Journal name: Journal of proteomics

1. Resolution and identification of major peanut allergens using a combination of fluorescence two-dimensional differential gel electrophoresis, Western blotting and Q-TOF mass spectrometry

Author:: Chassaigne, Hubert; Trégoat, Virginie; Nørgaard, Jørgen V.; Maleki, Soheila J.; Hengel, Arjon J. van
Source:: Journal of proteomics 2009 v.72 no.3 pp. 511-526
Subject:: peanuts; allergens; plant proteins; glycoproteins; fluorescence; gel electrophoresis; molecular weight; Western blotting; mass spectrometry; proteome
Abstract:: ... Peanut allergy is triggered by several proteins known as allergens. In this study, the complexity the peanut allergome is investigated with proteomic tools. The strength of this investigation resides in combining the high-resolving power and reproducibility of fluorescence two-dimensional differential gel electrophoresis with specific immunological detection as well as polypeptide sequencing by hi ...
Handle:: 10113/28692
DOI:: 10.1016/j.jprot.2009.02.002
: https://doi.org/10.1016/j.jprot.2009.02.002

2. The neuropeptidomics of Ixodes scapularis synganglion

Author:: Neupert, Susanne; Russell, William K.; Predel, Reinhard; Russell, David H.; Strey, Otto F.; Teel, Pete D.; Nachman, Ronald J.
Source:: Journal of proteomics 2009 v.72 no.6 pp. 1040-1045
Subject:: Ixodes scapularis; ticks; central nervous system; ganglia; neuropeptides; expressed sequence tags; sequence analysis; proteome; proteomics; mass spectrometry
Abstract:: ... Ticks (Ixodoidea) likely transmit the greatest variety of human and animal pathogens of any arthropod vector. Despite their medical significance little data is available about the messenger molecules in the central nervous system that coordinate all physiological processes in these animals, including behaviour. In our study, we performed the first comprehensive neuropeptidomic analysis of a tick s ...
Handle:: 10113/36309
DOI:: 10.1016/j.jprot.2009.06.007
: https://doi.org/10.1016/j.jprot.2009.06.007

3. Thioredoxin targets in plants: The first 30 years

Author:: Montrichard, Françoise; Alkhalfioui, Fatima; Yano, Hiroyuki; Vensel, William H.; Hurkman, William J.; Buchanan, Bob B.
Source:: Journal of proteomics 2009 v.72 no.3 pp. 452-474
Subject:: plant proteins; proteomics
Abstract:: ... The turn of the century welcomed major developments in redox biology. In plants, proteomics made possible the identification of proteins linked to thioredoxin (Trx), initially in chloroplasts and then other cell compartments. Two procedures, one based on thiol specific probes and the other on mutant Trx proteins, facilitated the labeling or isolation of potential Trx targets that were later identi ...
Handle:: 10113/28964
DOI:: 10.1016/j.jprot.2008.12.002
: https://doi.org/10.1016/j.jprot.2008.12.002

4. 2-D DIGE uterine endothelial proteomic profile for maternal chronic binge-like alcohol exposure

Author:: Jayanth Ramadoss; Ronald R. Magness
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2986-2994
ISSN:: 1874-3919
Subject:: binging; cluster analysis; cultured cells; endothelial cells; ethanol; ewes; oxidative stress; pathogenesis; pregnancy; proteins; proteome; proteomics; uterus
Abstract:: ... Little is known about alcohol effects on the utero-placental compartment during pregnancy. For the first time, we utilized 2-D DIGE quantitative proteomics to evaluate the role of the uterus in Fetal Alcohol Spectrum Disorders (FASD) pathogenesis. Uterine artery endothelial cells were isolated from pregnant ewes, FAC sorted, validated, and maintained in culture. To mimic maternal binge drinking pa ...
DOI:: 10.1016/j.jprot.2011.07.029
PubMed:: 21839868
PubMed Central:: PMC3215828
: https://doi.org/10.1016/j.jprot.2011.07.029

5. 2-D difference gel electrophoresis approach to assess protein expression profiles in Bathymodiolus azoricus from Mid-Atlantic Ridge hydrothermal vents

Author:: Rui Company; Oreto Antúnez; Maria João Bebianno; Miren P. Cajaraville; Amparo Torreblanca
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2909-2919
ISSN:: 1874-3919
Subject:: actin; catalase; chemical speciation; fluorescence; gel electrophoresis; gene expression regulation; mass spectrometry; metals; mussels; oxidative stress; principal component analysis; protein synthesis; proteome; temperature; toxic substances; toxicity; trypsin; ubiquinones
Abstract:: ... Hydrothermal vent mussels Bathymodiolus azoricus are naturally exposed to toxic chemical species originated directly from vent chimneys. The amount of toxic elements varies significantly among vent sites along the Mid-Atlantic Ridge and B. azoricus must be able to adapt to changes in hydrothermal fluid composition, temperature and pressure. The aim of this work was to study changes in the proteome ...
DOI:: 10.1016/j.jprot.2011.07.012
PubMed:: 21835277
: https://doi.org/10.1016/j.jprot.2011.07.012

6. 2-DE-based proteomic analysis of common bean (Phaseolus vulgaris L.) seeds

Author:: M. De La Fuente; A. Borrajo; J. Bermúdez; M. Lores; J. Alonso; M. López; M. Santalla; A.M. De Ron; C. Zapata; G. Alvarez
Source:: Journal of proteomics 2011 v.74 no.2 pp. 262-267
ISSN:: 1874-3919
Subject:: Phaseolus vulgaris; alpha-amylase; beans; carbohydrate metabolism; databases; gels; genome; humans; mass spectrometry; phaseolin; phenol; phytohemagglutinin; proteomics; seeds; stress response; two-dimensional gel electrophoresis
Abstract:: ... Common bean (Phaseolus vulgaris L.) is the most important grain legume for direct human consumption. Proteomic studies in legumes have increased significantly in the last years but few studies have been performed to date in P. vulgaris. We report here a proteomic analysis of bean seeds by two-dimensional electrophoresis (2-DE). Three different protein extraction methods (TCA–acetone, phenol and th ...
DOI:: 10.1016/j.jprot.2010.10.004
PubMed:: 20971221
: https://doi.org/10.1016/j.jprot.2010.10.004

7. 2-DE-based proteomic investigation of the saliva of the Amazonian triatomine vectors of Chagas disease: Rhodnius brethesi and Rhodnius robustus

Author:: Camila M. Costa; Marcelo V. Sousa; Carlos André O. Ricart; Jaime M. Santana; Antonio R.L. Teixeira; Peter Roepstorff; Sébastien Charneau
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1652-1663
ISSN:: 1874-3919
Subject:: Chagas disease; Rhodnius; Trypanosoma cruzi; amino acid sequences; blood; databases; gene duplication; genes; hematophagous insects; proteins; proteomics; saliva; two-dimensional gel electrophoresis
Abstract:: ... The triatomine bugs are obligatory haematophagous organisms that act as vectors of Chagas disease by transmitting the protozoan Trypanosoma cruzi. Their feeding success is strongly related to salivary proteins that allow these insects to access blood by counteracting host haemostatic mechanisms. Proteomic studies were performed on saliva from the Amazonian triatomine bugs: Rhodnius brethesi and R. ...
DOI:: 10.1016/j.jprot.2011.02.022
PubMed:: 21362504
: https://doi.org/10.1016/j.jprot.2011.02.022

8. 2D-DIGE analysis of phospho-enriched fractions from dasatinib-treated melanoma cell lines

Author:: Alex J. Eustace; Paul Dowling; Michael Henry; Padraig Doolan; Paula Meleady; Martin Clynes; John Crown; Norma O'Donovan
Source:: Journal of proteomics 2011 v.74 no.4 pp. 490-501
ISSN:: 1874-3919
Subject:: immunoblotting; melanoma; metastasis; phosphoproteins; phosphorylation; small interfering RNA; tyrosine
Abstract:: ... Current therapeutic regimes for metastatic melanoma have failed to provide robust clinical responses. Dasatinib has shown anti-proliferative and anti-invasive effects in vitro; however, not all melanoma cells tested were sensitive to dasatinib. We used 2D-DIGE analysis of phospho-enriched fractions to identify phosphoproteins involved in regulating response to dasatinib in an isogenic pair of mela ...
DOI:: 10.1016/j.jprot.2010.12.011
PubMed:: 21237296
: https://doi.org/10.1016/j.jprot.2010.12.011

9. A comparative proteome analysis links tyrosine kinase 2 (Tyk2) to the regulation of cellular glucose and lipid metabolism in response to poly(I:C)

Author:: Tom Grunert; Nicole R. Leitner; Martina Marchetti-Deschmann; Ingrid Miller; Barbara Wallner; Marta Radwan; Claus Vogl; Thomas Kolbe; Dagmar Kratky; Manfred Gemeiner; Günter Allmaier; Mathias Müller; Birgit Strobl
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2866-2880
ISSN:: 1874-3919
Subject:: metabolites; carbohydrate metabolism; proteome; glucose; cell-mediated immunity; macrophages; cytokines; gene expression regulation; pathogens; defense mechanisms; transcription factors; monitoring; tyrosine; immune response; double-stranded RNA; lipid metabolism; long-chain-fatty-acid-CoA ligase; triose-phosphate isomerase; protein synthesis; innate immunity
Abstract:: ... Tyrosine kinase 2 (Tyk2) is an integral part of the Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway which relays intracellular signals of various cytokines. Tyk2 crucially contributes to host defense mechanisms against microbial pathogens and to tumor surveillance but also facilitates immune pathologies. Here we investigated the impact of Tyk2 on the macrophage pro ...
DOI:: 10.1016/j.jprot.2011.07.006
PubMed:: 21787891
PubMed Central:: PMC3225013
: https://doi.org/10.1016/j.jprot.2011.07.006

10. A differential proteomic approach identifies structural and functional components that contribute to the differentiation of brain capillary endothelial cells

Author:: Gwënaël Pottiez; Sophie Duban-Deweer; Barbara Deracinois; Fabien Gosselet; Luc Camoin; Johan Hachani; Pierre-Olivier Couraud; Roméo Cecchelli; Marie-Pierre Dehouck; Laurence Fenart; Yannis Karamanos; Christophe Flahaut
Source:: Journal of proteomics 2011 v.75 no.2 pp. 628-641
ISSN:: 1874-3919
Subject:: Western blotting; actin; astrocytes; blood-brain barrier; brain; cattle; coculture; endothelial cells; gene expression; genes; messenger RNA; microfilaments; permeability; phenotype; protein metabolism; proteomics
Abstract:: ... When in the vicinity of astrocytes, brain capillary endothelial cells (BCECs) develop the characteristic structural and functional features of the blood-brain barrier (BBB). The latter has low cellular permeability and restricts various compounds from entering the brain. We recently reported that the cytoskeleton-related proteins actin, gelsolin and filamin-A undergo the largest quantitative chang ...
DOI:: 10.1016/j.jprot.2011.09.002
PubMed:: 21982828
: https://doi.org/10.1016/j.jprot.2011.09.002

11. A gel-based proteomic method reveals several protein pathway abnormalities in fetal Down syndrome brain

Author:: Yanwei Sun; Mara Dierssen; Nuria Toran; Daniela D. Pollak; Wei-Qiang Chen; Gert Lubec
Source:: Journal of proteomics 2011 v.74 no.4 pp. 547-557
ISSN:: 1874-3919
Subject:: Down syndrome; RNA-binding proteins; adults; brain; congenital abnormalities; cortex; creatine kinase; energy metabolism; fatty acid-binding proteins; potassium chloride; proteomics; retrotransposons; solutes; tubulin
Abstract:: ... A large series of protein pathway components have been shown to be dysregulated in Down syndrome (DS) brain. No information about pathomechanisms linked to the trisomic state can be obtained from adult DS brain, however, as neurodegeneration occurs from the fourth decade. The aim of the study was to search for protein dysregulation in fetal DS brain before neurodegenerative changes are observed. P ...
DOI:: 10.1016/j.jprot.2011.01.009
PubMed:: 21262400
: https://doi.org/10.1016/j.jprot.2011.01.009

12. A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer

Author:: Xiaoyang Luo; Yansheng Liu; Rui Wang; Haichuan Hu; Rong Zeng; Haiquan Chen
Source:: Journal of proteomics 2011 v.74 no.4 pp. 528-538
ISSN:: 1874-3919
Subject:: biomarkers; blood serum; enzyme-linked immunosorbent assay; gel electrophoresis; gene expression; liquid chromatography; lung neoplasms; patients; proteins; proteome; proteomics; tandem mass spectrometry
Abstract:: ... Cancer secretomes are a promising source for biomarker discovery. The analysis of cancer secretomes still faces some difficulties mainly related to the intracellular contamination, which hinders the qualification and follow-up validations. This study aimed to establish a high-quality secretome of A549 cells by using the cellular proteome as a reference and to test the merits of this refined secret ...
DOI:: 10.1016/j.jprot.2011.01.011
PubMed:: 21262398
: https://doi.org/10.1016/j.jprot.2011.01.011

13. A multidisciplinary study on the effects of phloem-limited viruses on the agronomical performance and berry quality of Vitis vinifera cv. Nebbiolo

Author:: Marzia Giribaldi; Micol Purrotti; Davide Pacifico; Deborah Santini; Franco Mannini; Piero Caciagli; Luca Rolle; Laura Cavallarin; Maria Gabriella Giuffrida; Cristina Marzachì
Source:: Journal of proteomics 2011 v.75 no.1 pp. 306-315
ISSN:: 1874-3919
Subject:: Grapevine leafroll-associated virus 1; Grapevine virus A; Vitis vinifera; analysis of variance; cell structures; cohesion; gels; grapes; metabolism; oxidative stress; proteins; proteome; proteomics; pulp; resveratrol; shoots; small fruits; texture; titratable acidity; vines; vineyards; viruses
Abstract:: ... Viral infections are known to have a detrimental effect on grapevine yield and performance, but there is still a lack of knowledge about their effect on the quality and safety of end products. Vines of Vitis vinifera cv. Nebbiolo clone 308, affected simultaneously by Grapevine leafroll-associated virus 1 (GLRaV-1), Grapevine virus A (GVA), and Rupestris stem pitting associated virus (RSPaV), were ...
DOI:: 10.1016/j.jprot.2011.08.006
PubMed:: 21856458
: https://doi.org/10.1016/j.jprot.2011.08.006

