Evidence for novel tomato seed allergens: IgE-reactive legumin and vicilin proteins identified by multidimensional protein fractionation-mass spectrometry and in silico epitope modeling.

abstract：:Fucosylated alpha-fetoprotein (AFP) is a specific tumor marker for hepatocellular carcinomas (HCC). However, the mechanisms underlying the increase in fucosylated AFP in serum of patients with HCC are largely unknown. Recently, we reported that fucosylation is a possible signal for the secretion of glycoproteins into ...

journal_title：Journal of proteome research

authors： Nakagawa T,Takeishi S,Kameyama A,Yagi H,Yoshioka T,Moriwaki K,Masuda T,Matsumoto H,Kato K,Narimatsu H,Taniguchi N,Miyoshi E

更新日期：2010-10-01 00:00:00

abstract：:Cold acclimation is the phenomenon in which plants are exposed to low, but nonfreezing, temperatures before exposure to drastic temperatures. To investigate how sunflower plants adjust their metabolism during cold treatment, a comparative proteomic approach, based on spectral counting data, was adopted to identify dif...

journal_title：Journal of proteome research

authors： Balbuena TS,Salas JJ,Martínez-Force E,Garcés R,Thelen JJ

更新日期：2011-05-06 00:00:00

abstract：:Deficiency of the sulfide metabolizing protein ETHE1 is the cause of ethylmalonic encephalopathy (EE), an inherited and severe metabolic disorder. To study the molecular effects of EE, we performed a proteomics study on mitochondria from cultured patient fibroblast cells. Samples from six patients were analyzed and re...

journal_title：Journal of proteome research

authors： Palmfeldt J,Vang S,Stenbroen V,Pavlou E,Baycheva M,Buchal G,Monavari AA,Augoustides-Savvopoulou P,Mandel H,Gregersen N

更新日期：2011-05-06 00:00:00

abstract：:Molecular imaging of tissue by MALDI mass spectrometry is a powerful tool for visualizing the spatial distribution of constituent analytes with high molecular specificity. Although the technique is relatively young, it has already contributed to the understanding of many diverse areas of human health. In recent years,...

journal_title：Journal of proteome research

authors： Chaurand P,Norris JL,Cornett DS,Mobley JA,Caprioli RM

更新日期：2006-11-01 00:00:00

abstract：:Dysregulated protein phosphorylation is a primary culprit in multiple physiopathological states. Hence, although analysis of signaling cascades on a proteome-wide scale would provide significant insight into both normal and aberrant cellular function, such studies are simultaneously limited by sheer biological complex...

journal_title：Journal of proteome research

authors： Ndassa YM,Orsi C,Marto JA,Chen S,Ross MM

更新日期：2006-10-01 00:00:00

abstract：:We present a novel straightforward method for enrichment of N-terminal peptides, utilizing charge-based fractional diagonal chromatography (ChaFRADIC). Our method is robust, easy to operate, fast, specific, and more sensitive than existing methods, enabling the differential quantitation of 1459 nonredundant N-terminal...

journal_title：Journal of proteome research

authors： Venne AS,Vögtle FN,Meisinger C,Sickmann A,Zahedi RP

更新日期：2013-09-06 00:00:00

abstract：:Cellular functions are largely carried out by noncovalent protein complexes that may exist within the cell as stable modules or as assemblies of dynamically changing composition, whose formation and decomposition are triggered in response to extracellular stimuli. The protein constituents of complexes often exhibit po...

journal_title：Journal of proteome research

authors： Przybylski C,Jünger MA,Aubertin J,Radvanyi F,Aebersold R,Pflieger D

更新日期：2010-10-01 00:00:00

abstract：:Increased serum haptoglobin concentration and changes in its glycosylation have been reported in certain cancer types. Information for hepatocellular carcinoma (HCC) has not yet been available. In this study, we aimed to carry out a systematic analysis of serum concentrations of haptoglobin (Hp) and its glycoforms in ...

journal_title：Journal of proteome research

authors： Ang IL,Poon TC,Lai PB,Chan AT,Ngai SM,Hui AY,Johnson PJ,Sung JJ

更新日期：2006-10-01 00:00:00

abstract：:In this report, we use a proteomic strategy to identify glycoproteins on the surface of exosomes derived from myeloid-derived suppressor cells (MDSCs), and then test if selected glycoproteins contribute to exosome-mediated chemotaxis and migration of MDSCs. We report successful modification of a surface chemistry meth...

journal_title：Journal of proteome research

authors： Chauhan S,Danielson S,Clements V,Edwards N,Ostrand-Rosenberg S,Fenselau C

更新日期：2017-01-06 00:00:00

abstract：:Protein interaction networks display approximate scale-free topology, in which hub proteins that interact with a large number of other proteins determine the overall organization of the network. In this study, we aim to determine whether hubs are distinguishable from other networked proteins by specific sequence featu...

