SearchGUI: A Highly Adaptable Common Interface for Proteomics Search and de Novo Engines.

abstract：:Proteomic studies were performed to identify the protein species involved in copper (Cu) stress responses in common wheat. Two-week-old wheat seedlings were exposed to 100 μM CuSO4 treatment for 3 days. Growth of shoots and roots was markedly inhibited and lipid peroxidation was greatly increased. Cu was readily absor...

journal_title：Journal of proteome research

authors： Li G,Peng X,Xuan H,Wei L,Yang Y,Guo T,Kang G

更新日期：2013-11-01 00:00:00

abstract：:To investigate the role of rpoS in gene expression of Escherichia coli cells grown as biofilms, we compared the proteomes of a rpoS mutant and the wild-type strain. Experiments were performed on planktonic cells (in exponential or stationary growth phase) and biofilms developed on glass wool. Spot-by-spot comparison o...

journal_title：Journal of proteome research

authors： Collet A,Cosette P,Beloin C,Ghigo JM,Rihouey C,Lerouge P,Junter GA,Jouenne T

更新日期：2008-11-01 00:00:00

abstract：:We assessed proteomic patterns in breast cancer using MALDI MS and laser capture microdissected cells. Protein and peptide expression in invasive mammary carcinoma versus normal mammary epithelium and estrogen-receptor positive versus estrogen-receptor negative tumors were compared. Biomarker candidates were identifie...

journal_title：Journal of proteome research

authors： Sanders ME,Dias EC,Xu BJ,Mobley JA,Billheimer D,Roder H,Grigorieva J,Dowsett M,Arteaga CL,Caprioli RM

更新日期：2008-04-01 00:00:00

abstract：:Pancreatic cystic neoplasms represent 10-15% of primary cystic masses of the pancreas. While pancreatic cysts are detected with an increasing frequency due to the use of advanced imaging modalities in clinical practice, the diagnosis of pancreatic cystic neoplasms remains unsatisfactory because available diagnostic te...

journal_title：Journal of proteome research

authors： Cuoghi A,Farina A,Z'graggen K,Dumonceau JM,Tomasi A,Hochstrasser DF,Genevay M,Lescuyer P,Frossard JL

更新日期：2011-05-06 00:00:00

abstract：:The effects of acute and chronic stress on the production of systemic metabolites were investigated in male Sprague-Dawley (SD) rats. Metabolites excreted in urine were analyzed using GC/MS in conjunction with multivariate and univariate statistical techniques. SD rats were subjected to two kinds of acute stress and c...

journal_title：Journal of proteome research

authors： Wang X,Zhao T,Qiu Y,Su M,Jiang T,Zhou M,Zhao A,Jia W

更新日期：2009-05-01 00:00:00

abstract：:IQGAP1 is a scaffolding protein that binds to a diverse array of signaling and structural molecules that are often associated with cell polarization and adhesion. Through interaction with its target proteins, IQGAP1 participates in multiple cellular functions, including Ca2+-calmodulin signaling, definition of cytoske...

journal_title：Journal of proteome research

authors： Meng X,Krokhin O,Cheng K,Ens W,Wilkins JA

更新日期：2007-02-01 00:00:00

abstract：:Direct tissue profiling and imaging mass spectrometry (MS) provides a detailed assessment of the complex protein pattern within a tissue sample. MALDI MS analysis of thin tissue sections results in over of 500 individual protein signals in the mass range of 2 to 70 kDa that directly correlate with protein composition ...

journal_title：Journal of proteome research

authors： Chaurand P,Schwartz SA,Caprioli RM

更新日期：2004-03-01 00:00:00

abstract：:Incomplete recovery from the LC column is identified as a major cause for poor detection efficiency of phosphopeptides by LC-MS/MS. It is proposed that metal ions adsorbed on the stationary phase interact with the phosphate group of phosphopeptides via an ion-pairing mechanism related to IMAC (IMAC: immobilized metal ...

journal_title：Journal of proteome research

authors： Winter D,Seidler J,Ziv Y,Shiloh Y,Lehmann WD

更新日期：2009-01-01 00:00:00

abstract：:Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively exp...

journal_title：Journal of proteome research

authors： Miller MG

更新日期：2007-02-01 00:00:00

abstract：:Gaining insights into the molecular events that govern the progression from melanoma in situ to advanced melanoma and understanding how the local microenvironment at the melanoma site influences this progression are two clinically pivotal aspects that to date are largely unexplored. In an effort to identify key regula...

journal_title：Journal of proteome research

authors： Hood BL,Grahovac J,Flint MS,Sun M,Charro N,Becker D,Wells A,Conrads TP

更新日期：2010-07-02 00:00:00

abstract：:The presence of the fungal pathogen, Botrytis cinerea, in the vineyard causes reductions in both quality and quantity of grapes and wine. Because proteins are involved in the foam stabilization of sparkling wines, we have undertaken, for the first time, a thorough proteomic analysis of two champagne base wines prepare...