14. A novel polyclonal antibody library for expression profiling of poorly characterized, membrane and secreted human proteins

Author:: Renata Grifantini; Massimiliano Pagani; Andrea Pierleoni; Alberto Grandi; Matteo Parri; Susanna Campagnoli; Piero Pileri; Davide Cattaneo; Elena Canidio; Angela Pontillo; Elisa De Camilli; Alberto Bresciani; Federica Marinoni; Eros Pedrazzoli; Renzo Nogarotto; Sergio Abrignani; Giuseppe Viale; Paolo Sarmientos; Guido Grandi
Source:: Journal of proteomics 2011 v.75 no.2 pp. 532-547
ISSN:: 1874-3919
Subject:: Escherichia coli; Western blotting; animal ovaries; biomarkers; colon; databases; gene expression regulation; humans; immunohistochemistry; mice; microarray technology; microscopy; neoplasms; polyclonal antibodies; protein synthesis; proteins
Abstract:: ... The YOMICS™ antibody library (http://www.yomics.com/) presented in this article is a new collection of 1559 murine polyclonal antibodies specific for 1287 distinct human proteins. This antibody library is designed to target marginally characterized membrane-associated and secreted proteins. It was generated against human proteins annotated as transmembrane or secreted in GenBank, EnsEMBL, Vega and ...
DOI:: 10.1016/j.jprot.2011.08.018
PubMed:: 21920474
: https://doi.org/10.1016/j.jprot.2011.08.018

15. A proteomic analysis of the wound response in Medicago leaves reveals the early activation of a ROS-sensitive signal pathway

Author:: Nelson C. Soares; Jolanta Wojtkowska; Phil A. Jackson
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1411-1420
ISSN:: 1874-3919
Subject:: Medicago truncatula; hydrogen peroxide; leaves; proteins; proteomics; signal transduction
Abstract:: ... Wounded Medicago truncatula leaves produce a burst of O₂ ⁻ (phase I) between 1 and 15min, then of O₂ ⁻ and H₂O₂ (phase II) between 1 and 3h. Our previous results suggest reactive oxygen species (ROS) may provide signals to mobilise early (6h), apoplastic, wound-responsive proteins (WRPs). 2DE and MALDI-TOF/TOF were used to analyse how the suppression of ROS production at different time points by d ...
DOI:: 10.1016/j.jprot.2011.03.017
PubMed:: 21440688
: https://doi.org/10.1016/j.jprot.2011.03.017

16. A proteomic approach to investigate the differential antigenic profile of two Coxiella burnetii strains

Author:: Anastasia Papadioti; Stavroula Markoutsa; Iosif Vranakis; Yiannis Tselentis; Michael Karas; Anna Psaroulaki; Georgios Tsiotis
Source:: Journal of proteomics 2011 v.74 no.7 pp. 1150-1159
ISSN:: 1874-3919
Subject:: Coxiella burnetii; Gram-negative bacteria; Q fever; animal models; antigens; blood serum; diagnostic techniques; endocarditis; outer membrane proteins; pathogenesis; pathogens; patients; polyacrylamide gel electrophoresis; proteomics; virulence; zoonoses
Abstract:: ... Q fever is a widespread zoonosis caused by Coxiella burnetii, an obligate intracellular Gram-negative bacterium. Current diagnostics of Q fever is based on serological testing of patient serum. Biological distinction among C. burnetii strains has been referred at the genetic level as well as in virulence in animal models of Q fever. Disclosure of strain specific antigens might show insight into th ...
DOI:: 10.1016/j.jprot.2011.04.016
PubMed:: 21565289
: https://doi.org/10.1016/j.jprot.2011.04.016

17. A proteomic study of in-root interactions between chickpea pathogens: The root-knot nematode Meloidogyne artiellia and the soil-borne fungus Fusarium oxysporum f. sp. ciceris race 5

Author:: Juan E. Palomares-Rius; Pablo Castillo; Juan A. Navas-Cortés; Rafael M. Jiménez-Díaz; Manuel Tena
Source:: Journal of proteomics 2011 v.74 no.10 pp. 2034-2051
ISSN:: 1874-3919
Subject:: Fusarium oxysporum; Fusarium wilt; Meloidogyne; biotic stress; chickpeas; cultivars; disease control; fungi; mixed infection; pathogens; proteins; proteome; proteomics; root-knot nematodes; soil-borne diseases; two-dimensional gel electrophoresis
Abstract:: ... Fusarium wilt caused by the fungus Fusarium oxysporum f. sp. ciceris (Foc) is the main soil-borne disease limiting chickpea production. Management of this disease is achieved mainly by the use of resistant cultivars. However, co-infection of a Foc-resistant plant by the fungus and the root-knot nematode Meloidogyne artiellia (Ma) causes breakdown of the resistance and thus limits its efficacy in t ...
DOI:: 10.1016/j.jprot.2011.05.026
PubMed:: 21640211
: https://doi.org/10.1016/j.jprot.2011.05.026

18. A proteomics view of programmed cell death mechanisms during host–parasite interactions

Author:: Patricia Cuervo; Nilma Fernandes; Jose Batista de Jesus
Source:: Journal of proteomics 2011 v.75 no.1 pp. 246-256
ISSN:: 1874-3919
Subject:: Protozoa; apoptosis; burden of disease; cell viability; host-parasite relationships; parasites; proteomics; vaccine development
Abstract:: ... Protozoan parasites are responsible for an impressive disease burden in developing and less-developed countries. The development of vaccines and effective new therapies for dealing with these organisms are among the main gaps to be filled in the control of protozoan parasite diseases. Programmed cell death (PCD) pathways have gained attention in recent years because they comprise complex signallin ...
DOI:: 10.1016/j.jprot.2011.07.027
PubMed:: 21843666
: https://doi.org/10.1016/j.jprot.2011.07.027

19. A proteomics view on the role of drought-induced senescence and oxidative stress defense in enhanced stem reserves remobilization in wheat

Author:: Mitra Mohammadi Bazargani; Elham Sarhadi; Ali-Akbar Shahnejat Bushehri; Andrea Matros; Hans-Peter Mock; Mohammad-Reza Naghavi; Vahid Hajihoseini; Mohsen Mardi; Mohammad-Reza Hajirezaei; Foad Moradi; Bahman Ehdaie; Ghasem Hosseini Salekdeh
Source:: Journal of proteomics 2011 v.74 no.10 pp. 1959-1973
ISSN:: 1874-3919
Subject:: filling period; cell death; flowering; peduncle; signal transduction; drought; wheat; crop yield; carbon; gels; mass spectrometry; oxidative stress; two-dimensional gel electrophoresis; proteome; landraces; carbohydrates; water stress; gene expression; Triticum aestivum; photosynthesis; gene expression regulation; leaves; stem cells; proteomics; proteins; protein synthesis; drying
Abstract:: ... Drought is one of the major factors limiting the yield of wheat (Triticum aestivum L.) particularly during grain filling. Under terminal drought condition, remobilization of pre-stored carbohydrates in wheat stem to grain has a major contribution in yield. To determine the molecular mechanism of stem reserve utilization under drought condition, we compared stem proteome patterns of two contrasting ...
DOI:: 10.1016/j.jprot.2011.05.015
PubMed:: 21621021
: https://doi.org/10.1016/j.jprot.2011.05.015

20. A quantitative view of the morphological phases of Paracoccidioides brasiliensis using proteomics

Author:: Tereza C.V. Rezende; Clayton L. Borges; Adriana D. Magalhães; Marcelo Valle de Sousa; Carlos A.O. Ricart; Alexandre M. Bailão; Célia M.A. Soares
Source:: Journal of proteomics 2011 v.75 no.2 pp. 572-587
ISSN:: 1874-3919
Subject:: Paracoccidioides brasiliensis; Western blotting; conidia; gene expression regulation; mass spectrometry; morphogenesis; mycelium; pathogens; proteins; proteome; proteomics; reverse transcriptase polymerase chain reaction; two-dimensional gel electrophoresis; virulence; yeasts
Abstract:: ... Paracoccidioides brasiliensis is a fungal pathogen with a broad distribution in Latin American countries. The mycelia-to-yeast morphological transition of P. brasiliensis is involved in the virulence of this pathogen, and this event is essential to the establishment of infection. Here, we report the first proteomic comparison between the mycelia, the mycelia-to-yeast transition and the yeast cells ...
DOI:: 10.1016/j.jprot.2011.08.020
PubMed:: 21920475
: https://doi.org/10.1016/j.jprot.2011.08.020

21. A quantitative view on Mycobacterium leprae antigens by proteomics

Author:: Harald G. Wiker; Gisele G. Tomazella; Gustavo A. de Souza
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1711-1719
ISSN:: 1874-3919
Subject:: DNA libraries; Mycobacterium leprae; antigens; bioinformatics; genomics; immune response; leprosy; pathogens; prediction; proteins; proteomics; pseudogenes; recombinant DNA; virulence
Abstract:: ... Leprosy is an ancient disease and the focus of the researchers' scrutiny for more than a century. However, many of the molecular aspects related to transmission, virulence, antigens and immune responses are far from known. Initially, the implementation of recombinant DNA library screens raised interesting antigen candidates. Finally, the availability of Mycobacterium leprae genomic information sho ...
DOI:: 10.1016/j.jprot.2011.01.004
PubMed:: 21278007
: https://doi.org/10.1016/j.jprot.2011.01.004

22. A workflow for peptide-based proteomics in a poorly sequenced plant: A case study on the plasma membrane proteome of banana

Author:: A. Vertommen; A.L.B. Møller; J.H.G. Cordewener; R. Swennen; B. Panis; C. Finnie; A.H.P. America; S.C. Carpentier
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1218-1229
ISSN:: 1874-3919
Subject:: bananas; case studies; leaves; membrane proteins; peptides; plasma membrane; proteome; proteomics; sequence homology; solubility
Abstract:: ... Membrane proteins are an interesting class of proteins because of their functional importance. Unfortunately their analysis is hampered by low abundance and poor solubility in aqueous media. Since shotgun methods are high-throughput and partly overcome these problems, they are preferred for membrane proteomics. However, their application in non-model plants demands special precautions to prevent f ...
DOI:: 10.1016/j.jprot.2011.02.008
PubMed:: 21334471
: https://doi.org/10.1016/j.jprot.2011.02.008

23. Abundance of tegument surface proteins in the human blood fluke Schistosoma mansoni determined by QconCAT proteomics

Author:: William Castro-Borges; Deborah M. Simpson; Adam Dowle; Rachel S. Curwen; Jane Thomas-Oates; Robert J. Beynon; R. Alan Wilson
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1519-1533
ISSN:: 1874-3919
Subject:: Schistosoma mansoni; antigens; aquaporins; arginine; flukes; immunity; immunoglobulin G; lysine; models; peptides; proteomics; surface proteins; transporters; trypsin
Abstract:: ... The schistosome tegument provides a major interface with the host blood stream in which it resides. Our recent proteomic studies have identified a range of proteins present in the complex tegument structure, and two models of protective immunity have implicated surface proteins as mediating antigens. We have used the QconCAT technique to evaluate the relative and absolute amounts of tegument prote ...
DOI:: 10.1016/j.jprot.2011.06.011
PubMed:: 21704203
: https://doi.org/10.1016/j.jprot.2011.06.011

24. Activity-based proteomics: Identification of ABHD11 and ESD activities as potential biomarkers for human lung adenocarcinoma

Author:: T. Wiedl; S. Arni; B. Roschitzki; J. Grossmann; S. Collaud; A. Soltermann; S. Hillinger; R. Aebersold; W. Weder
Source:: Journal of proteomics 2011 v.74 no.10 pp. 1884-1894
ISSN:: 1874-3919
Subject:: adenocarcinoma; biomarkers; enzyme activity; humans; lung neoplasms; mass spectrometry; metastasis; models; patients; prognosis; proteomics; survival rate
Abstract:: ... Lung cancer is the leading cause of all cancer related deaths with a worldwide mortality of 1.2 million each year. The 5-year survival rate ranges from 80% in early stages to a dismal 5% in advanced disease. Prognosis is currently mostly determined based on the extension of disease at diagnosis. Thereby it has become evident that predicted and real outcomes can vary significantly, even for patient ...
DOI:: 10.1016/j.jprot.2011.04.030
PubMed:: 21596165
: https://doi.org/10.1016/j.jprot.2011.04.030

25. Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani

Author:: Dirk Schmidt-Arras; Olivier Leclercq; Pier Federico Gherardini; Manuela Helmer-Citterich; Wolfgang Faigle; Damarys Loew; Gerald F. Späth
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1644-1651
ISSN:: 1874-3919
Subject:: Leishmania donovani; adenosinetriphosphatase; drugs; hosts; humans; insects; pH; parasites; pathogens; protein kinases; protein phosphorylation; proteins; signal transduction; temperature; two-dimensional gel electrophoresis
Abstract:: ... The protozoan parasite Leishmania donovani undergoes various developmental transitions during its infectious cycle that are triggered by environmental signals encountered inside insect and vertebrate hosts. Intracellular differentiation of the pathogenic amastigote stage is induced by pH and temperature shifts that affect protein kinase activities and downstream protein phosphorylation. Identifica ...
DOI:: 10.1016/j.jprot.2011.03.024
PubMed:: 21443974
: https://doi.org/10.1016/j.jprot.2011.03.024

26. Advances in top-down proteomics for disease biomarker discovery

Author:: David Calligaris; Claude Villard; Daniel Lafitte
Source:: Journal of proteomics 2011 v.74 no.7 pp. 920-934
ISSN:: 1874-3919
Subject:: biochemical pathways; bioinformatics; biomarkers; evolution; instrumentation; mass spectrometry; proteins; proteomics
Abstract:: ... Top-down mass spectrometry strategies allow identification and characterization of proteins and protein networks by direct fragmentation. These analytical processes involve a panel of fragmentation mechanisms, some of which preserve protein post-translational modifications. Thus top-down is of special interest in clinical biochemistry to probe modified proteins as potential disease biomarkers. Thi ...
DOI:: 10.1016/j.jprot.2011.03.030
PubMed:: 21477672
: https://doi.org/10.1016/j.jprot.2011.03.030