journal_title：Journal of proteome research

authors： Dosztányi Z,Chen J,Dunker AK,Simon I,Tompa P

更新日期：2006-11-01 00:00:00

abstract：:Almond, as a part of the nut family, is an important source of biological compounds, and specifically, almond skins have been considered an important source of polyphenols, including flavan-3-ols and flavonols. Polyphenol metabolism may produce several classes of metabolites that could often be more biologically activ...

journal_title：Journal of proteome research

authors： Llorach R,Garrido I,Monagas M,Urpi-Sarda M,Tulipani S,Bartolome B,Andres-Lacueva C

更新日期：2010-11-05 00:00:00

abstract：:Histones regulate a variety of chromatin templated events by their post-translational modifications (PTMs). Although there are extensive reports on the PTMs of canonical histones, the information on the histone variants remains very scanty. Here, we report the identification of different PTMs, such as acetylation, met...

journal_title：Journal of proteome research

authors： Pentakota SK,Sandhya S,P Sikarwar A,Chandra N,Satyanarayana Rao MR

更新日期：2014-12-05 00:00:00

abstract：:Over the past few years, awareness has risen that for mass-spectrometry-based proteomics methods to mature into everyday analytical and clinical practices, extensive quality assessment is mandatory. A currently overlooked source of qualitative information originates from the mass spectrometer itself. Apart from the ac...

journal_title：Journal of proteome research

authors： Bittremieux W,Willems H,Kelchtermans P,Martens L,Laukens K,Valkenborg D

更新日期：2015-05-01 00:00:00

abstract：:A "one-pot" alternative method for processing proteins and isolating peptide mixtures from bacterial samples is presented for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and data reduction. The conventional in-solution digestion of the protein contents of bacteria is compared to a small disposab...

journal_title：Journal of proteome research

authors： Jabbour RE,Deshpande SV,Stanford MF,Wick CH,Zulich AW,Snyder AP

更新日期：2011-02-04 00:00:00

abstract：:Campylobacter jejuni, an important foodborne microorganism, poses severe and emergent threats to human health as antibiotic resistance becomes increasingly prevalent. The mechanisms of drug resistance are hard to decipher, and little is known at the metabolic level. Here we apply metabolomic profiling to discover meta...

journal_title：Journal of proteome research

authors： Li H,Xia X,Li X,Naren G,Fu Q,Wang Y,Wu C,Ding S,Zhang S,Jiang H,Li J,Shen J

更新日期：2015-02-06 00:00:00

abstract：:Sensitive detection of molecular biomarkers in clinical samples is crucially important in disease diagnostics. This paper reports the development of an aptamer microarray platform combined with sol-gel technology to identify low-abundance targets in complex serum samples. Because of the nanoporous structure of the sol...

journal_title：Journal of proteome research

authors： Ahn JY,Lee SW,Kang HS,Jo M,Lee DK,Laurell T,Kim S

更新日期：2010-11-05 00:00:00

abstract：:In shotgun proteomics analysis, user-specified parameters are critical to database search performance and therefore to the yield of confident peptide-spectrum matches (PSMs). Two of the most important parameters are related to the accuracy of the mass spectrometer. Precursor mass tolerance defines the peptide candidat...

journal_title：Journal of proteome research

authors： May DH,Tamura K,Noble WS

更新日期：2017-04-07 00:00:00

abstract：:Differentiating and quantifying protein differences in complex samples produces significant challenges in sensitivity and specificity. Label-free quantification can draw from two different information sources: precursor intensities and spectral counts. Intensities are accurate for calculating protein relative abundanc...

journal_title：Journal of proteome research

authors： Chen YY,Chambers MC,Li M,Ham AJ,Turner JL,Zhang B,Tabb DL

更新日期：2013-09-06 00:00:00

abstract：:Clostridium difficile in recent years has undergone rapid evolution and has emerged as a serious human pathogen. Proteomic approaches can improve the understanding of the diversity of this important pathogen, especially in comparing the adaptive ability of different C. difficile strains. In this study, TMT labeling an...

journal_title：Journal of proteome research

authors： Chen JW,Scaria J,Mao C,Sobral B,Zhang S,Lawley T,Chang YF

更新日期：2013-03-01 00:00:00

abstract：:Deamidation of asparaginyl residues in proteins produces a mixture of asparaginyl, n-aspartyl, and isoaspartyl residues, which affects the proteins' structure, function, and stability. Thus, it is important to identify and quantify the products to evaluate the effects in biological systems. It is still a challenging t...

journal_title：Journal of proteome research

authors： Hao P,Qian J,Dutta B,Cheow ES,Sim KH,Meng W,Adav SS,Alpert A,Sze SK

更新日期：2012-03-02 00:00:00

abstract：:Protein biomarkers are fundamental tools for the characterization of stem cells and for tracking their differentiation and maturation down developmental lineages. Technology development allowing increased coverage of difficult cellular proteomes should allow for the discovery of new and novel membrane protein biomarke...

