Comparison of software tools to improve the detection of carcinogen induced changes in the rat liver proteome by analyzing SELDI-TOF-MS spectra.

abstract：:Major depressive disorder (MDD) is a socially detrimental psychiatric disorder, contributing to increased healthcare expenditures and suicide rates. However, no empirical laboratory-based tests are available to support the diagnosis of MDD. In this study, a NMR-based plasma metabonomic method for the diagnosis of MDD ...

journal_title：Journal of proteome research

authors： Zheng P,Gao HC,Li Q,Shao WH,Zhang ML,Cheng K,Yang DY,Fan SH,Chen L,Fang L,Xie P

更新日期：2012-03-02 00:00:00

abstract：:Automated sequencing of unknowns in bottom-up proteomics makes the data produced susceptible to process control errors, which can be propagated into mistakes in analyte identification. Inclusion of an unintrusive internal standard, such as lysozyme, allows monitoring all phases of the proteomics process including samp...

journal_title：Journal of proteome research

authors： Riter LS,Hodge BD,Gooding KM,Julian RK Jr

更新日期：2005-01-01 00:00:00

abstract：:Bacillus thuringiensis, a Gram-positive endospore-forming bacterium, is characterized by the formation of parasporal crystals consisting of insecticidal crystal proteins (ICPs) during sporulation. We reveal gene expression profiles and regulatory mechanisms associated with spore and parasporal crystal formation based ...

journal_title：Journal of proteome research

authors： Wang J,Mei H,Qian H,Tang Q,Liu X,Yu Z,He J

更新日期：2013-12-06 00:00:00

abstract：:Campylobacter jejuni is the most common cause of bacterial gastroenteritis in the developed world. Immunoproteomics highlighted a 42-45 kDa antigen that comigrated on two-dimensional (2-DE) gels with the C. jejuni major outer membrane protein (MOMP). Predictive analysis revealed two candidates for the identity of the ...

journal_title：Journal of proteome research

authors： Scott NE,Bogema DR,Connolly AM,Falconer L,Djordjevic SP,Cordwell SJ

更新日期：2009-10-01 00:00:00

abstract：:The plant cell wall is a dynamic cellular compartment consisting of a complex matrix of components that can change dramatically in response to environmental stresses. During pathogen attack, for instance, a wide spectrum of proteins that participate in various sequential processes involved in plant defense is secreted...

journal_title：Journal of proteome research

authors： Cheng FY,Blackburn K,Lin YM,Goshe MB,Williamson JD

更新日期：2009-01-01 00:00:00

abstract：:Hepatocellular carcinoma (HCC) is a major liver malignancy possessing a high mortality rate and is particularly prevalent in China and Asia. While surgery is the most effective treatment for liver tumor, about 80% of HCC patients are inoperable at presentation and die early due to late diagnosis. For early cancer dete...

journal_title：Journal of proteome research

authors： Sun S,Xu MZ,Poon RT,Day PJ,Luk JM

更新日期：2010-01-01 00:00:00

abstract：:Enzyme-mediated 18O/16O differential labeling of proteome samples often suffers from incomplete exchange of the carboxy-terminus oxygen atoms, resulting in ambiguity in the measurable abundance differences. In this study, an 18O/16O labeling strategy was optimized for and applied to the solution-based comparative anal...

journal_title：Journal of proteome research

authors： Blonder J,Hale ML,Chan KC,Yu LR,Lucas DA,Conrads TP,Zhou M,Popoff MR,Issaq HJ,Stiles BG,Veenstra TD

更新日期：2005-03-01 00:00:00

abstract：:This study presents a comparative proteomic analysis of the membrane subproteome of whole Arabidopsis seedlings using 2% Brij-58 or 60% methanol to enrich and solubilize membrane proteins for strong cation exchange fractionation and reversed-phase liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 4...

journal_title：Journal of proteome research

authors： Mitra SK,Gantt JA,Ruby JF,Clouse SD,Goshe MB

更新日期：2007-05-01 00:00:00

abstract：:14-3-3s are phosphoserine/phosphotreonine binding proteins that play pivotal roles as regulators of multiple cellular processes in eukaryotes. The flagellated protozoan parasite Giardia duodenalis, the causing agent of giardiasis, is a valuable simplified eukaryotic model. A single 14-3-3 isoform (g14-3-3) is expresse...

journal_title：Journal of proteome research

authors： Lalle M,Camerini S,Cecchetti S,Sayadi A,Crescenzi M,Pozio E

更新日期：2012-05-04 00:00:00

abstract：:Glycoproteins influence numerous indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to th...