27. Agricultural recovery of a formerly radioactive area: II. Systematic proteomic characterization of flax seed development in the remediated Chernobyl area

Author:: Katarína Klubicová; Maksym Danchenko; Ludovit Skultety; Valentyna V. Berezhna; Andrea Hricová; Namik M. Rashydov; Martin Hajduch
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1378-1384
ISSN:: 1874-3919
Subject:: Linum usitatissimum; crops; enzymes; flax; glycolysis; linseed; proteins; proteomics; seed development; tandem mass spectrometry; two-dimensional gel electrophoresis
Abstract:: ... Molecular characterization of crop plants grown in remediated, formerly radioactive, areas could establish a framework for future agricultural use of these areas. Recently, we have established a quantitative reference map for mature flax seed proteins (Linum usitatissimum L.) harvested from a remediated plot in Chernobyl town. Herein we describe results from our ongoing studies of this subject, an ...
DOI:: 10.1016/j.jprot.2011.02.029
PubMed:: 21385628
: https://doi.org/10.1016/j.jprot.2011.02.029

28. Alteration of plasma membrane-bound redox systems of iron deficient pea roots by chitosan

Author:: Claudia-Nicole Meisrimler; Sebastien Planchon; Jenny Renaut; Kjell Sergeant; Sabine Lüthje
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1437-1449
ISSN:: 1874-3919
Subject:: chitosan; elicitors; iron; mass spectrometry; nutrient deficiencies; pathogenicity; pathogens; peas; peroxidases; plasma membrane; polyacrylamide gel electrophoresis; proteome; roots; transport proteins
Abstract:: ... Iron is essential for all living organisms and plays a crucial role in pathogenicity. This study presents the first proteome analysis of plasma membranes isolated from pea roots. Protein profiles of four different samples (+Fe, +Fe/Chitosan, −Fe, and −Fe/Chitosan) were compared by native IEF-PAGE combined with in-gel activity stains and DIGE. Using DIGE, 89 proteins of interest were detected in pl ...
DOI:: 10.1016/j.jprot.2011.01.012
PubMed:: 21310270
: https://doi.org/10.1016/j.jprot.2011.01.012

29. An analysis of the Caenorhabditis elegans lipid raft proteome using geLC-MS/MS

Author:: Wei Rao; R. Elwyn Isaac; Jeffrey N. Keen
Source:: Journal of proteomics 2011 v.74 no.2 pp. 242-253
ISSN:: 1874-3919
Subject:: Caenorhabditis elegans; models; phospholipids; prediction; proteins; proteome; proteomics
Abstract:: ... Lipid rafts are microdomains of the phospholipid bilayer, proposed to form semi-stable “islands” that act as a platform for several important cellular processes; major classes of raft-resident proteins include signalling proteins and glycosylphosphatidylinositol (GPI)-anchored proteins. Proteomic studies into lipid rafts have been mainly carried out in mammalian cell lines and single cell organism ...
DOI:: 10.1016/j.jprot.2010.11.001
PubMed:: 21070894
: https://doi.org/10.1016/j.jprot.2010.11.001

30. An in vivo characterization of colostrum protein uptake in porcine gut during early lactation

Author:: Marianne Danielsen; Lene Juul Pedersen; Emøke Bendixen
Source:: Journal of proteomics 2011 v.74 no.1 pp. 101-109
ISSN:: 1874-3919
Subject:: beta-lactoglobulin; bioactive properties; casein; colostrum; early lactation; humans; neonates; piglets; proteolysis; small intestine; stomach; veterinary medicine
Abstract:: ... Understanding the bioactive roles of colostrum proteins has gained much attention, and in particular, their potential use in human and veterinary medicine has been extensively studied. However, studies of bioactivity have mainly been conducted in vitro, but it has not yet been well characterized at the individual protein level which colostrum components are internalized by the intestinal tissue of ...
DOI:: 10.1016/j.jprot.2010.08.011
PubMed:: 20831910
: https://doi.org/10.1016/j.jprot.2010.08.011

31. An insight into the sialotranscriptome and proteome of the coarse bontlegged tick, Hyalomma marginatum rufipes

Author:: Ivo M.B. Francischetti; Jennifer M. Anderson; Nicholas Manoukis; Van M. Pham; José M.C. Ribeiro
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2892-2908
ISSN:: 1874-3919
Subject:: Hyalomma marginatum rufipes; amino acid sequences; blood; cDNA libraries; cattle; complementary DNA; diet; evolution; expressed sequence tags; hemostasis; hosts; inflammation; ions; mites; new family; proteins; proteome; salivary glands; ticks; transcriptome; vaccines
Abstract:: ... Ticks are mites specialized in acquiring blood from vertebrates as their sole source of food and are important disease vectors to humans and animals. Among the specializations required for this peculiar diet, ticks evolved a sophisticated salivary potion that can disarm their host's hemostasis, inflammation, and immune reactions. Previous transcriptome analysis of tick salivary proteins has reveal ...
Handle:: 10113/54168
DOI:: 10.1016/j.jprot.2011.07.015
PubMed:: 21851864
PubMed Central:: PMC3215792
: https://doi.org/10.1016/j.jprot.2011.07.015

32. An integrated proteomics and genomics analysis to unravel a heterogeneous platelet secretion defect

Author:: Michela Di Michele; Chantal Thys; Etienne Waelkens; Lut Overbergh; Wannes D'Hertog; Chantal Mathieu; Rita De Vos; Kathelijne Peerlinck; Chris Van Geet; Kathleen Freson
Source:: Journal of proteomics 2011 v.74 no.6 pp. 902-913
ISSN:: 1874-3919
Subject:: adenosine diphosphate; collagen; cytoskeleton; electron microscopy; epinephrine; gene expression regulation; genes; genomics; granules; hemorrhage; messenger RNA; patients; platelet aggregation; protein synthesis; proteomics; quantitative polymerase chain reaction; secretion
Abstract:: ... Eight patients with clinical bleeding problems have evidence for platelet storage pool disease as they present with impaired platelet aggregation and secretion with low concentrations of ADP and collagen and an absence of second phase aggregation with epinephrine. Electron microscopy analysis further showed a reduced but not absent amount of platelet dense granules, and CD63 staining was decreased ...
DOI:: 10.1016/j.jprot.2011.03.007
PubMed:: 21406263
: https://doi.org/10.1016/j.jprot.2011.03.007

33. Analysis of proteome changes in doxorubicin-treated adult rat cardiomyocyte

Author:: Suresh N. Kumar; Eugene A. Konorev; Deepika Aggarwal; Balaraman Kalyanaraman
Source:: Journal of proteomics 2011 v.74 no.5 pp. 683-697
ISSN:: 1874-3919
Subject:: proteins; proteome; cardiomyopathy; protein synthesis; oxidative stress; reactive oxygen species; stress response; cardiomyocytes; adults; patients; rats; proteomics; solubilization; apoptosis
Abstract:: ... Doxorubicin-induced cardiomyopathy in cancer patients is well established. The proposed mechanism of cardiac damage includes generation of reactive oxygen species, mitochondrial dysfunction and cardiomyocyte apoptosis. Exposure of adult rat cardiomyocytes to low levels of DOX for 48h induced apoptosis. Analysis of protein expression showed a differential regulation of several key proteins includin ...
DOI:: 10.1016/j.jprot.2011.02.013
PubMed:: 21338723
PubMed Central:: PMC3298037
: https://doi.org/10.1016/j.jprot.2011.02.013

34. Analysis of site-specific N-homocysteinylation of human serum albumin in vitro and in vivo using MALDI-ToF and LC-MS/MS mass spectrometry

Author:: Łukasz Marczak; Marta Sikora; Maciej Stobiecki; Hieronim Jakubowski
Source:: Journal of proteomics 2011 v.74 no.7 pp. 967-974
ISSN:: 1874-3919
Subject:: blood; homocysteine; human serum albumin; humans; lysine; mass spectrometry; neurodegenerative diseases
Abstract:: ... Elevated levels of homocysteine (Hcy) are associated with cardiovascular and neurodegenerative diseases in humans. Hcy becomes a component of human proteins as a result of N-homocysteinylation of protein lysine residues by Hcy-thiolactone, which affects the protein's structure and function, and contributes to Hcy-related pathology. Albumin is the major target for N-homocysteinylation in human bloo ...
DOI:: 10.1016/j.jprot.2011.01.021
PubMed:: 21329771
: https://doi.org/10.1016/j.jprot.2011.01.021

35. Analysis of the variability of human normal urine by 2D-GE reveals a “public” and a “private” proteome

Author:: Laurence Molina; Nicolas Salvetat; Randa Ben Ameur; Sabine Peres; Nicolas Sommerer; Fayçal Jarraya; Hammadi Ayadi; Franck Molina; Claude Granier
Source:: Journal of proteomics 2011 v.75 no.1 pp. 70-80
ISSN:: 1874-3919
Subject:: biomarkers; gels; humans; mass spectrometry; proteins; proteome; temperature; urine
Abstract:: ... The characterization of the normal urinary proteome is steadily progressing and represents a major interest in the assessment of clinical urinary biomarkers. To estimate quantitatively the variability of the normal urinary proteome, urines of 20 healthy people were collected. We first evaluated the impact of the sample conservation temperature on urine proteome integrity. Keeping the urine sample ...
DOI:: 10.1016/j.jprot.2011.06.031
PubMed:: 21787893
: https://doi.org/10.1016/j.jprot.2011.06.031

36. Annexin C4 in A. Fumigatus: A proteomics approach to understand the function

Author:: Vahid Khalaj; Bahareh Azarian; Somayeh Enayati; Behrouz Vaziri
Source:: Journal of proteomics 2011 v.74 no.10 pp. 1950-1958
ISSN:: 1874-3919
Subject:: Aspergillus fumigatus; electron transport chain; fungi; humans; oxidative stress; pathogens; proteins; proteomics; sporulation; stress response
Abstract:: ... Annexin C4 has been identified as a new member of fungal annexin family. In search of function, we have generated an annexin C4 disruptant strain of human pathogen, Aspergillus fumigatus. Detailed phenotypic analysis confirmed a non essential role of annexin C4 in the growth and sporulation of this pathogen. We applied a comparative proteomics strategy to understand the possible role of this prote ...
DOI:: 10.1016/j.jprot.2011.05.018
PubMed:: 21640208
: https://doi.org/10.1016/j.jprot.2011.05.018

37. Application of proteomics to the assessment of the response to ionising radiation in Arabidopsis thaliana

Author:: Morgane Gicquel; Marie-Andrée Esnault; Jesùs V. Jorrín-Novo; Francisco Cabello-Hurtado
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1364-1377
ISSN:: 1874-3919
Subject:: Arabidopsis thaliana; databases; gene expression regulation; leaves; proteins; proteome; proteomics; roots; statistical analysis
Abstract:: ... Ionising radiation (IR) affects cellular and tissue function. However, the biological effects and interactions induced by IR are unclear. The aim of this study was to decipher the proteomic patterns that influence these pathways. The proteomes of Arabidopsis thaliana roots and rosettes were analysed in response to sub-lethal IR doses (0, 10, and 40Gy). For each dose, the dynamic response was obser ...
DOI:: 10.1016/j.jprot.2011.03.025
PubMed:: 21447410
: https://doi.org/10.1016/j.jprot.2011.03.025

38. Assessment of allergenicity of diploid and hexaploid wheat genotypes: Identification of allergens in the albumin/globulin fraction

Author:: C. Larré; R. Lupi; G. Gombaud; C. Brossard; G. Branlard; D.A. Moneret-Vautrin; H. Rogniaux; S. Denery-Papini
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1279-1289
ISSN:: 1874-3919
Subject:: albumins; allergenicity; allergens; celiac disease; cultivars; diet; diploidy; electrophoresis; enzyme-linked immunosorbent assay; food allergies; genotype; gluten; hexaploidy; immunoblotting; immunoglobulin E; mass spectrometry; patients; wheat
Abstract:: ... Wheat is an important part of the daily diet of millions of people. However, this staple food is also responsible for food allergies. Ancient cultivars of wheat are gaining interest today but nothing is known about their allergenicity. Many wheat proteins have been reported as causative food allergens, including some prolamin-type gluten proteins, and salt soluble proteins of the albumin/globulin ...
DOI:: 10.1016/j.jprot.2011.03.014
PubMed:: 21473946
: https://doi.org/10.1016/j.jprot.2011.03.014

39. Assigning statistical significance to proteotypic peptides via database searches

Author:: Gelio Alves; Aleksey Y. Ogurtsov; Yi-Kuo Yu
Source:: Journal of proteomics 2011 v.74 no.2 pp. 199-211
ISSN:: 1874-3919
Subject:: amino acids; databases; peptide libraries
Abstract:: ... Querying MS/MS spectra against a database containing only proteotypic peptides reduces data analysis time due to reduction of database size. Despite the speed advantage, this search strategy is challenged by issues of statistical significance and coverage. The former requires separating systematically significant identifications from less confident identifications, while the latter arises when the ...
DOI:: 10.1016/j.jprot.2010.10.005
PubMed:: 21055489
PubMed Central:: PMC3186061
: https://doi.org/10.1016/j.jprot.2010.10.005

40. Back to the basics: Maximizing the information obtained by quantitative two dimensional gel electrophoresis analyses by an appropriate experimental design and statistical analyses

Author:: Luis Valledor; Jesús Jorrín
Source:: Journal of proteomics 2011 v.74 no.1 pp. 1-18
ISSN:: 1874-3919
Subject:: experimental design; planning; proteomics; statistical analysis; two-dimensional gel electrophoresis
Abstract:: ... Two dimensional gel electrophoresis has been one of the techniques most used for protein separation in proteomics experiments and still continues to be so for some species such as plants. Despite the constant technical advances and continuous improvements in the field of 2-DE, the experimental design and analysis of protein abundance data continue to be ignored or not properly documented in the li ...
DOI:: 10.1016/j.jprot.2010.07.007
PubMed:: 20656082
: https://doi.org/10.1016/j.jprot.2010.07.007

