In-depth mass spectrometric mapping of the human vitreous proteome
Mapping of proteins involved in normal eye functions is a prerequisite to identify pathological changes during eye disease processes. We therefore analysed the proteome of human vitreous by applying in-depth proteomic screening technologies. For ethical reasons human vitreous samples were obtained by vitrectomy from "surrogate normal patients" with epiretinal gliosis that is considered to constitute only negligible pathological vitreoretinal changes. We applied different protein prefractionation strategies including liquid phase isoelectric focussing, 1D SDS gel electrophoresis and a combination of both and compared the nu...
Source: Proteome Science - May 20, 2013 Category: Bioinformatics Authors: Sebastian AretzTim KrohneKerstin KammererUwe WarnkenAgnes Hotz-WagenblattMarion BergmannBoris StanzelTore KempfFrank HolzMartina SchnölzerJürgen Kopitz Source Type: research
Interactions by 2D Gel Electrophoresis Overlap (iGEO): a novel high fidelity
approach to identify constituents of protein complexes
Conclusions:
The iGEO strategy confirmed a core complex comprised of PINCH, RSU1, ILK, and
ILK binding partner Parvin. Our iGEO method also identified five novel
protein partners that specifically interacted with PINCH in
Drosophila S2 cell culture. Because of the improved
reproducibility of 2D-GE methodology and the increasing affordability of the
required labeling reagents, iGEO is a method that is accessible to most
moderately well-equipped biological laboratories. The biochemical
co-purifications inherent in iGEO allow for rapid and unambiguous
identification of the cons...
Source: Proteome Science - May 12, 2013 Category: Bioinformatics Authors: Masaaki YoshigiStephen PronovostJulie Kadrmas Source Type: research
Interactions by 2D Gel Electrophoresis Overlap (iGEO): a novel high fidelity approach to identify constituents of protein complexes
Conclusions:
The iGEO strategy confirmed a core complex comprised of PINCH, RSU1, ILK, and ILK binding partner Parvin. Our iGEO method also identified five novel protein partners that specifically interacted with PINCH in Drosophila S2 cell culture. Because of the improved reproducibility of 2D-GE methodology and the increasing affordability of the required labeling reagents, iGEO is a method that is accessible to most moderately well-equipped biological laboratories. The biochemical co-purifications inherent in iGEO allow for rapid and unambiguous identification of the constituents of protein complexes, without the need f...
Source: Proteome Science - May 12, 2013 Category: Bioinformatics Authors: Masaaki YoshigiStephen PronovostJulie Kadrmas Source Type: research
Comparative proteome analysis of Tumor necrosis factor ¿-stimulated human Vascular Smooth Muscle Cells in response to melittin
Conclusion:
Taken together, these data established that the expression of some proteins was significantly changed by melittin treatment in tumor necrosis factor alpha stimulated the cells and provided insights into the mechanism of the melittin function for its potential use as an anti-inflammatory agent. (Source: Proteome Science)
Source: Proteome Science - May 7, 2013 Category: Bioinformatics Authors: Hyun-Ji ChoJeong-Han KangKwan-Kyu ParkJung-Yoon ChoeYoon-Yub ParkYong-Suk MoonIl-Kyung ChungHyeun-Wook ChangCheorl-Ho KimYung ChoiWun-Jae KimSung-Kwon MoonYoung-Chae Chang Source Type: research
Comparative proteome analysis of Tumor necrosis factor alpha-stimulated human Vascular Smooth Muscle Cells in response to melittin
Conclusion:
Taken together, these data established that the expression of some proteins was significantly changed by melittin treatment in tumor necrosis factor alpha stimulated the cells and provided insights into the mechanism of the melittin function for its potential use as an anti-inflammatory agent. (Source: Proteome Science)
Source: Proteome Science - May 7, 2013 Category: Bioinformatics Authors: Hyun-Ji ChoJeong-Han KangKwan-Kyu ParkJung-Yoon ChoeYoon-Yub ParkYong-Suk MoonIl-Kyung ChungHyeun-Wook ChangCheorl-Ho KimYung ChoiWun-Jae KimSung-Kwon MoonYoung-Chae Chang Source Type: research
A SELDI mass spectrometry study of experimental autoimmune encephalomyelitis: sample preparation, reproducibility, and differential protein expression patterns
Background:
Experimental autoimmune encephalomyelitis (EAE) is an autoimmune, inflammatory disease of the central nervous system that is widely used as a model of multiple sclerosis (MS). Mitochondrial dysfunction appears to play a role in the development of neuropathology in MS and may also play a role in disease pathology in EAE. Here, surface enhanced laser desorption ionization mass spectrometry (SELDI-MS) has been employed to obtain protein expression profiles from mitochondrially enriched fractions derived from EAE and control mouse brain. To gain insight into experimental variation, the reproducibility of sub-cellul...