journal_title：Journal of proteome research

authors： Cilindre C,Jégou S,Hovasse A,Schaeffer C,Castro AJ,Clément C,Van Dorsselaer A,Jeandet P,Marchal R

更新日期：2008-03-01 00:00:00

abstract：:Porphyromonas gingivalis is a keystone periodontal pathogen that has been associated with autoimmune disorders. The cell surface proteases Lys-gingipain (Kgp) and Arg-gingipains (RgpA and RgpB) are major virulence factors, and their proteolytic activity is enhanced by small peptides such as glycylglycine (GlyGly). The...

journal_title：Journal of proteome research

authors： Zhang L,Veith PD,Huq NL,Chen YY,Seers CA,Cross KJ,Gorasia DG,Reynolds EC

更新日期：2018-08-03 00:00:00

abstract：:We report the structural analysis of cap-binding proteins using a chemical probe/ultraviolet photodissociation (UVPD) mass spectrometry strategy for evaluating solvent accessibility of proteins. Our methodology utilized a chromogenic probe (NN) to probe the exposed amine residues of wheat eukaryotic translation initia...

journal_title：Journal of proteome research

authors： O'Brien JP,Mayberry LK,Murphy PA,Browning KS,Brodbelt JS

更新日期：2013-12-06 00:00:00

abstract：:Workflows in urinary proteomics studies are often complex and require many steps to enrich, purify, deplete, and separate the complex mixture. Many of these methods are laborious, are time-consuming, and have the potential for error. Although individual steps of these methods have been previously studied, their downst...

journal_title：Journal of proteome research

authors： Vaezzadeh AR,Briscoe AC,Steen H,Lee RS

更新日期：2010-11-05 00:00:00

abstract：:Urine is an ideal material to study the cancer-related protein biomarkers in bladder, whereas exploration to these candidates is confronting technique challenges. Herein, we propose a comprehensive strategy of searching the urine proteins related with bladder cancer. The strategy consists of three core combinations, s...

journal_title：Journal of proteome research

authors： Guo J,Ren Y,Hou G,Wen B,Xian F,Chen Z,Cui P,Xie Y,Zi J,Lin L,Wu S,Li Z,Wu L,Lou X,Liu S

更新日期：2016-07-01 00:00:00

abstract：:Plastids are essential organelles because they contribute to primary and secondary metabolism and plant signaling networks. A high-quality inventory of the plastid proteome is therefore a critical tool in plant research. We present reference plastid proteomes for maize (Zea mays) and Arabidopsis (Arabidopsis thaliana)...

journal_title：Journal of proteome research

authors： Huang M,Friso G,Nishimura K,Qu X,Olinares PD,Majeran W,Sun Q,van Wijk KJ

更新日期：2013-01-04 00:00:00

abstract：:Many pressing medical challenges, such as diagnosing disease, enhancing directed stem-cell differentiation, and classifying cancers, have long been hindered by limitations in our ability to quantify proteins in single cells. Mass spectrometry (MS) is poised to transcend these limitations by developing powerful methods...

journal_title：Journal of proteome research

authors： Specht H,Slavov N

更新日期：2018-08-03 00:00:00

abstract：:Glycoproteins are potentially important biomarkers of disease and therapeutic targets. In particular, the N-linked glycoproteins are a focus of interest as they can be found in the extracellular environment and body fluids. In this study, we have sampled the tears, the extracellular fluid of the epithelial cells cover...

journal_title：Journal of proteome research

authors： Lei Z,Beuerman RW,Chew AP,Koh SK,Cafaro TA,Urrets-Zavalia EA,Urrets-Zavalia JA,Li SF,Serra HM

更新日期：2009-04-01 00:00:00

abstract：:The majority of mitochondrial preproteins are targeted via N-terminal presequences that are cleaved upon import into the organelle. The essential mitochondrial processing protease (MPP) is assumed to cleave the majority of incoming precursors; however, only a small fraction of mitochondrial precursors have been experi...

journal_title：Journal of proteome research

authors： Burkhart JM,Taskin AA,Zahedi RP,Vögtle FN

更新日期：2015-11-06 00:00:00

abstract：:To estimate the potential of the state-of-the-art proteomics technologies on full coverage of the encoding gene products, the Chinese Human Chromosome Proteome Consortium (CCPC) applied a multiomics strategy to systematically analyze the transciptome, translatome, and proteome of the same cultured hepatoma cells with ...

journal_title：Journal of proteome research

authors： Chang C,Li L,Zhang C,Wu S,Guo K,Zi J,Chen Z,Jiang J,Ma J,Yu Q,Fan F,Qin P,Han M,Su N,Chen T,Wang K,Zhai L,Zhang T,Ying W,Xu Z,Zhang Y,Liu Y,Liu X,Zhong F,Shen H,Wang Q,Hou G,Zhao H,Li G,Liu S,G

更新日期：2014-01-03 00:00:00

abstract：:Vascular leakage is a hallmark of severe dengue infection. Although extensive studies have been conducted during the past several decades, the molecular mechanisms underlying vascular leakage in dengue shock syndrome (DSS) remain unclear. We thus performed a proteomics study to characterize responses in human endothel...