41. Bacterial proteins with cleaved or uncleaved signal peptides of the general secretory pathway

Author:: Gustavo A. de Souza; Nils A. Leversen; Hiwa Målen; Harald G. Wiker
Source:: Journal of proteomics 2011 v.75 no.2 pp. 502-510
ISSN:: 1874-3919
Subject:: Bacillus subtilis; Mycobacterium tuberculosis; bacteria; bacterial proteins; cell viability; mammals; outer membrane proteins; peptides; proteomics; screening; signal peptide
Abstract:: ... Correct protein compartmentalization is a key step for molecular function and cell viability, and this is especially true for membrane and externalized proteins of bacteria. Recent proteomic reports of Bacillus subtilis have shown that many proteins with Sec-like signal peptides and absence of a transmembrane helix domain are still observed in membrane-enriched fractions, but further evidence abou ...
DOI:: 10.1016/j.jprot.2011.08.016
PubMed:: 21920479
: https://doi.org/10.1016/j.jprot.2011.08.016

42. Bioinformatic strategies for unambiguous identification of prostate specific antigen in clinical samples

Author:: Ákos Végvári; Melinda Rezeli; Jari Häkkinen; Carina Sihlbom; Elisabet Carlsohn; Johan Malm; Hans Lilja; Thomas Laurell; György Marko-Varga
Source:: Journal of proteomics 2011 v.75 no.1 pp. 202-210
ISSN:: 1874-3919
Subject:: antigens; bioinformatics; biomarkers; computer software; databases; diagnostic techniques; immunoassays; peptides; prostatic neoplasms
Abstract:: ... Prostate specific antigen (PSA), as a widely used clinical biomarker in prostate cancer diagnostics, exists in multiple molecular forms. However, all of these forms might not be recognized in a given sample by the standard immunoassays. Therefore, we have investigated PSA isoforms, separated by size, using mass spectrometric analyses. The objective of these developments was to identify and specify ...
DOI:: 10.1016/j.jprot.2011.06.008
PubMed:: 21723425
PubMed Central:: PMC3220806
: https://doi.org/10.1016/j.jprot.2011.06.008

43. Biomarkers of disease and post-mortem changes — Heat stabilization, a necessary tool for measurement of protein regulation

Author:: Kim Kultima; Karl Sköld; Mats Borén
Source:: Journal of proteomics 2011 v.75 no.1 pp. 145-159
ISSN:: 1874-3919
Subject:: biomarkers; enzyme activity; heat; proteins; proteomics
Abstract:: ... This review focuses on post sampling changes and how the Stabilizor system has been used to control this natural biological process and potential implications on cancer-specific biomarkers due to post sampling changes. Tissue sampling is a major traumatic event that can have drastic effects within a very short timeframe at the molecular level [1] resulting in loss of sample quality due to post-mor ...
DOI:: 10.1016/j.jprot.2011.06.009
PubMed:: 21708298
: https://doi.org/10.1016/j.jprot.2011.06.009

44. Biomolecular characterization of allergenic proteins in snow crab (Chionoecetes opilio) and de novo sequencing of the second allergen arginine kinase using tandem mass spectrometry

Author:: Anas M. Abdel Rahman; Sandip D. Kamath; Andreas L. Lopata; John J. Robinson; Robert J. Helleur
Source:: Journal of proteomics 2011 v.74 no.2 pp. 231-241
ISSN:: 1874-3919
Subject:: Chionoecetes opilio; allergens; arginine kinase; bioinformatics; blood serum; chromatography; crabs; desorption; hypersensitivity; immunoblotting; ionization; legs; monitoring; muscles; patients; polyacrylamide gel electrophoresis; proteins; smooth endoplasmic reticulum; tandem mass spectrometry
Abstract:: ... Snow crab (Chionoecetes opilio) proteins have been recognized as an important source of both food and occupational allergens. While snow crab causes a significant occupational allergy, only one novel allergen has recently been fully characterized. The muscle proteins from snow crab legs were profiled by SDS-PAGE. Several of these proteins were characterized using tandem mass spectrometry. Five pro ...
DOI:: 10.1016/j.jprot.2010.10.010
PubMed:: 21059421
: https://doi.org/10.1016/j.jprot.2010.10.010

45. Boric acid gel enrichment of glycosylated proteins in human wound fluids

Author:: Christoph Krisp; Caroline Kubutat; Andreas Kyas; Lars Steinsträßer; Frank Jacobsen; Dirk Wolters
Source:: Journal of proteomics 2011 v.74 no.4 pp. 502-509
ISSN:: 1874-3919
Subject:: Western blotting; affinity chromatography; boric acid; cattle; diabetes mellitus; fetuins; gels; glycoproteins; glycosylation; humans; mass spectrometry; pathogenesis; patients; quantitative analysis
Abstract:: ... The enrichment of glycosylated proteins by glycocapturing materials plays a pivotal role for the investigation of polysaccharide containing proteins in disease pathogenesis. Hence, we investigated a boric acid gel as a binding material for glycoprotein enrichment. The bovine proteins alpha-1-acid-glycoprotein (A1AG) and alpha-2-HS-glycoprotein (fetuin A) were spiked in human chronic wound fluids a ...
DOI:: 10.1016/j.jprot.2011.01.005
PubMed:: 21278005
: https://doi.org/10.1016/j.jprot.2011.01.005

46. Challenges and solutions for the identification of membrane proteins in non-model plants

Author:: A. Vertommen; B. Panis; R. Swennen; S.C. Carpentier
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1165-1181
ISSN:: 1874-3919
Subject:: gels; membrane proteins; polyacrylamide gel electrophoresis; proteome; proteomics; solubility; two-dimensional gel electrophoresis
Abstract:: ... The workhorse for proteomics in non-model plants is classical two-dimensional electrophoresis, a combination of iso-electric focusing and SDS-PAGE. However, membrane proteins with multiple membrane spanning domains are hardly detected on classical 2-DE gels because of their low abundance and poor solubility in aqueous media. In the current review, solutions that have been proposed to handle these ...
DOI:: 10.1016/j.jprot.2011.02.016
PubMed:: 21354347
: https://doi.org/10.1016/j.jprot.2011.02.016

47. Changes in the leaf proteome profile of Mentha arvensis in response to Alternaria alternata infection

Author:: Ragini Sinha; Sharmila Chattopadhyay
Source:: Journal of proteomics 2011 v.74 no.3 pp. 327-336
ISSN:: 1874-3919
Subject:: Alternaria alternata; Mentha arvensis; crops; desorption; energy metabolism; gene expression regulation; ionization; leaves; pathogenesis; plant pathogenic fungi; proteins; proteome; proteomics; spectroscopy; two-dimensional gel electrophoresis
Abstract:: ... Plant pathogenic fungi cause important yield losses in crops. A proteomic approach was used to study the changes in the leaf proteome profile of the plant Mentha arvensis infected with a necrotrophic fungus, Alternaria alternata. High-resolution two-dimensional gel electrophoresis (2-DE) followed by colloidal Coomassie staining and mass spectrometric analysis was used to identify highly abundant p ...
DOI:: 10.1016/j.jprot.2010.11.009
PubMed:: 21111074
: https://doi.org/10.1016/j.jprot.2010.11.009

48. Changes in the plant proteome resulting from salt stress: Toward the creation of salt-tolerant crops?

Author:: Hamid Sobhanian; Keyvan Aghaei; Setsuko Komatsu
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1323-1337
ISSN:: 1874-3919
Subject:: agricultural land; arable soils; food crops; genes; proteins; proteome; proteomics; salinity; salt stress; salt tolerance; toxicity
Abstract:: ... Salinity in agricultural land is a major problem worldwide, placing a severe constraint on crop growth and productivity in many regions, and increased salinization of arable land is expected to have devastating global effects. Though plants vary in their sensitivity to salt stress, high salinity causes water deficit and ion toxicity in many plant species. Considerable efforts have therefore been m ...
DOI:: 10.1016/j.jprot.2011.03.018
PubMed:: 21440686
: https://doi.org/10.1016/j.jprot.2011.03.018

49. Characterisation of the variation of mouse brain proteome by two-dimensional electrophoresis

Author:: István Földi; Géza Müller; Botond Penke; Tamás Janáky
Source:: Journal of proteomics 2011 v.74 no.6 pp. 894-901
ISSN:: 1874-3919
Subject:: brain; experimental design; genetic background; human diseases; laboratory animals; mice; models; proteome; proteomics; two-dimensional gel electrophoresis; variance
Abstract:: ... Neuroproteomics is aimed to study the molecular organisation of the nervous system at the protein level. Two-dimensional electrophoresis is the most frequently used technique in quantitative proteomics. The aim of this study was to assess the experimental and biological variations on this proteomic platform using mouse brain tissue. Mice are the most generally used lab animals for modelling human ...
DOI:: 10.1016/j.jprot.2011.03.006
PubMed:: 21406261
: https://doi.org/10.1016/j.jprot.2011.03.006

50. Characterization of mitochondrial proteome in a severe case of ETF-QO deficiency

Author:: H. Rocha; R. Ferreira; J. Carvalho; R. Vitorino; C. Santa; L. Lopes; N. Gregersen; L. Vilarinho; F. Amado
Source:: Journal of proteomics 2011 v.75 no.1 pp. 221-228
ISSN:: 1874-3919
Subject:: acyl-CoA dehydrogenase; antioxidants; apoptosis; electron transfer; fatty acids; fibroblasts; gene expression regulation; mitochondria; mutation; oxidation; pathogenesis; patients; phenotype; protein synthesis; proteins; proteome; riboflavin
Abstract:: ... Multiple acyl-CoA dehydrogenase deficiency (MADD) is a mitochondrial fatty acid oxidation disorder caused by mutations that affect electron transfer flavoprotein (ETF) or ETF:ubiquinone oxidoreductase (ETF-QO) or even due to unidentified disturbances of riboflavin metabolism. Besides all the available data on the molecular basis of FAO disorders, including MADD, the pathophysiological mechanisms u ...
DOI:: 10.1016/j.jprot.2011.04.025
PubMed:: 21596162
: https://doi.org/10.1016/j.jprot.2011.04.025

51. Characterization of the B-Raf interactome in mouse hippocampal neuronal cells

Author:: Juan J. Bonfiglio; Giuseppina Maccarrone; Christiane Rewerts; Florian Holsboer; Eduardo Arzt; Christoph W. Turck; Susana Silberstein
Source:: Journal of proteomics 2011 v.74 no.2 pp. 186-198
ISSN:: 1874-3919
Subject:: actin; cytoskeleton; gel electrophoresis; messenger RNA; metabolism; mice; mitogen-activated protein kinase; molecular chaperones; neurons; proteomics; receptors; signal transduction; translation (genetics); tubulin
Abstract:: ... B-Raf links a variety of extracellular stimuli downstream of cell surface receptors, constituting a determining factor in the ability of neurons to activate ERK. A detailed study of the B-Raf interactome is necessary to clarify the intricacy of B-Raf-dependent signal transduction. We used a mouse hippocampal cell line (HT22) that expresses B-Raf at high levels, to identify B-Raf associated protein ...
DOI:: 10.1016/j.jprot.2010.10.006
PubMed:: 21055488
: https://doi.org/10.1016/j.jprot.2010.10.006

52. Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: Evaluation in proteomic studies using peptide-centric database searches

Author:: Lázaro H. Betancourt; Aniel Sánchez; Yasset Pérez; Jorge Fernandez de Cossio; Jeovanis Gil; Patricia Toledo; Seiji Iguchi; Saburo Aimoto; Luis J. González; Gabriel Padrón; Toshifumi Takao; Vladimir Besada
Source:: Journal of proteomics 2011 v.74 no.10 pp. 2210-2213
ISSN:: 1874-3919
Subject:: cation exchange chromatography; databases; peptides; proteomics
Abstract:: ... Here we describe an integrated approach for the selective separation of peptides from complex mixtures using strong cation-exchange chromatography. The procedure exploits the charge differences produced by reversible modification of primary amino groups in peptides, enabling their separation into three major fractions: 1) neutral peptides 2) peptides with one positive charge and 3) peptides with 2 ...
DOI:: 10.1016/j.jprot.2011.04.029
PubMed:: 21596166
: https://doi.org/10.1016/j.jprot.2011.04.029

53. Cibacron Blue and proteomics: The mystery of the platoon missing in action

Author:: Francesco Di Girolamo; Pier Giorgio Righetti; Alfonsina D'Amato; Maxey C.M. Chung
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2856-2865
ISSN:: 1874-3919
Subject:: adsorption; albumins; biomarkers; blood proteins; boiling; dyeing; genes; hydrophobic bonding; proteome; proteomics; sodium chloride; thiourea; urea
Abstract:: ... The use of Cibacron Blue columns (HiTrapBlue) in proteome analysis for removal of plasma albumin, for facilitating biomarker discovery, has not borne any fruit. In fact, the visibility of low-abundance proteins was obscured. It is here reported that, upon albumin sequestering from plasma, there is adsorption, via hydrophobic interaction, of a substantial number of plasma proteins, which are lost f ...
DOI:: 10.1016/j.jprot.2011.06.033
PubMed:: 21787892
: https://doi.org/10.1016/j.jprot.2011.06.033

54. Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS

Author:: Irene Granlund; Thomas Kieselbach; Rikard Alm; Wolfgang P. Schröder; Cecilia Emanuelsson
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1190-1200
ISSN:: 1874-3919
Subject:: Arabidopsis; amino acids; chloroplasts; gels; genome; peptides; protein isoforms; proteins; proteome; proteomics; screening; spinach
Abstract:: ... It is an established fact that allelic variation and post-translational modifications create different variants of proteins, which are observed as isoelectric and size subspecies in two-dimensional gel based proteomics. Here we explore the stromal proteome of spinach and Arabidopsis chloroplast and show that clustering of mass spectra is a useful tool for investigating such variants and detecting ...
DOI:: 10.1016/j.jprot.2011.04.008
PubMed:: 21539947
: https://doi.org/10.1016/j.jprot.2011.04.008