journal_title：Journal of proteome research

authors： Kim JW,Hwang H,Lim JS,Lee HJ,Jeong SK,Yoo JS,Paik YK

更新日期：2016-11-04 00:00:00

abstract：:Peroxiredoxin V, an atypical thioredoxin peroxidase, is widely expressed in mammalian tissues. In addition, Prdx V is localized in mitochondria, peroxisome, cytosol, and the nucleus. Prdx V has been reported to protect a wide range of cellular environments as an antioxidant enzyme, and its dysfunctions may be implicat...

journal_title：Journal of proteome research

authors： Yang HY,Kwon J,Cho EJ,Choi HI,Park C,Park HR,Park SH,Chung KJ,Ryoo ZY,Cho KO,Lee TH

更新日期：2010-08-06 00:00:00

abstract：:The enormous challenges of mass spectrometry-based metaproteomics are primarily related to the analysis and interpretation of the acquired data. This includes reliable identification of mass spectra and the meaningful integration of taxonomic and functional meta-information from samples containing hundreds of unknown ...

journal_title：Journal of proteome research

authors： Muth T,Behne A,Heyer R,Kohrs F,Benndorf D,Hoffmann M,Lehtevä M,Reichl U,Martens L,Rapp E

更新日期：2015-03-06 00:00:00

abstract：:Mass spectrometry is the main analytical technique currently used to address the challenges of glycomics as it offers unrivalled levels of sensitivity and the ability to handle complex mixtures of different glycan variations. Determination of glycan structures from analysis of MS data is a major bottleneck in high-thr...

journal_title：Journal of proteome research

authors： Ceroni A,Maass K,Geyer H,Geyer R,Dell A,Haslam SM

更新日期：2008-04-01 00:00:00

abstract：:Selenite has been a touted cancer chemopreventative agent but generates conflicting outcomes. Multiple mechanisms of selenite cytotoxicity in cancer cells are thought to be induced by metabolites of selenite. We observed that intracellular metabolism of selenite generates endogenous selenium nanoparticles (SeNPs) in c...

journal_title：Journal of proteome research

authors： Bao P,Chen Z,Tai RZ,Shen HM,Martin FL,Zhu YG

更新日期：2015-02-06 00:00:00

abstract：:Many proteins possess intrinsic disorder (ID) and lack a rigid three-dimensional structure in at least part of their sequence. ID has been hypothesized to influence protein-protein and protein-ligand interactions. We calculated ID for nearly 400 vertebrate and invertebrate members of the biomedically important nuclear...

journal_title：Journal of proteome research

authors： Krasowski MD,Reschly EJ,Ekins S

更新日期：2008-10-01 00:00:00

abstract：:Improvements in proteome analysis of erythrocyte membrane proteins by two-dimensional electrophoresis are here reported. In particular, a differential extraction procedure was set up allowing separation of integral membrane proteins from peripheral species. Moreover, the use of dilute Immobiline gels (down to as low a...

journal_title：Journal of proteome research

authors： Bruschi M,Seppi C,Arena S,Musante L,Santucci L,Balduini C,Scaloni A,Lanciotti M,Righetti PG,Candiano G

更新日期：2005-07-01 00:00:00

abstract：:Spontaneous preterm birth (SPTB) is a major contributor to perinatal morbidity and mortality. However, the diagnosis of preterm labor (PTL) that leads to preterm birth is difficult, and there is a pressing need for improved diagnosis. We utilized multidimensional liquid chromatography-tandem mass spectrometry (LC/LC-M...

journal_title：Journal of proteome research

authors： Pereira L,Reddy AP,Jacob T,Thomas A,Schneider KA,Dasari S,Lapidus JA,Lu X,Rodland M,Roberts CT Jr,Gravett MG,Nagalla SR

更新日期：2007-04-01 00:00:00

abstract：:In the past few years, the focus of phosphoproteomics has shifted from merely qualitative to quantitative and targeted studies. Tryptic digestion is a critical step that directly affects quantification and that can be impaired by phosphorylation. Therefore, we systematically characterized the digestion efficiency of 1...

journal_title：Journal of proteome research

authors： Dickhut C,Feldmann I,Lambert J,Zahedi RP

更新日期：2014-06-06 00:00:00

abstract：:Patients with triple-negative breast cancer (TNBC) are unresponsive to endocrine and anti-HER2 pharmacotherapy, limiting their therapeutic options to chemotherapy. TNBC is frequently associated with abnormalities in the PI3K/AKT/mTOR signaling pathway; drugs targeting this pathway are currently being evaluated in thes...

journal_title：Journal of proteome research

authors： Euceda LR,Hill DK,Stokke E,Hatem R,El Botty R,Bièche I,Marangoni E,Bathen TF,Moestue SA

更新日期：2017-05-05 00:00:00

abstract：:Energy imbalance is a primary cause of obesity. While the classical approach to attenuate weight gain includes an increase in energy expenditure through exercise, dietary manipulation such as the inclusion of dairy products has also been proven effective. In the present study, we explored the potential mechanisms by w...

