for clinical proteome analysis (19).…”

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confidence: 99%

Serum Proteomic Signature of Human Chagasic Patients for the Identification of Novel Potential Protein Biomarkers of Disease

Wen¹,

Zago

Nuñez³

et al. 2012

Molecular & Cellular Proteomics

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Chagas disease is initiated upon infection by Trypanosoma cruzi. Among the health consequences is a decline in heart function, and the pathophysiological mechanisms underlying this manifestation are not well understood. To explore the possible mechanisms, we employed IgY LC10 affinity chromatography in conjunction with ProteomeLab PF2D and two-dimensional gel electrophoresis to resolve the proteome signature of high and low abundance serum proteins in chagasic patients. MALDI-TOF MS/MS analysis yielded 80 and 14 differentially expressed proteins associated with cardiomyopathy of chagasic and other etiologies, respectively. The extent of oxidative stress-induced carbonyl modifications of the differentially expressed proteins (n ‫؍‬ 26) was increased and coupled with a depression of antioxidant proteins. Functional annotation of the top networks developed by ingenuity pathway analysis of proteome database identified dysregulation of inflammation/acute phase response signaling and lipid metabolism relevant to production of prostaglandins and arachidonic acid in chagasic patients. Overlay of the major networks identified prothrombin and plasminogen at a nodal position with connectivity to proteome signature indicative of heart disease (i.e., thrombosis, angiogenesis, vasodilatation of blood vessels or the aorta, and increased permeability of blood vessel and endothelial tubes), and inflammatory responses (e.g., platelet aggregation, complement activation, and phagocyte activation and migration). The detection of cardiac proteins (myosin light chain 2 and myosin heavy chain 11) and increased levels of vinculin and plasminogen provided a comprehensive set of biomarkers of cardiac muscle injury and development of clinical Chagas disease in human patients. These results provide an impetus for biomarker validation in large cohorts of clinically characterized chagasic patients. Molecular & Cellular

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confidence: 99%

Serum Proteomic Signature of Human Chagasic Patients for the Identification of Novel Potential Protein Biomarkers of Disease

Wen¹,

Zago

Nuñez³

et al. 2012

Molecular & Cellular Proteomics

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“…In contrast, other proteomics analytical methods, such as two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and LC-MS/MS, isotope-coded affinity tags (ICAT) and isobaric tags for relative and absolute quantification (iTRAQ), require certain pre-treatment steps (precipitation, clean-up with column, and enzymatic protein digestion 4) ). In this paper, we describe the history of the development of the FD-LC-MS/MS method and its application as a comprehensive differential proteomics approach to extracts of mouse liver, 5) mouse brain, 6) thoroughbred horse muscle, 7) and breast cancer cell lines 8) as well as fluctuations in protein levels in tissues and cells to elucidate intracellular biochemical events.…”

Section: Challenge Of Mass Spectrometry Toward the Elucidation Of Lifmentioning

confidence: 99%

“…13) Multidimensional LC, one of the standard methods for proteomics analysis, has been used to separate enzymatically digested peptides followed by identification by MS/MS. 4) In most LC-based methods, a mixture of the digested isotope-labeled peptides is separated by reversed-phase chromatography, and then the eluate is analyzed directly by mass spectrometry. Two typical stable-isotope labeling reagents, ICAT 15) and iTRAQ, 16) were developed in recent years and utilized for quantitative proteomics analyses.…”

Section: Development Of a Novel Proteomics Ap-proach: Fd-lc-ms/msmentioning

confidence: 99%

FD-LC-MS/MS Method for Determining Protein Expression and Elucidating Biochemical Events in Tissues and Cells

Ichibangase

Imai

2012

Biological & Pharmaceutical Bulletin

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To study biochemical events in tissues and cells, we have developed a novel proteomics approach, FD-LC-MS/MS, which consists of fluorogenic derivatization (FD), LC separation and detection/quantification of proteins in a biological sample, followed by the isolation and tryptic digestion of target proteins, and then their identification using nano-HPLC-MS/MS. Fluorogenic reagents such as 7-chloro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulphonamide (DAABD-Cl) were designed to have high sensitivity for HPLC-fluorescence and -MS/MS detection and reactivity for cysteine residues in proteins. This comprehensive differential proteomics approach was applied to several tissues, such as mouse liver, mouse brain, horse muscle, breast cancer cell lines, and mouse heart, in order to study fluctuations in protein levels in tissues and cells.

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“…Different strategies have been reported for the study of post-translational modifications of proteins, quantitative peptidomic or quantitative proteomic studies, in which labels, or Isotopic Coded Affinity Tags (ICAT), are applied for comparisons between levels of peptides or proteins in biological samples (e.g., treated vs untreated). These conventional quantification procedures are generally employed on the basis of a relative quantification, as calculations are made from at least two different samples [9,10]. System biology requires an accurate quantification of a specified set of peptides/proteins across multiple samples.…”

Section: Introductionmentioning

confidence: 99%