55. Comparative proteome analyses of host protein expression in response to Enterovirus 71 and Coxsackievirus A16 infections

Author:: Jia Jun Lee; Joey Bing Kai Seah; Vincent Tak Kwong Chow; Chit Laa Poh; Eng Lee Tan
Source:: Journal of proteomics 2011 v.74 no.10 pp. 2018-2024
ISSN:: 1874-3919
Subject:: Enterovirus A; calreticulin; children; desmin; encephalitis; etiological agents; foot-and-mouth disease; gene expression regulation; hand, foot and mouth disease; immune system; meningitis; muscle contraction; myocarditis; myocytes; paralysis; protein disulfide-isomerase; protein synthesis; proteome
Abstract:: ... Enterovirus 71 (EV71) and Coxsackievirus A16 (CA16) are the main etiological agents of Hand, Foot and Mouth Disease (HFMD), a common disease among children and had caused several outbreaks in the Asia-Pacific region. Although being genetically close to each other, EV71 infection can cause serious and fatal neurological complications like encephalitis, myocarditis, acute flaccid paralysis (AFP) and ...
DOI:: 10.1016/j.jprot.2011.05.022
PubMed:: 21621020
: https://doi.org/10.1016/j.jprot.2011.05.022

56. Comparative proteome analysis of Brucella abortus 2308 and its virB type IV secretion system mutant reveals new T4SS-related candidate proteins

Author:: Vladimir Paredes-Cervantes; Raúl Flores-Mejía; Martha C. Moreno-Lafont; Humberto Lanz-Mendoza; Ángel T. Tello-López; Jane Castillo-Vera; Victoria Pando-Robles; Gerardo Hurtado-Sil; Edith González-González; Octavio Rodríguez-Cortés; Adriana Gutiérrez-Hoya; María T. Vega-Ramírez; Rubén López-Santiago
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2959-2971
ISSN:: 1874-3919
Subject:: Brucella melitensis biovar Abortus; endoplasmic reticulum; gene overexpression; mutants; mutation; proteins; proteome; secretion; vacuoles; virulence
Abstract:: ... Brucella abortus is an alpha-2 proteobacteria with a type IV secretion system (T4SS) known as virB, which is necessary to gain virulence by building up a replicative vacuole associated with the endoplasmic reticulum of the host cell. A virB T4SS mutant of the B. abortus 2308 strain and its wild-type strain were grown in acid medium in order to obtain and analyze their proteomes, looking for putati ...
DOI:: 10.1016/j.jprot.2011.07.020
PubMed:: 21875698
: https://doi.org/10.1016/j.jprot.2011.07.020

57. Comparative proteomic analysis of Fasciola hepatica juveniles and Schistosoma bovis schistosomula

Author:: E. De la Torre Escudero; R. Manzano-Román; L. Valero; A. Oleaga; R. Pérez-Sánchez; A. Hernández-González; M. Siles-Lucas
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1534-1544
ISSN:: 1874-3919
Subject:: Fasciola hepatica; Schistosoma bovis; juveniles; mass spectrometry; methanol; parasites; peptides; proteins; proteome; proteomics; ruminants; schistosomula; trypsin
Abstract:: ... Protein interactions between host and parasites can influence the infection success and severity. The aim of this investigation was to identify the proteins from two trematodes potentially localized at the host–parasite interface. We performed the proteomic profiles from in vivo obtained immature lung stage Schistosoma bovis schistosomula and in vitro excysted juveniles from Fasciola hepatica, par ...
DOI:: 10.1016/j.jprot.2011.05.024
PubMed:: 21621657
: https://doi.org/10.1016/j.jprot.2011.05.024

58. Comparative proteomic analysis of four Bacillus clausii strains: Proteomic expression signature distinguishes protein profile of the strains

Author:: Rosa Lippolis; Antonio Gnoni; Anna Abbrescia; Damiano Panelli; Stefania Maiorano; Maria Stefania Paternoster; Anna Maria Sardanelli; Sergio Papa; Antonio Gaballo
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2846-2855
ISSN:: 1874-3919
Subject:: Bacillus clausii; alcohol dehydrogenase; aldehyde dehydrogenase; enzyme activity; image analysis; mass spectrometry; protein synthesis; proteins; proteome; proteomics; reverse transcriptase polymerase chain reaction; two-dimensional gel electrophoresis
Abstract:: ... A comparative proteomic approach, using two dimensional gel electrophoresis and mass spectrometry, has been developed to compare and elucidate the differences among the cellular proteomes of four closely related isogenic O/C, SIN, N/R and T, B. clausii strains during both exponential and stationary phases of growth. Image analysis of the electropherograms reveals a high degree of concordance among ...
DOI:: 10.1016/j.jprot.2011.06.032
PubMed:: 21810490
: https://doi.org/10.1016/j.jprot.2011.06.032

59. Comparative proteomics of spinal cords of rat fetuses with spina bifida aperta

Author:: Yang Fan; Lili Wang; Fenghua Zhou; Yi Zhang; Hui Li; Liping Shan; Zhengwei Yuan
Source:: Journal of proteomics 2011 v.75 no.2 pp. 668-676
ISSN:: 1874-3919
Subject:: apoptosis; cell adhesion; congenital abnormalities; fetus; gene expression regulation; mass spectrometry; messenger RNA; protein folding; proteins; proteomics; quantitative polymerase chain reaction; rats; signal transduction; spina bifida; spinal cord; therapeutics; two-dimensional gel electrophoresis; uterus
Abstract:: ... Neural tube defects (NTDs) are complex congenital anomalies of the central nervous system, with a prevalence of 5 per 10,000 worldwide. However, current therapeutics for NTDs are unsatisfactory. The neurological complications remain the main problem for therapy. Neurological dysfunction could result from the primary defect or injuries to the uncovered neural tissue in the uterus. However, the path ...
DOI:: 10.1016/j.jprot.2011.09.006
PubMed:: 21945729
: https://doi.org/10.1016/j.jprot.2011.09.006

60. Comparison of blood serum peptide enrichment methods by Tricine SDS-PAGE and mass spectrometry

Author:: Grazia Biosa; Maria Filippa Addis; Alessandro Tanca; Salvatore Pisanu; Tonina Roggio; Sergio Uzzau; Daniela Pagnozzi
Source:: Journal of proteomics 2011 v.75 no.1 pp. 93-99
ISSN:: 1874-3919
Subject:: biomarkers; blood serum; fractionation; mass spectrometry; molecular weight; peptides; polyacrylamide gel electrophoresis; proteins; solubilization; ultrafiltration
Abstract:: ... Characterisation of blood serum peptides can provide valuable information on physiological and pathological processes. However, the analysis of raw serum samples by MS results in the identification of a limited number of peptides. In order to improve sensitivity, many peptide enrichment methods have been proposed during the last ten years. Here, we present a comparison of fractionation methods aim ...
DOI:: 10.1016/j.jprot.2011.06.025
PubMed:: 21757041
: https://doi.org/10.1016/j.jprot.2011.06.025

61. Comprehensive proteomic profiling of adult Angiostrongylus costaricensis, a human parasitic nematode

Author:: Karina M. Rebello; Juliana S.L. Barros; Ester M. Mota; Paulo C. Carvalho; Jonas Perales; Henrique L. Lenzi; Ana G.C. Neves-Ferreira
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1545-1559
ISSN:: 1874-3919
Subject:: Angiostrongylus; adults; data collection; genes; heat shock proteins; helminths; human diseases; humans; pH; proteomics; stress response; Latin America
Abstract:: ... Angiostrongylus costaricensis is a nematode helminth that causes an intestinal acute inflammatory process known as abdominal angiostrongyliasis, which is a poorly understood human disease occurring in Latin America. Our aim was to study the proteomic profiles of adult parasites focusing on immunogenic proteins. Total cellular extracts from both genders showed similar 2-DE profiles, with 60% of all ...
DOI:: 10.1016/j.jprot.2011.04.031
PubMed:: 21596163
: https://doi.org/10.1016/j.jprot.2011.04.031

62. Confident identification of 3-nitrotyrosine modifications in mass spectral data across multiple mass spectrometry platforms

Author:: Bensheng Li; Jason M. Held; Birgit Schilling; Steven R. Danielson; Bradford W. Gibson
Source:: Journal of proteomics 2011 v.74 no.11 pp. 2510-2521
ISSN:: 1874-3919
Subject:: chromatography; instrumentation; mass spectrometry; peptides; post-translational modification; proteomics; spectral analysis; stoichiometry
Abstract:: ... 3-nitrotyrosine (3NT) is an oxidative posttranslational modification associated with many diseases. Determining the specific sites of this modification remains a challenge due to the low stoichiometry of 3NT modifications in biological samples. Mass spectrometry-based proteomics is a powerful tool for identifying 3NT modifications, however several reports identifying 3NT sites were later demonstra ...
DOI:: 10.1016/j.jprot.2011.04.007
PubMed:: 21514405
PubMed Central:: PMC3191283
: https://doi.org/10.1016/j.jprot.2011.04.007

63. Contribution of proteomics of Leishmania spp. to the understanding of differentiation, drug resistance mechanisms, vaccine and drug development

Author:: Daniel Paape; Toni Aebischer
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1614-1624
ISSN:: 1874-3919
Subject:: Leishmania; developmental stages; drug resistance; drugs; genome; humans; parasites; phosphorylation; proteins; proteome; proteomics; resistance mechanisms
Abstract:: ... Leishmania spp., protozoan parasites with a digenetic life cycle, cause a spectrum of diseases in humans. Recently several Leishmania spp. have been sequenced which significantly boosted the number and quality of proteomic studies conducted. Here a historic review will summarize work of the pre-genomic era and then focus on studies after genome information became available. Firstly works comparing ...
DOI:: 10.1016/j.jprot.2011.05.005
PubMed:: 21621022
: https://doi.org/10.1016/j.jprot.2011.05.005

64. Copper exposure effects on yeast mitochondrial proteome

Author:: Lucia Banci; Ivano Bertini; Simone Ciofi-Baffoni; Annamaria D'Alessandro; Deepa Jaiswal; Valeria Marzano; Sara Neri; Maurizio Ronci; Andrea Urbani
Source:: Journal of proteomics 2011 v.74 no.11 pp. 2522-2535
ISSN:: 1874-3919
Subject:: Saccharomyces cerevisiae; copper; electrophoresis; hydrogen peroxide; liquid chromatography; meta-analysis; mitochondria; oxidative stress; proteome; proteomics; stress response; tandem mass spectrometry; yeasts
Abstract:: ... Mitochondria play an important role on the entire cellular copper homeostatic mechanisms. Alteration of cellular copper levels may thus influence mitochondrial proteome and its investigation represents an important contribution to the general understanding of copper-related cellular effects. In these study we have performed an organelle targeted proteomic investigation focusing our attention on th ...
DOI:: 10.1016/j.jprot.2011.04.014
PubMed:: 21549866
: https://doi.org/10.1016/j.jprot.2011.04.014

65. CrossWork: Software-assisted identification of cross-linked peptides

Author:: Morten I. Rasmussen; Jan C. Refsgaard; Li Peng; Gunnar Houen; Peter Højrup
Source:: Journal of proteomics 2011 v.74 no.10 pp. 1871-1883
ISSN:: 1874-3919
Subject:: complement; crosslinking; data collection; peptides; protein structure; proteins
Abstract:: ... The increased interest in chemical cross-linking for probing protein structure and interaction has led to a large increase in literature describing new cross-linkers and search programs. However, this has not led to a corresponding increase in the analysis of large and complex proteins. A major obstacle is that the new cross-linkers are either not readily available and/or have a low reactivity. In ...
DOI:: 10.1016/j.jprot.2011.04.019
PubMed:: 21600323
: https://doi.org/10.1016/j.jprot.2011.04.019

66. DIGE analysis of proteome changes accompanying large resveratrol production by grapevine (Vitis vinifera cv. Gamay) cell cultures in response to methyl-β-cyclodextrin and methyl jasmonate elicitors

Author:: M.J. Martinez-Esteso; S. Sellés-Marchart; J.C. Vera-Urbina; M.A. Pedreño; R. Bru-Martinez
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1421-1436
ISSN:: 1874-3919
Subject:: Vitis vinifera; cell culture; cell growth; cyclodextrins; databases; elicitors; enzymes; extracellular space; growth retardation; methyl jasmonate; pathogenesis-related proteins; phytoalexins; proteome; resveratrol
Abstract:: ... We had previously shown that Vitis vinifera cv. Gamay cell suspension accumulates extracellularly large amounts of the phytoalexin trans-resveratrol (tR) in response to elicitation with methylated cyclodextrins (MBCD), which can be triplicated when the elicitor is combined with methyl jasmonate (MeJA). In parallel, new pathogenesis-related proteins accumulated in the apoplast-like extracellular sp ...
DOI:: 10.1016/j.jprot.2011.02.035
PubMed:: 21426946
: https://doi.org/10.1016/j.jprot.2011.02.035

67. Dasatinib, imatinib and staurosporine capture compounds — Complementary tools for the profiling of kinases by Capture Compound Mass Spectrometry (CCMS)

Author:: Jenny J. Fischer; Christian Dalhoff; Anna K. Schrey; Olivia Y. Graebner neé Baessler; Simon Michaelis; Kathrin Andrich; Mirko Glinski; Friedrich Kroll; Michael Sefkow; Mathias Dreger; Hubert Koester
Source:: Journal of proteomics 2011 v.75 no.1 pp. 160-168
ISSN:: 1874-3919
Subject:: proteins; human cell lines; humans; drugs; proteomics; sorting; phosphotransferases (kinases); mass spectrometry; liquid chromatography
Abstract:: ... Capture Compound Mass Spectrometry (CCMS) is a platform technology for the functional isolation of subproteomes. Here we report the synthesis of two new kinase Capture Compounds (CCs) based on the tyrosine-kinase specific inhibitors dasatinib and imatinib and compare their interaction profiles to that of our previously reported staurosporine-CCs. CCs are tri-functional molecules: they comprise a s ...
DOI:: 10.1016/j.jprot.2011.05.035
PubMed:: 21664307
: https://doi.org/10.1016/j.jprot.2011.05.035