Source: Proteome Science - May 1, 2013 Category: Bioinformatics Authors: Sausan AzzamLaurie BroadwaterShuo LiErnest FreemanJennifer McDonoughRoger Gregory Source Type: research
Members of the high mobility group B protein family are dynamically expressed in embryonic neural stem cells
We report the predominance of small diameter HMGB2-/- neurospheres in comparison to wild-type, which correlated with increased proliferation in these smaller HMGB2-/- neurospheres. Our data suggest that HMGB2 plays a regulatory role in NSC cell proliferation and maintenance pathways. (Source: Proteome Science)
Source: Proteome Science - April 27, 2013 Category: Bioinformatics Authors: Ariel AbrahamRobert BronsteinEmily ChenAntonius KollerLorenza RonfaniMirjana Maletic-SavaticStella Tsirka Source Type: research
Retraction: clinical and technical phosphoproteomic research
ErratumThe citation and references ([1] Lopez E, Lopez I, Ferreira A, Sequi J: Clinical and Technical Phosphoproteomic Research.Proteome Sci 2011, 9(1):27. [2] Lopez E, Matthiesen R, Lopez I, Ashman K, Mendieta J, Wesselink JJ, Gomez-Puertas P, Ferreira A: Functional phosphoproteomics tools for current immunological disorders research. Journal of integrated omics 2011, 1(1):1-16. [3] Ashman K, Villar EL: Phosphoproteomics and cancer research. Clin Transl Oncol 2009,11(6):356-62. [4] Choudhary C, Mann M: Decoding signalling networks by mass spectrometry-based proteomics. Nature Reviews Molecular Cell Biology 2010, 11, 427-4...
Source: Proteome Science - April 23, 2013 Category: Bioinformatics Authors: Elena LópezIsabel LópezAntonio FerreiraJulia Sequí Source Type: research
Whole gel processing procedure for GeLC-MS/MS based proteomics
Background:
SDS-PAGE followed by in-gel digestion (IGD) is a popular workflow in mass spectrometry-based proteomics. In GeLC-MS/MS, a protein lysate of a biological sample is separated by SDS-PAGE and each gel lane is sliced in 5--20 slices which, after IGD, are analyzed by LC-MS/MS. The database search results for all slices of a biological sample are combined yielding global protein identification and quantification for each sample. In large scale GeLC-MS/MS experiments the manual processing steps including washing, reduction and alkylation become a bottleneck. Here we introduce the whole gel (WG) procedure where, prior ...
Source: Proteome Science - April 23, 2013 Category: Bioinformatics Authors: Sander PiersmaMarc WarmoesMeike de WitInge de ReusJaco KnolConnie Jiménez Source Type: research
Retraction Note: clinical and technical phosphoproteomic research
(Source: Proteome Science)
Source: Proteome Science - April 23, 2013 Category: Bioinformatics Authors: Elena López, Isabel López, Antonio Ferreira and Julia Sequí Source Type: research
Proteomics approach combined with biochemical attributes to elucidate compatible and incompatible plant-virus interactions between Vigna mungo and Mungbean Yellow Mosaic India Virus
Conclusions:
Biochemical and proteomic analyses revealed early accumulation of the defense/stress related proteins involved in ROS metabolism during incompatible interaction. The robustness in induction of defense/stress and signal transduction related proteins is the key factor in inducing resistance. The mechanism of MYMIV-resistance in V. mungo involves redirection of carbohydrate flux towards pentose phosphate pathway. Some of these identified, differentially regulated proteins are also conferring abiotic stress responses illustrating harmony amongst different stress responses. To the best of our knowledge, this is the...
Source: Proteome Science - April 15, 2013 Category: Bioinformatics Authors: Subrata KunduDipjyoti ChakrabortyAnirban KunduAmita Pal Source Type: research
Profiling and annotation of human kidney glomerulus proteome
Conclusions:
A high-confidence, non-redundant dataset of proteins created by comprehensive proteomic analysis could provide a more extensive understanding of human glomerulus proteome and could be useful as a resource for the discovery of biomarkers and disease-relevant proteins. (Source: Proteome Science)
Source: Proteome Science - April 8, 2013 Category: Bioinformatics Authors: Zenyui CuiYutaka YoshidaBo XuYing ZhangMasaaki NametaSameh MagdeldinTomoo MakiguchiToshikazu IkomaHidehiko FujinakaEishin YaoitaTadashi Yamamoto Source Type: research
Plasma proteome changes associated with refractory anemia and refractory anemia with ringed sideroblasts in patients with myelodysplastic syndrome
Conclusions:
This study describes plasma proteome changes associated with MDS patients with refractory anemia and refractory anemia with ringed sideroblasts. Changes observed in the inter-alpha-trypsin inhibitor heavy chain H4 fragments were in agreement with our previous studies of other MDS subgroups: refractory cytopenia with multilineage dysplasia and refractory anemia with excess blasts subtype 1. Mass spectrometry-based relative quantification of retinol-binding protein 4 peptides has shown that there are differences in the modification of this protein between refractory anemia with excess blasts subtype 1 patients a...
Source: Proteome Science - April 8, 2013 Category: Bioinformatics Authors: Pavel MájekZuzana Riedelová-ReicheltováJi¿í SuttnarKlára Pe¿ánkováJaroslav ¿ermákJan Dyr Source Type: research
Proteomic analysis of elite soybean jidou17 and its parents using iTRAQ-based quantitative approaches
Conclusions:
This study applied a proven technique to study proteomics in 14-day-old soybean leaves and explored the depth and breadth of soybean protein research. The results provide new data for further understanding the mechanisms of elite cultivar development. (Source: Proteome Science)
Source: Proteome Science - March 26, 2013 Category: Bioinformatics Authors: Jun QinFeng GuDuan LiuChangcheng YinShuangjin ZhaoHao ChenJianan ZhangChunyan YangXu ZhanMengchen Zhang Source Type: research
The 3T3-L1 adipocyte glycogen proteome
Conclusions:
These data provide new molecular insights into the regulation of glycogen-bound proteins that are associated with the maintenance, organization and localization of the adipocyte glycogen particle. (Source: Proteome Science)
Source: Proteome Science - March 22, 2013 Category: Bioinformatics Authors: David StapletonChad NelsonKrishna ParsawarMarcelo Flores-OpazoDonald McClainGlendon Parker Source Type: research