journal_title：Journal of proteome research

authors： Kanlaya R,Pattanakitsakul SN,Sinchaikul S,Chen ST,Thongboonkerd V

更新日期：2009-05-01 00:00:00

abstract：:While the proteome defines the expressed gene products, the metabolome results from reactions controlled by such gene products. Plasma represents an accessible "window" to the metabolome both in regard of availability and content. The wide range of the plasma metabolome, in terms of molecular diversity and abundance, ...

journal_title：Journal of proteome research

authors： Griffiths WJ,Hornshaw M,Woffendin G,Baker SF,Lockhart A,Heidelberger S,Gustafsson M,Sjövall J,Wang Y

更新日期：2008-08-01 00:00:00

abstract：:Formalin-fixed, paraffin-embedded (FFPE) tissues have been used to discover disease-associated protein changes using mass spectrometry. Protein post-translational modifications such as glycosylation are known to associate with disease development. In this study, we investigated whether FFPE tissues preserve such modif...

journal_title：Journal of proteome research

authors： Tian Y,Gurley K,Meany DL,Kemp CJ,Zhang H

更新日期：2009-04-01 00:00:00

abstract：:Ozone (O3), a potent air pollutant and a significant greenhouse gas, has been recognized as a major component of global climate change. However, current increasing trends in its background level are projecting a more severe threat to natural and cultivated plants in the near future. The present study has been designed...

journal_title：Journal of proteome research

authors： Sarkar A,Rakwal R,Bhushan Agrawal S,Shibato J,Ogawa Y,Yoshida Y,Kumar Agrawal G,Agrawal M

更新日期：2010-09-03 00:00:00

abstract：:Two-dimensional differential gel electrophoresis (2-D DIGE) was used to analyze human serum following the removal of albumin and five other high-abundant serum proteins. After protein removal, serum was analyzed by SDS-PAGE as a preliminary screen, and significant differences between four high-abundant protein removal...

journal_title：Journal of proteome research

authors： Chromy BA,Gonzales AD,Perkins J,Choi MW,Corzett MH,Chang BC,Corzett CH,McCutchen-Maloney SL

更新日期：2004-11-01 00:00:00

abstract：:Francisella tularensis is a Gram-negative bacterium that causes the zoonotic disease tularemia. The historical development of tularemia as a biological weapon has led to it being characterized by the CDC as a category A biothreat agent. Neither posttranslational modification (PTM) of proteins, in particular lysine ace...

journal_title：Journal of proteome research

authors： Marakasova E,Ii A,Nelson KT,van Hoek ML

更新日期：2020-04-03 00:00:00

abstract：:Colorectal cancer (CRC) is the third most common cancer worldwide and has poor prognosis. To identify the proteins involved in colorectal carcinogenesis, we employed 2-DE and MALDI-TOF/TOF-based proteomics approach to study the differentially expressed proteins in tumor and adjacent nontumor tissue samples. Samples fr...

journal_title：Journal of proteome research

authors： Ma YL,Peng JY,Zhang P,Huang L,Liu WJ,Shen TY,Chen HQ,Zhou YK,Zhang M,Chu ZX,Qin HL

更新日期：2009-10-01 00:00:00

abstract：:When analyzing proteins in complex samples using tandem mass spectrometry of peptides generated by proteolysis, the inference of proteins can be ambiguous, even with well-validated peptides. Unresolved questions include whether to show all possible proteins vs a minimal list, what to do when proteins are inferred ambi...

journal_title：Journal of proteome research

authors： Meyer-Arendt K,Old WM,Houel S,Renganathan K,Eichelberger B,Resing KA,Ahn NG

更新日期：2011-07-01 00:00:00

abstract：:Protein biomarker discovery in the low concentration range of human body fluids requires the enrichment of the proteins of interest. Here we report on a tandem affinity strategy: In the first step, we isolated a human plasma glyco-subproteome of healthy individuals by wheat germ agglutinin (WGA) lectin affinity chroma...

journal_title：Journal of proteome research

authors： Mortezai N,Harder S,Schnabel C,Moors E,Gauly M,Schlüter H,Wagener C,Buck F

更新日期：2010-12-03 00:00:00

abstract：:The purpose of this study was to evaluate the use of high resolution LC-MS together with metabolomics and D(4)-cholic acid (D(4)-CA) as a metabolic tracer to measure the metabolism and reconjugation of bile acids (BAs) in vitro and in vivo. Metabolic tracers are very important because they allow for the direct detecti...

journal_title：Journal of proteome research

authors： Castro-Perez JM,Roddy TP,Shah V,Wang SP,Ouyang X,Ogawa A,McLaren DG,Tadin-Strapps M,Robinson MJ,Bartz SR,Ason B,Chen Y,Previs SF,Wong KK,Vreeken RJ,Johns DG,Hubbard BK,Hankemeier T,Mitnaul L

更新日期：2011-10-07 00:00:00