68. Deciphering the iron response in Acinetobacter baumannii: A proteomics approach

Author:: Chika C. Nwugo; Jennifer A. Gaddy; Daniel L. Zimbler; Luis A. Actis
Source:: Journal of proteomics 2011 v.74 no.1 pp. 44-58
ISSN:: 1874-3919
Subject:: Acinetobacter baumannii; RNA; bacteria; biosynthesis; chelation; correlation; cultured cells; energy; gels; gene expression regulation; mass spectrometry; protein synthesis; proteomics; receptors; siderophores
Abstract:: ... Iron is an essential nutrient that plays a role in bacterial differential gene expression and protein production. Accordingly, the comparative analysis of total lysate and outer membrane fractions isolated from A. baumannii ATCC 19606ᵀ cells cultured under iron-rich and -chelated conditions using 2-D gel electrophoresis-mass spectrometry resulted in the identification of 58 protein spots different ...
DOI:: 10.1016/j.jprot.2010.07.010
PubMed:: 20692388
PubMed Central:: PMC2997898
: https://doi.org/10.1016/j.jprot.2010.07.010

69. Deconvolution of overlapping isotopic clusters improves quantification of stable isotope–labeled peptides

Author:: Salvatore Cappadona; Javier Muñoz; Wim P.E. Spee; Teck Y. Low; Shabaz Mohammed; Bas van Breukelen; Albert J.R. Heck
Source:: Journal of proteomics 2011 v.74 no.10 pp. 2204-2209
ISSN:: 1874-3919
Subject:: mass spectrometry; models; peptides; stable isotopes
Abstract:: ... High-resolution mass spectrometry and the use of stable isotopes have greatly improved our ability to quantify proteomes. Typically, the relative abundance of peptides is estimated by identifying the isotopic clusters and by comparing the peak intensities of peptide pairs. However, when the mass shift between the labeled peptides is small, there can be the possibility for overlap of the isotopic c ...
DOI:: 10.1016/j.jprot.2011.04.022
PubMed:: 21616183
: https://doi.org/10.1016/j.jprot.2011.04.022

70. Deep insights into the plant proteome by pretreatment with combinatorial hexapeptide ligand libraries

Author:: Andreas Fröhlich; Christian Lindermayr
Source:: Journal of proteomics 2011 v.74 no.8 pp. 1182-1189
ISSN:: 1874-3919
Subject:: proteins; proteome; fractionation; humans; proteomics; technology
Abstract:: ... Proteome analyses suffer from the large complexity of even small proteomes. Additionally, in many protein samples a few highly abundant proteins are hindering detailed proteomic studies, since they mask low abundant proteins. Recently, a new technology has emerged, which reduces dynamic range of protein concentrations within a given sample using combinatorial hexapeptide ligand libraries (CPLLs). ...
DOI:: 10.1016/j.jprot.2011.02.019
PubMed:: 21354349
: https://doi.org/10.1016/j.jprot.2011.02.019

71. Deeper in the human cornea proteome using nanoLC–Orbitrap MS/MS: An improvement for future studies on cornea homeostasis and pathophysiology

Author:: Stéphane D. Galiacy; Carine Froment; Emmanuelle Mouton-Barbosa; Angélique Erraud; Karima Chaoui; Laurence Desjardins; Bernard Monsarrat; François Malecaze; Odile Burlet-Schiltz
Source:: Journal of proteomics 2011 v.75 no.1 pp. 81-92
ISSN:: 1874-3919
Subject:: alcohols; cornea; corneal diseases; data collection; genes; homeostasis; humans; oxidative stress; pathophysiology; proteins; proteome; proteomics
Abstract:: ... The cornea is a transparent, avascular, and highly specialized connective tissue that provides the majority of light refraction in the optical system of the eye. The human cornea is composed of several layers interacting in a complex manner and possessing specific functions, like eye protection and optical clearness. Only few proteomic studies of mammalian cornea have been performed leading to the ...
DOI:: 10.1016/j.jprot.2011.09.020
PubMed:: 21989269
: https://doi.org/10.1016/j.jprot.2011.09.020

72. Determination of the Plasmodium vivax schizont stage proteome

Author:: Wanlapa Roobsoong; Sittiruk Roytrakul; Jetsumon Sattabongkot; Jianyong Li; Rachanee Udomsangpetch; Liwang Cui
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1701-1710
ISSN:: 1874-3919
Subject:: Plasmodium vivax; Western blotting; antibodies; antigens; antiserum; binding proteins; blood serum; drugs; genome; humoral immunity; malaria; parasites; patients; protein synthesis; proteome; tandem mass spectrometry; two-dimensional gel electrophoresis
Abstract:: ... With the genome of the malaria parasite Plasmodium vivax sequenced, it is important to determine the proteomes of the parasite in order to assist efforts in antigen and drug target discovery. Since a method for continuous culture of P. vivax parasite is not available, we tried to study the proteome of the erythrocytic stages using fresh parasite isolates from patients. In schizont-enriched samples ...
DOI:: 10.1016/j.jprot.2011.03.035
PubMed:: 21515433
PubMed Central:: PMC3156846
: https://doi.org/10.1016/j.jprot.2011.03.035

73. Development of quantitative plasma N-glycoproteomics using label-free 2-D LC-MALDI MS and its applicability for biomarker discovery in hepatocellular carcinoma

Author:: Takeshi Ishihara; Isao Fukuda; Atsushi Morita; Yoshihiko Takinami; Hiroyuki Okamoto; Shin-Ichiro Nishimura; Yoshito Numata
Source:: Journal of proteomics 2011 v.74 no.10 pp. 2159-2168
ISSN:: 1874-3919
Subject:: detection limit; ferroxidase; hepatoma; blood proteins; humans; biomarkers; quantitative analysis; bioinformatics; patients; computer software; proteomics; glycopeptides
Abstract:: ... There has been rapid progress in the development of clinical proteomic methodologies with improvements in mass spectrometric technologies and bioinformatics, leading to many new methodologies for biomarker discovery from human plasma. However, it is not easy to find new biomarkers because of the wide dynamic range of plasma proteins and the need for their quantification. Here, we report a new meth ...
DOI:: 10.1016/j.jprot.2011.06.010
PubMed:: 21704746
: https://doi.org/10.1016/j.jprot.2011.06.010

74. Developments for a growing Japanese patient population: Facilitating new technologies for future health care

Author:: Harubumi Kato; Toshihide Nishimura; Norihiko Ikeda; Tesshi Yamada; Tadashi Kondo; Nagahiro Saijo; Kazuto Nishio; Junichiro Fujimoto; Masaharu Nomura; Yoshiya Oda; Bertil Lindmark; Jiro Maniwa; Hitoshi Hibino; Michiaki Unno; Toshinori Ito; Yoshiki Sawa; Hiromasa Tojo; Shin Egawa; Goutham Edula; Mary Lopez; Murray Wigmore; Naohiko Inase; Yasuyuki Yoshizawa; Fumio Nomura; György Marko-Varga
Source:: Journal of proteomics 2011 v.74 no.6 pp. 759-764
ISSN:: 1874-3919
Subject:: diagnostic techniques; elderly; health care costs; drug therapy; image analysis; cardiovascular diseases; lung neoplasms; biomarkers; drugs; medicine; infrastructure; models; technology; phenotype; patients; proteomics; computed tomography; mortality; Japan
Abstract:: ... Lung cancer, COPD and cardiovascular diseases are highlighted as some of the most common disease that cause mortality, and for that reason are the most active areas for drug development. This perspective paper overviews the urgent need to develop a health care system for a rapidly growing patient population in Japan, including forthcoming demands on clinical care, expecting outcomes, and economics ...
DOI:: 10.1016/j.jprot.2010.12.006
PubMed:: 21184850
: https://doi.org/10.1016/j.jprot.2010.12.006

75. Different target surfaces for the analysis of peptides, peptide mixtures and peptide mass fingerprints by AP-MALDI ion trap-mass spectrometry

Author:: Ernst Pittenauer; Alexander Kassler; Roland Haubner; Günter Allmaier
Source:: Journal of proteomics 2011 v.74 no.7 pp. 975-981
ISSN:: 1874-3919
Subject:: desorption; electron microscopy; ionization; peptides; proteomics; roughness; spectroscopy; stainless steel; surface roughness; titanium
Abstract:: ... The desorption/ionization behavior of individual peptides, an equimolare peptide mixture and a tryptic digest was investigated by AP-MALDI-IT-MS using four different target materials (gold-covered stainless steel (SS), titanium nitride-covered SS, hand-polished SS, and microdiamond-covered hardmetal) under identical conditions. Gold-covered as well as polished SS targets yielded comparable mass sp ...
DOI:: 10.1016/j.jprot.2010.10.003
PubMed:: 20970531
: https://doi.org/10.1016/j.jprot.2010.10.003

76. Differential expression of Trypanosoma cruzi I associated with clinical forms of Chagas disease: Overexpression of oxidative stress proteins in acute patient isolate

Author:: M.L. Díaz; A. Solari; C.I. González
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1673-1682
ISSN:: 1874-3919
Subject:: Chagas disease; Trypanosoma cruzi; Western blotting; adhesion; amastigotes; antioxidants; biomarkers; cytoskeleton; disease course; drugs; gene expression regulation; genetic variation; geographical distribution; oxidative stress; patients; peroxidase; protein synthesis; proteins; trypomastigotes; virulence; Colombia
Abstract:: ... Chagas disease has a variable clinical course with different manifestations and heterogenous geographical distribution. Some studies suggest that this clinical variability could be influenced by the genetic variability of T. cruzi. Here we present the differential protein expression among trypomastigotes and amastigotes of T. cruzi group I isolates from patients with acute and chronic form of Chag ...
DOI:: 10.1016/j.jprot.2011.05.001
PubMed:: 21642025
: https://doi.org/10.1016/j.jprot.2011.05.001

77. Differential proteomics of plant development

Author:: Tomáš Takáč; Tibor Pechan; Jozef Šamaj
Source:: Journal of proteomics 2011 v.74 no.5 pp. 577-588
ISSN:: 1874-3919
Subject:: cell differentiation; cell division; cell fractionation; cytoskeleton; molecular cloning; plant development; protein folding; proteins; proteome; proteomics
Abstract:: ... In this mini-review, recent advances in plant developmental proteomics are summarized. The growing interest in plant proteomics continually produces large numbers of developmental studies on plant cell division, elongation, differentiation, and formation of various organs. The brief overview of changes in proteome profiles emphasizes the participation of stress-related proteins in all developmenta ...
DOI:: 10.1016/j.jprot.2011.02.002
PubMed:: 21315196
: https://doi.org/10.1016/j.jprot.2011.02.002

78. Digestion protocol for small protein amounts for nano-HPLC-MS(MS) analysis

Author:: Lilla Turiák; Oliver Ozohanics; Fabio Marino; László Drahos; Károly Vékey
Source:: Journal of proteomics 2011 v.74 no.7 pp. 942-947
ISSN:: 1874-3919
Subject:: evaporation; high performance liquid chromatography; protein content; proteins; tandem mass spectrometry
Abstract:: ... A miniaturized tryptic digestion protocol for protein analysis has been developed, which works well for small amounts of proteins using small volume of reagents. The protocol starts from 10μL sample volume with total protein content in the low pmol or fmol range (alternatively expressed, in the low ng range). After adding various reagents the total volume of the tryptic digest will increase to 15μ ...
DOI:: 10.1016/j.jprot.2011.01.007
PubMed:: 21256993
: https://doi.org/10.1016/j.jprot.2011.01.007

79. Direct characterization of target podocyte antigens and auto-antibodies in human membranous glomerulonephritis: Alfa-enolase and borderline antigens

Author:: Maurizio Bruschi; Maria Luisa Carnevali; Corrado Murtas; Giovanni Candiano; Andrea Petretto; Marco Prunotto; Rita Gatti; Lucia Argentiero; Riccardo Magistroni; Giacomo Garibotto; Francesco Scolari; Pietro Ravani; Loreto Gesualdo; Landino Allegri; Gian Marco Ghiggeri
Source:: Journal of proteomics 2011 v.74 no.10 pp. 2008-2017
ISSN:: 1874-3919
Subject:: antigens; autoimmunity; blood serum; electron microscopy; glomerulonephritis; humans; immunoglobulin G; pathogenesis; patients
Abstract:: ... The identification of glomerular auto-antigens in idiopathic human membranous glomerulonephritis (MGN) is a crucial step towards the definition of the mechanisms of the disease. Recent ‘in vivo’ studies demonstrated a heterogeneous composition of glomerular immune-deposits in MGN biopsies only a part of which have been characterized. We studied with a proteomical approach IgGs eluted from laser ca ...
DOI:: 10.1016/j.jprot.2011.05.021
PubMed:: 21640210
: https://doi.org/10.1016/j.jprot.2011.05.021

80. Discovery of putative pancreatic cancer biomarkers using subcellular proteomics

Author:: Kimberly Q. McKinney; Yong-Yook Lee; Hyun-Su Choi; Gale Groseclose; David A. Iannitti; John B. Martinie; Mark W. Russo; Deborah H. Lundgren; David K. Han; Herbert L. Bonkovsky; Sun-Il Hwang
Source:: Journal of proteomics 2011 v.74 no.1 pp. 79-88
ISSN:: 1874-3919
Subject:: biomarkers; computer software; cytoskeleton; cytosol; fractionation; gel electrophoresis; gene expression regulation; liquid chromatography; molecular weight; pancreas; pancreatic neoplasms; patients; protein synthesis; proteins; proteomics; resection; statistical analysis; tandem mass spectrometry; trypsin
Abstract:: ... Pancreatic cancer (PC) is a highly aggressive disease that frequently remains undetected until it has progressed to an advanced, systemic stage. Successful treatment of PC is hindered by the lack of early detection. The application of proteomic analysis to PC combined with subcellular fractionation has introduced new possibilities in the field of biomarker discovery. We utilized matched pairs of p ...
DOI:: 10.1016/j.jprot.2010.08.006
PubMed:: 20807598
: https://doi.org/10.1016/j.jprot.2010.08.006