journal_title：Journal of proteome research

authors： McQuade LR,Schmidt U,Pascovici D,Stojanov T,Baker MS

更新日期：2009-12-01 00:00:00

abstract：:T lymphocytes mediate cellular and humoral defense against foreign bodies or autoantigens. An understanding of T-cell information processing furthers studies of the immunological response. We describe a large-scale phosphorylation analysis of primary T cells using a multidimensional separation strategy, involving prep...

journal_title：Journal of proteome research

authors： Carrascal M,Ovelleiro D,Casas V,Gay M,Abian J

更新日期：2008-12-01 00:00:00

abstract：:Metabolically engineered Escherichia coli has previously been used to degrade cis-1,2-dichloroethylene (cis-DCE). The strains express the six genes of an evolved toluene ortho-monooxygenase from Burkholderia cepacia G4 (TOM-Green, which formed a reactive epoxide) with either (1) gamma-glutamylcysteine synthetase (GSHI...

journal_title：Journal of proteome research

authors： Lee J,Cao L,Ow SY,Barrios-Llerena ME,Chen W,Wood TK,Wright PC

更新日期：2006-06-01 00:00:00

abstract：:Ribosomal proteins of the model gram-positive bacterium B. subtilis 168 were extensively characterized in a proteomic study. Mass spectra of the 52 proteins expected to be constitutive components of the 70S ribosome were recorded. Peptide MS/MS analysis with an average sequence coverage of 85% supported the identifica...

journal_title：Journal of proteome research

authors： Lauber MA,Running WE,Reilly JP

更新日期：2009-09-01 00:00:00

abstract：:MS-based de novo peptide sequencing has been improved remarkably with significant development of mass-spectrometry and computational approaches but still lacks quality-control methods. Here we proposed a novel algorithm pSite to evaluate the confidence of each amino acid rather than the full-length peptides obtained b...

journal_title：Journal of proteome research

authors： Yang H,Chi H,Zhou WJ,Zeng WF,Liu C,Wang RM,Wang ZW,Niu XN,Chen ZL,He SM

更新日期：2018-01-05 00:00:00

abstract：:Hydrogen peroxide (H(2)O(2)) and nitric oxide ((•)NO) elicit numerous processes in plants. However, our knowledge of H(2)O(2) and (•)NO-responsive proteins is limited. The present study aimed to identify proteins whose accumulation levels were regulated by these signaling molecules in citrus leaves. To address this qu...

journal_title：Journal of proteome research

authors： Tanou G,Job C,Belghazi M,Molassiotis A,Diamantidis G,Job D

更新日期：2010-11-05 00:00:00

abstract：:Large-scale metabolomics studies involving thousands of samples present multiple challenges in data analysis, particularly when an untargeted platform is used. Studies with multiple cohorts and analysis platforms exacerbate existing problems such as peak alignment and normalization. Therefore, there is a need for robu...

journal_title：Journal of proteome research

authors： Karaman I,Ferreira DL,Boulangé CL,Kaluarachchi MR,Herrington D,Dona AC,Castagné R,Moayyeri A,Lehne B,Loh M,de Vries PS,Dehghan A,Franco OH,Hofman A,Evangelou E,Tzoulaki I,Elliott P,Lindon JC,Ebbels TM

更新日期：2016-12-02 00:00:00

abstract：:Vascular endothelial growth factor receptor-2 (VEGFR-2) is an important receptor tyrosine kinase (RTK) that plays critical roles in both physiologic and pathologic angiogenesis. The extracellular domain of VEGFR-2 is composed of seven immunoglobulin-like domains, each with multiple potential N-glycosylation sites (seq...

journal_title：Journal of proteome research

authors： Chandler KB,Leon DR,Meyer RD,Rahimi N,Costello CE

更新日期：2017-02-03 00:00:00

abstract：:The missing human proteome comprises predicted protein-coding genes with no credible protein level evidence detected so far and constitutes ~18% of the human protein coding genes (neXtProt release 19/9/2014). The missing proteins may be of pharmacological interest as many of these are membrane receptors, thus requirin...

journal_title：Journal of proteome research

authors： Kumar D,Jain A,Dash D

更新日期：2015-12-04 00:00:00

abstract：:Mycobacterium tuberculosis, the causative agent of tuberculosis, accounts for 1.5 million human deaths annually worldwide. Despite efforts to eradicate tuberculosis, it still remains a deadly disease. The two best characterized strains of M. tuberculosis, virulent H37Rv and avirulent H37Ra, provide a unique platform t...

journal_title：Journal of proteome research

authors： Verma R,Pinto SM,Patil AH,Advani J,Subba P,Kumar M,Sharma J,Dey G,Ravikumar R,Buggi S,Satishchandra P,Sharma K,Suar M,Tripathy SP,Chauhan DS,Gowda H,Pandey A,Gandotra S,Prasad TS

更新日期：2017-04-07 00:00:00