81. Distinct cell surface proteome profiling by biotin labeling and glycoprotein capturing

Author:: Kohji Nagano; Takashi Shinkawa; Kuniyasu Kato; Noriyuki Inomata; Nami Yabuki; Masayuki Haramura
Source:: Journal of proteomics 2011 v.74 no.10 pp. 1985-1993
ISSN:: 1874-3919
Subject:: biotin; glycoproteins; glycosylation; membrane proteins; plasma membrane; proteome; surface proteins
Abstract:: ... We performed here MS-based cell surface proteome profiling of HCT-116 cells by two distinct methods based on biotin labeling and glycoprotein capturing. In total, 742 biotinylated and 219 glycosylated proteins were identified by the biotin labeling and glycoprotein capturing, of which 224 and 138 proteins known to be located on plasma membrane were included, respectively, according to ingenuity pa ...
DOI:: 10.1016/j.jprot.2011.05.019
PubMed:: 21621025
: https://doi.org/10.1016/j.jprot.2011.05.019

82. Distinction of thioredoxin transnitrosylation and denitrosylation target proteins by the ICAT quantitative approach

Author:: Changgong Wu; Andrew Myles Parrott; Tong Liu; Mohit Raja Jain; Yanfei Yang; Junichi Sadoshima; Hong Li
Source:: Journal of proteomics 2011 v.74 no.11 pp. 2498-2509
ISSN:: 1874-3919
Subject:: biotin; cyclophilins; peptides; peroxiredoxin; proteins
Abstract:: ... S-Nitrosylation is a reversible PTM for regulating protein function. Thioredoxin-1 (Trx1) catalyzes either transnitrosylation or denitrosylation of specific proteins, depending on the redox status of the cysteines within its conserved oxidoreductase CXXC motif. With a disulfide bond formed between the two catalytic cysteines, Trx1 is not only inactive as a denitrosylase, but it may also be nitrosy ...
DOI:: 10.1016/j.jprot.2011.06.001
PubMed:: 21704743
PubMed Central:: PMC3253718
: https://doi.org/10.1016/j.jprot.2011.06.001

83. Diversity of anti-haemostatic proteins in the salivary glands of Rhodnius species transmitters of Chagas disease in the greater Amazon

Author:: Ana C.M. Bussacos; Ernesto S. Nakayasu; Mariana M. Hecht; Juliana A. Parente; Célia M.A. Soares; Antônio R.L. Teixeira; Igor C. Almeida
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1664-1672
ISSN:: 1874-3919
Subject:: Rhodnius; Trypanosoma cruzi; blood; glutathione; humans; insecticides; insects; myo-inositol; platelet aggregation; proteins; salivary glands; sialome; transcriptome
Abstract:: ... The triatomines in the tribe Rhodniini are the main vectors of the Trypanosoma cruzi to humans in recent outbreaks of acute Chagas disease in the Amazon. These insects dwelling in palm trees do not colonize the human domicile. Their success to transmit the infection relies partially on the efficacy of their salivary gland apparatuses. Here we show the transcriptome of the Rhodnius brethesi and Rho ...
DOI:: 10.1016/j.jprot.2011.06.022
PubMed:: 21742069
: https://doi.org/10.1016/j.jprot.2011.06.022

84. Diversity of human skeletal muscle in health and disease: Contribution of proteomics

Author:: Cecilia Gelfi; Michele Vasso; Paolo Cerretelli
Source:: Journal of proteomics 2011 v.74 no.6 pp. 774-795
ISSN:: 1874-3919
Subject:: actin; animal models; biomarkers; cold; enzymes; exercise; functional properties; humans; hypoxia; insulin resistance; muscles; myosin; myositis; patients; proteome; proteomics; skeletal muscle; tropomyosins
Abstract:: ... Muscle represents a large fraction of the human body mass. It is an extremely heterogeneous tissue featuring in its contractile structure various proportions of heavy- and light-chain slow type 1 and fast types 2A and 2X myosins, actins, tropomyosins, and troponin complexes as well as metabolic proteins (enzymes and most of the players of the so-called excitation–transcription coupling). Muscle is ...
DOI:: 10.1016/j.jprot.2011.02.028
PubMed:: 21414428
: https://doi.org/10.1016/j.jprot.2011.02.028

85. Docosohaexanoic acid-supplemented PACA44 cell lines and over-activation of Krebs cycle: An integrated proteomic, metabolomic and interactomic overview

Author:: Angelo D'Alessandro; Gian Maria D'Amici; Anna Maria Timperio; Nicolò Merendino; Lello Zolla
Source:: Journal of proteomics 2011 v.74 no.10 pp. 2138-2158
ISSN:: 1874-3919
Subject:: NADP (coenzyme); apoptosis; cytoskeleton; energy flow; enzymes; extrusion; fatty acids; glutathione; glycolysis; growth retardation; homeostasis; humans; metabolomics; oxidative stress; pancreatic neoplasms; pentose phosphate cycle; proteomics; tricarboxylic acid cycle
Abstract:: ... Recent investigations have pointed out the ability of fatty acids, in particular of docosohaexanoic acid (DHA), to induce growth inhibition and apoptosis in the human PaCa-44 pancreatic cancer cell line through a series of mechanisms which has been hypothesized to mimic apoptosis. While preliminary evidences indicated the involvement of lipid-targeting oxidative stress in DHA-induced apoptotic pro ...
DOI:: 10.1016/j.jprot.2011.06.006
PubMed:: 21723426
: https://doi.org/10.1016/j.jprot.2011.06.006

86. Drug localization in different lung cancer phenotypes by MALDI mass spectrometry imaging

Author:: György Marko-Varga; Thomas E. Fehniger; Melinda Rezeli; Balázs Döme; Thomas Laurell; Ákos Végvári
Source:: Journal of proteomics 2011 v.74 no.7 pp. 982-992
ISSN:: 1874-3919
Subject:: adenocarcinoma; drug therapy; drugs; epidermal growth factor receptors; image analysis; instrumentation; lung neoplasms; matrix-assisted laser desorption-ionization mass spectrometry; mortality; patients; phenotype; physicochemical properties; risk factors; smoking (habit); somatic mutation
Abstract:: ... Lung cancer is a common cause of cancer mortality in the world, largely due to the risk factor of tobacco smoking. The drug therapy at the molecular level includes targeting the epidermal growth factor receptor (EGFR) tyrosine kinase activity by using inhibitors, such as erlotinib (Tarceva) and gefitinib (Iressa). The heterogeneity of disease phenotypes and the somatic mutations presented in patie ...
DOI:: 10.1016/j.jprot.2011.03.019
PubMed:: 21440690
: https://doi.org/10.1016/j.jprot.2011.03.019

87. Early biosignature of oxidative stress in the retinal pigment epithelium

Author:: Hilal Arnouk; Hyunju Lee; Ruonan Zhang; Hyewon Chung; Richard C. Hunt; Wan Jin Jahng
Source:: Journal of proteomics 2011 v.74 no.2 pp. 254-261
ISSN:: 1874-3919
Subject:: cell differentiation; energy metabolism; epithelium; gene expression regulation; homeostasis; mass spectrometry; models; oxidative stress; phagocytosis; photoreceptors; polyacrylamide gel electrophoresis; protein folding; protein synthesis; proteome; proteomics; retinal diseases
Abstract:: ... The retinal pigment epithelium (RPE) is essential for retinoid recycling and phagocytosis of photoreceptors. Understanding of proteome changes that mediate oxidative stress-induced degeneration of RPE cells may provide further insight into the molecular mechanisms of retinal diseases. In the current study, comparative proteomics has been applied to investigate global changes of RPE proteins under ...
DOI:: 10.1016/j.jprot.2010.11.004
PubMed:: 21074641
PubMed Central:: PMC5173386
: https://doi.org/10.1016/j.jprot.2010.11.004

88. Early dysregulation of the mitochondrial proteome in a mouse model of Alzheimer's disease

Author:: Jose L. Chou; Deepa V. Shenoy; Nicy Thomas; Pankaj K. Choudhary; Frank M. LaFerla; Steven R. Goodman; Gail A.M. Breen
Source:: Journal of proteomics 2011 v.74 no.4 pp. 466-479
ISSN:: 1874-3919
Subject:: Alzheimer disease; amyloid; animal models; apoptosis; fatty acids; gel electrophoresis; gene expression regulation; genetically modified organisms; glycolysis; humans; ion transport; mice; mitochondria; mutation; oxidation; oxidative phosphorylation; oxidative stress; pathogenesis; protein synthesis; proteome; proteomics; pyruvic acid; tandem mass spectrometry; transgenes; tricarboxylic acid cycle
Abstract:: ... Mitochondrial structural and functional alterations appear to play to an important role in the pathogenesis of Alzheimer's disease (AD). In the present study, we used a quantitative comparative proteomic profiling approach to analyze changes in the mitochondrial proteome in AD. A triple transgenic mouse model of AD (3xTg-AD) which harbors mutations in three human transgenes, APPSwₑ, PS1M₁₄₆V and T ...
DOI:: 10.1016/j.jprot.2010.12.012
PubMed:: 21237293
: https://doi.org/10.1016/j.jprot.2010.12.012

89. Effect of diethylcarbamazine, butylated hydroxy anisole and methyl substituted chalcone on filarial parasite Setaria cervi: Proteomic and biochemical approaches

Author:: Sushma Rathaur; Marshleen Yadav; Neetu Singh; Alka Singh
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1595-1606
ISSN:: 1874-3919
Subject:: DNA fragmentation; Setaria cervi; apoptosis; butylated hydroxyanisole; chalcone; cytochrome P-450; cytotoxicity; death; diethylcarbamazine; enzymes; homeostasis; metabolic detoxification; neutralization; nitric oxide; oxidative stress; parasites; proteomics; viability
Abstract:: ... For survival, parasite exerts several lines of defense of which drug neutralization is one of the major phenomena. Lack of phase I cytochrome P450 in some of the nematode render them depend on the phase II detoxification system involving GST as a major detoxifying enzymes. In present study, the antifilarial DEC, phenolic compound BHA and methyl chalcone have been evaluated for proteomic and bioche ...
DOI:: 10.1016/j.jprot.2011.04.020
PubMed:: 21571110
: https://doi.org/10.1016/j.jprot.2011.04.020

90. Effect of post-harvest heat treatment on proteome change of peach fruit during ripening

Author:: Li Zhang; Zhifang Yu; Li Jiang; Juan Jiang; Haibo Luo; Linran Fu
Source:: Journal of proteomics 2011 v.74 no.7 pp. 1135-1149
ISSN:: 1874-3919
Subject:: temperature; proteins; proteome; peaches; stress response; glycolysis; proteomics; gene expression; gels; ripening; cell structures; heat treatment; electrophoresis; databases; fruiting
Abstract:: ... The extracted proteins from the heat-treated peach fruit (dipped in hot water at 48°C for 10min and then stored at room temperature (20°C–25°C) for up to 6days) were used for proteomic analysis in order to understand the response of post-harvest peach fruit to heat treatment during ripening stage at proteomic level. After two dimensional gels electrophoresis (2-DE) was conducted, more than 600 pro ...
DOI:: 10.1016/j.jprot.2011.04.012
PubMed:: 21550427
: https://doi.org/10.1016/j.jprot.2011.04.012

91. Effects of Clostridium difficile Toxin A on the proteome of colonocytes studied by differential 2D electrophoresis

Author:: Johannes J. Zeiser; Jennifer Klodmann; Hans-Peter Braun; Ralf Gerhard; Ingo Just; Andreas Pich
Source:: Journal of proteomics 2011 v.75 no.2 pp. 469-479
ISSN:: 1874-3919
Subject:: Clostridium difficile; actin; colitis; cytoskeleton; diarrhea; electrophoresis; humans; metabolism; oxidative stress; pathogens; proteome; stress response; ubiquitin; virulence
Abstract:: ... Clostridium difficile is a spore-forming anaerobic pathogen, commonly associated with severe diarrhea or life-threatening pseudomembraneous colitis. Its main virulence factors are the single-chain, multi-domain toxin A (TcdA) and B (TcdB). Their glucosyltransferase domain selectively inactivates Rho proteins leading to a reorganization of the cytoskeleton. To study exclusively glucosyltransferase- ...
DOI:: 10.1016/j.jprot.2011.08.012
PubMed:: 21890007
: https://doi.org/10.1016/j.jprot.2011.08.012

92. Emerging nanoproteomics approaches for disease biomarker detection: A current perspective

Author:: Sandipan Ray; Panga Jaipal Reddy; Sandeep Choudhary; Dinesh Raghu; Sanjeeva Srivastava
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2660-2681
ISSN:: 1874-3919
Subject:: biomarkers; carbon nanotubes; disease course; early diagnosis; gold; human diseases; humans; nanoparticles; nanowires; nucleotide sequences; pathogens; proteomics; quantum dots; silicon
Abstract:: ... Availability of genome sequence of human and different pathogens has advanced proteomics research for various clinical applications. One of the prime goals of proteomics is identification and characterization of biomarkers for cancer and other fatal human diseases to aid an early diagnosis and monitor disease progression. However, rapid detection of low abundance biomarkers from the complex biolog ...
DOI:: 10.1016/j.jprot.2011.04.027
PubMed:: 21596164
: https://doi.org/10.1016/j.jprot.2011.04.027

93. Ending the drought: New strategies for improving the flow of affordable, effective antivenoms in Asia and Africa

Author:: David J. Williams; José-María Gutiérrez; Juan J. Calvete; Wolfgang Wüster; Kavi Ratanabanangkoon; Owen Paiva; Nicholas I. Brown; Nicholas R. Casewell; Robert A. Harrison; Paul D. Rowley; Mark O'Shea; Simon D. Jensen; Kenneth D. Winkel; David A. Warrell
Source:: Journal of proteomics 2011 v.74 no.9 pp. 1735-1767
ISSN:: 1874-3919
Subject:: World Health Organization; antigens; antivenoms; children; clinical trials; community health; drought; funding; humans; leadership; medicine; men; patients; poverty; proteomics; snake bites; snakes; toxins; venoms; viability; women; Africa; Asia
Abstract:: ... The development of snake antivenoms more than a century ago should have heralded effective treatment of the scourge of snakebite envenoming in impoverished, mostly rural populations around the world. That snakebite still exists today, as a widely untreated illness that maims, kills and terrifies men, women and children in vulnerable communities, is a cruel anachronism. Antivenom can be an effectiv ...
DOI:: 10.1016/j.jprot.2011.05.027
PubMed:: 21640209
: https://doi.org/10.1016/j.jprot.2011.05.027

94. Farm animal proteomics — A review

Author:: Emøke Bendixen; Marianne Danielsen; Kristin Hollung; Elisabetta Gianazza; Ingrid Miller
Source:: Journal of proteomics 2011 v.74 no.3 pp. 282-293
ISSN:: 1874-3919
Subject:: animal production; animal products; cattle; food production; physiology; proteomics; swine
Abstract:: ... In agricultural sciences as in all other areas of life science, the implementation of proteomics and other post-genomic tools is an important step towards more detailed understanding of the complex biological systems that control physiology and pathology of living beings. Farm animals are raised in large-scale operations, with the aim to obtain animal products for human consumption. Hence, underst ...
DOI:: 10.1016/j.jprot.2010.11.005
PubMed:: 21112346
: https://doi.org/10.1016/j.jprot.2010.11.005

95. Filter-aided sample preparation with dimethyl labeling to identify and quantify milk fat globule membrane proteins

Author:: Jing Lu; S. Boeren; S.C. de Vries; H.J.F. van Valenberg; J. Vervoort; K. Hettinga
Source:: Journal of proteomics 2011 v.75 no.1 pp. 34-43
ISSN:: 1874-3919
Subject:: carbohydrates; casein; cattle; environmental factors; fat globules; lipids; membrane proteins; micelles; milk; milk fat; minerals; protein composition; proteomics; vitamins
Abstract:: ... Bovine milk is a major nutrient source in many countries and it is produced at an industrial scale. Milk is a complex mixture of proteins, fats, carbohydrates, vitamins and minerals. The composition of the bovine milk samples can vary depending on the genetic makeup of the bovine species as well as environmental factors. It is therefore important to study the qualitative and quantitative differenc ...
DOI:: 10.1016/j.jprot.2011.07.031
PubMed:: 21907314
: https://doi.org/10.1016/j.jprot.2011.07.031

96. Francisella tularensis membrane complexome by blue native/SDS-PAGE

Author:: Jiri Dresler; Jana Klimentova; Jiri Stulik
Source:: Journal of proteomics 2011 v.75 no.1 pp. 257-269
ISSN:: 1874-3919
Subject:: Francisella tularensis; bacteria; biosynthesis; cell division; mass spectrometry; membrane proteins; microbial physiology; oxidative phosphorylation; pathogenesis; phospholipids; polyacrylamide gel electrophoresis; stoichiometry; tularemia; virulence
Abstract:: ... The study of membrane proteins and membrane protein complexes (MPC) provides crucial information in the field of bacterial physiology and pathogenesis research. The method of blue native polyacrylamide gel electrophoresis and its combination with SDS-PAGE (BN/SDS-PAGE) were here employed to study the membrane complexome of an intracellular bacterium Francisella tularensis, the causative agent of a ...
DOI:: 10.1016/j.jprot.2011.05.006
PubMed:: 21601022
: https://doi.org/10.1016/j.jprot.2011.05.006

97. From SELDI-TOF MS to protein identification by on-chip elution

Author:: Mari Mæland Nilsen; Kai-Erik Uleberg; Emiel A.M. Janssen; Jan P.A. Baak; Odd Ketil Andersen; Anne Hjelle
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2995-2998
ISSN:: 1874-3919
Subject:: Gadus morhua; biomarkers; cation exchange; cod (fish); peptides; proteins
Abstract:: ... SELDI-TOF MS has been demonstrated as a powerful tool for biomarker discovery. However, a major disadvantage of SELDI-TOF MS is the lack of direct identification of the discriminatory peaks discovered. We describe a novel experimental identification strategy where peptides/proteins captured to a weak cation exchange ProteinArray surface (CM10) are eluted, and thereafter identified by utilizing a s ...
DOI:: 10.1016/j.jprot.2011.06.027
PubMed:: 21798383
: https://doi.org/10.1016/j.jprot.2011.06.027

98. From in silico target prediction to multi-target drug design: Current databases, methods and applications

Author:: Alexios Koutsoukas; Benjamin Simms; Johannes Kirchmair; Peter J. Bond; Alan V. Whitmore; Steven Zimmer; Malcolm P. Young; Jeremy L. Jenkins; Meir Glick; Robert C. Glen; Andreas Bender
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2554-2574
ISSN:: 1874-3919
Subject:: bioactive properties; databases; drugs; prediction; protein structure; screening
Abstract:: ... Given the tremendous growth of bioactivity databases, the use of computational tools to predict protein targets of small molecules has been gaining importance in recent years. Applications span a wide range, from the ‘designed polypharmacology’ of compounds to mode-of-action analysis. In this review, we firstly survey databases that can be used for ligand-based target prediction and which have gro ...
DOI:: 10.1016/j.jprot.2011.05.011
PubMed:: 21621023
: https://doi.org/10.1016/j.jprot.2011.05.011

99. Fucosylated glycoproteomic approach to identify a complement component 9 associated with squamous cell lung cancer (SQLC)

Author:: Arul Narayanasamy; Jung-Mo Ahn; Hye-Jin Sung; Deok-Hoon Kong; Kwon-Soo Ha; Soo-Youn Lee; Je-Yoel Cho
Source:: Journal of proteomics 2011 v.74 no.12 pp. 2948-2958
ISSN:: 1874-3919
Subject:: Western blotting; biomarkers; complement; enzyme-linked immunosorbent assay; glycoproteins; humans; hybrids; lectins; lung neoplasms; mortality; patients; polyacrylamide gel electrophoresis; proteomics
Abstract:: ... Human lung cancer is a major cause of cancer mortality worldwide. Understanding the pathophysiological features and the development of novel biomarkers for diagnosis as well as treatment are major tasks. In the present study, sera from ten SQLC patients and healthy control (HEC) were collected and pooled, respectively. The pooled sera were depleted via an immunoaffinity method and further subjecte ...
DOI:: 10.1016/j.jprot.2011.07.019
PubMed:: 21840429
: https://doi.org/10.1016/j.jprot.2011.07.019

100. Functional analysis of beef tenderness

Author:: Nicolas Guillemin; Muriel Bonnet; Catherine Jurie; Brigitte Picard
Source:: Journal of proteomics 2011 v.75 no.2 pp. 352-365
ISSN:: 1874-3919
Subject:: beef; genomics; meat tenderness; proteins; tenderizing
Abstract:: ... Meat tenderness represents a complex assembly of different cellular pathways. As a consequence, genomics studies have revealed many different proteins considered as tenderness markers. So it is difficult to have an overview of tenderness in terms of cellular pathways. In this work cellular pathways of tenderness were analyzed, an interactome of 330 proteins was designed, and explanations of tender ...
DOI:: 10.1016/j.jprot.2011.07.026
PubMed:: 21855665
: https://doi.org/10.1016/j.jprot.2011.07.026

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1. Resolution and identification of major peanut allergens using a combination of fluorescence two-dimensional differential gel electrophoresis, Western blotting and Q-TOF mass spectrometry

2. The neuropeptidomics of Ixodes scapularis synganglion

3. Thioredoxin targets in plants: The first 30 years

4. 2-D DIGE uterine endothelial proteomic profile for maternal chronic binge-like alcohol exposure

5. 2-D difference gel electrophoresis approach to assess protein expression profiles in Bathymodiolus azoricus from Mid-Atlantic Ridge hydrothermal vents

6. 2-DE-based proteomic analysis of common bean (Phaseolus vulgaris L.) seeds

7. 2-DE-based proteomic investigation of the saliva of the Amazonian triatomine vectors of Chagas disease: Rhodnius brethesi and Rhodnius robustus

8. 2D-DIGE analysis of phospho-enriched fractions from dasatinib-treated melanoma cell lines

9. A comparative proteome analysis links tyrosine kinase 2 (Tyk2) to the regulation of cellular glucose and lipid metabolism in response to poly(I:C)

10. A differential proteomic approach identifies structural and functional components that contribute to the differentiation of brain capillary endothelial cells

11. A gel-based proteomic method reveals several protein pathway abnormalities in fetal Down syndrome brain

12. A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer

13. A multidisciplinary study on the effects of phloem-limited viruses on the agronomical performance and berry quality of Vitis vinifera cv. Nebbiolo

14. A novel polyclonal antibody library for expression profiling of poorly characterized, membrane and secreted human proteins

15. A proteomic analysis of the wound response in Medicago leaves reveals the early activation of a ROS-sensitive signal pathway

16. A proteomic approach to investigate the differential antigenic profile of two Coxiella burnetii strains

17. A proteomic study of in-root interactions between chickpea pathogens: The root-knot nematode Meloidogyne artiellia and the soil-borne fungus Fusarium oxysporum f. sp. ciceris race 5

18. A proteomics view of programmed cell death mechanisms during host–parasite interactions

19. A proteomics view on the role of drought-induced senescence and oxidative stress defense in enhanced stem reserves remobilization in wheat

20. A quantitative view of the morphological phases of Paracoccidioides brasiliensis using proteomics

21. A quantitative view on Mycobacterium leprae antigens by proteomics

22. A workflow for peptide-based proteomics in a poorly sequenced plant: A case study on the plasma membrane proteome of banana

23. Abundance of tegument surface proteins in the human blood fluke Schistosoma mansoni determined by QconCAT proteomics

24. Activity-based proteomics: Identification of ABHD11 and ESD activities as potential biomarkers for human lung adenocarcinoma

25. Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani

26. Advances in top-down proteomics for disease biomarker discovery

27. Agricultural recovery of a formerly radioactive area: II. Systematic proteomic characterization of flax seed development in the remediated Chernobyl area

28. Alteration of plasma membrane-bound redox systems of iron deficient pea roots by chitosan

29. An analysis of the Caenorhabditis elegans lipid raft proteome using geLC-MS/MS

30. An in vivo characterization of colostrum protein uptake in porcine gut during early lactation

31. An insight into the sialotranscriptome and proteome of the coarse bontlegged tick, Hyalomma marginatum rufipes

32. An integrated proteomics and genomics analysis to unravel a heterogeneous platelet secretion defect

33. Analysis of proteome changes in doxorubicin-treated adult rat cardiomyocyte

34. Analysis of site-specific N-homocysteinylation of human serum albumin in vitro and in vivo using MALDI-ToF and LC-MS/MS mass spectrometry

35. Analysis of the variability of human normal urine by 2D-GE reveals a “public” and a “private” proteome

36. Annexin C4 in A. Fumigatus: A proteomics approach to understand the function

37. Application of proteomics to the assessment of the response to ionising radiation in Arabidopsis thaliana

38. Assessment of allergenicity of diploid and hexaploid wheat genotypes: Identification of allergens in the albumin/globulin fraction

39. Assigning statistical significance to proteotypic peptides via database searches

40. Back to the basics: Maximizing the information obtained by quantitative two dimensional gel electrophoresis analyses by an appropriate experimental design and statistical analyses

41. Bacterial proteins with cleaved or uncleaved signal peptides of the general secretory pathway

42. Bioinformatic strategies for unambiguous identification of prostate specific antigen in clinical samples

43. Biomarkers of disease and post-mortem changes — Heat stabilization, a necessary tool for measurement of protein regulation

44. Biomolecular characterization of allergenic proteins in snow crab (Chionoecetes opilio) and de novo sequencing of the second allergen arginine kinase using tandem mass spectrometry

45. Boric acid gel enrichment of glycosylated proteins in human wound fluids

46. Challenges and solutions for the identification of membrane proteins in non-model plants

47. Changes in the leaf proteome profile of Mentha arvensis in response to Alternaria alternata infection

48. Changes in the plant proteome resulting from salt stress: Toward the creation of salt-tolerant crops?

49. Characterisation of the variation of mouse brain proteome by two-dimensional electrophoresis

50. Characterization of mitochondrial proteome in a severe case of ETF-QO deficiency

51. Characterization of the B-Raf interactome in mouse hippocampal neuronal cells

52. Charge state-selective separation of peptides by reversible modification of amino groups and strong cation-exchange chromatography: Evaluation in proteomic studies using peptide-centric database searches

53. Cibacron Blue and proteomics: The mystery of the platoon missing in action

54. Clustering of MS spectra for improved protein identification rate and screening for protein variants and modifications by MALDI-MS/MS

55. Comparative proteome analyses of host protein expression in response to Enterovirus 71 and Coxsackievirus A16 infections

56. Comparative proteome analysis of Brucella abortus 2308 and its virB type IV secretion system mutant reveals new T4SS-related candidate proteins

57. Comparative proteomic analysis of Fasciola hepatica juveniles and Schistosoma bovis schistosomula

58. Comparative proteomic analysis of four Bacillus clausii strains: Proteomic expression signature distinguishes protein profile of the strains

59. Comparative proteomics of spinal cords of rat fetuses with spina bifida aperta

60. Comparison of blood serum peptide enrichment methods by Tricine SDS-PAGE and mass spectrometry

61. Comprehensive proteomic profiling of adult Angiostrongylus costaricensis, a human parasitic nematode

62. Confident identification of 3-nitrotyrosine modifications in mass spectral data across multiple mass spectrometry platforms

63. Contribution of proteomics of Leishmania spp. to the understanding of differentiation, drug resistance mechanisms, vaccine and drug development

64. Copper exposure effects on yeast mitochondrial proteome

65. CrossWork: Software-assisted identification of cross-linked peptides

66. DIGE analysis of proteome changes accompanying large resveratrol production by grapevine (Vitis vinifera cv. Gamay) cell cultures in response to methyl-β-cyclodextrin and methyl jasmonate elicitors

67. Dasatinib, imatinib and staurosporine capture compounds — Complementary tools for the profiling of kinases by Capture Compound Mass Spectrometry (CCMS)

68. Deciphering the iron response in Acinetobacter baumannii: A proteomics approach

69. Deconvolution of overlapping isotopic clusters improves quantification of stable isotope–labeled peptides