journal_title：Journal of proteome research

authors： Mayengbam S,Mickiewicz B,Trottier SK,Mu C,Wright DC,Reimer RA,Vogel HJ,Shearer J

更新日期：2019-11-01 00:00:00

abstract：:Ethylene has been hypothesised to be a regulator of root nodule development in legumes, but its molecular mechanisms of action remain unclear. The skl mutant is an ethylene-insensitive legume mutant showing a hypernodulation phenotype when inoculated with its symbiont Sinorhizobium meliloti. We used the skl mutant to ...

journal_title：Journal of proteome research

authors： Prayitno J,Imin N,Rolfe BG,Mathesius U

更新日期：2006-11-01 00:00:00

abstract：:Advancements in studies on the evolutionary mechanisms underlying bacterial antibiotic resistance are unclear. This study aimed to investigate the evolutionary mechanism underlying bacterial antibiotic resistance using isobaric tags for relative and absolute quantitation-based quantitative proteomics along with functi...

journal_title：Journal of proteome research

authors： Du GF,Zheng YD,Chen J,He QY,Sun X

更新日期：2019-11-01 00:00:00

abstract：:Cystinuria is a purely renal, rare genetic disease caused by mutations in cystine transporter genes and characterized by defective cystine reabsorption leading to kidney stones. In 14% of cases, patients undergo nephrectomy, but given the difficulty to predict the evolution of the disease, the identification of marker...

journal_title：Journal of proteome research

authors： Bourderioux M,Nguyen-Khoa T,Chhuon C,Jeanson L,Tondelier D,Walczak M,Ollero M,Bekri S,Knebelmann B,Escudier E,Escudier B,Edelman A,Guerrera IC

更新日期：2015-01-02 00:00:00

abstract：:The Halobacterium salinarum gas vesicle (GV) is an extremely stable intracellular organelle with air trapped inside a proteinaceous membrane. Reported here is a comparative proteomics analysis of GV and GV depleted lysate (GVD) to reveal the membrane structural proteins. Ten proteins encoded by gvp-1 (gvpMLKJIHGFED-1 ...

journal_title：Journal of proteome research

authors： Chu LJ,Chen MC,Setter J,Tsai YS,Yang H,Fang X,Ting YS,Shaffer SA,Taylor GK,von Haller PD,Goodlett DR,Ng WV

更新日期：2011-03-04 00:00:00

abstract：:Histones are subjected to extensive post-translational modifications (PTMs) that are known to play key roles in many biological processes. In this study, we report a fast, efficient, highly reproducible, and easily automated method involving ultra-high performance liquid chromatography (UHPLC) coupled to a high resolu...

journal_title：Journal of proteome research

authors： Contrepois K,Ezan E,Mann C,Fenaille F

更新日期：2010-10-01 00:00:00

abstract：:The present study reports an in-depth proteome analysis of two Lactobacillus rhamnosus strains, the well-known probiotic strain GG and the dairy strain Lc705. We used GeLC-MS/MS, in which proteins are separated using 1-DE and identified using nanoLC-MS/MS, to generate high-quality protein catalogs. To maximize the num...

journal_title：Journal of proteome research

authors： Savijoki K,Lietzén N,Kankainen M,Alatossava T,Koskenniemi K,Varmanen P,Nyman TA

更新日期：2011-08-05 00:00:00

abstract：:Moving from macroscale preparative systems in proteomics to micro- and nanotechnologies offers researchers the ability to deeply profile smaller numbers of cells that are more likely to be encountered in clinical settings. Herein a recently developed microscale proteomic method, microdroplet processing in one pot for ...

journal_title：Journal of proteome research

authors： Weke K,Singh A,Uwugiaren N,Alfaro JA,Wang T,Hupp TR,O'Neill JR,Vojtesek B,Goodlett DR,Williams SM,Zhou M,Kelly RT,Zhu Y,Dapic I

更新日期：2021-01-25 00:00:00

abstract：:Metabolic phenotyping of tissues uses metabolomics and lipidomics to measure the relative polar and nonpolar (lipid) metabolite levels in biological samples. This approach aims to understand disease biochemistry and identify biochemical markers of disease. Sample preparation methods must be reproducible, sensitive (hi...

journal_title：Journal of proteome research

authors： Southam AD,Pursell H,Frigerio G,Jankevics A,Weber RJM,Dunn WB

更新日期：2021-01-01 00:00:00

abstract：:Decoy database searches are used to filter out false positive protein identifications derived from search engines, but there is no consensus about which decoy is "the best". We evaluate nine different decoy designs using public data sets from samples of known composition. Statistically significant performance differen...

journal_title：Journal of proteome research

authors： Blanco L,Mead JA,Bessant C

更新日期：2009-04-01 00:00:00

abstract：:Polygalacturonase inhibiting proteins (PGIPs) are members of the leucine rich repeat family of proteins, involved in plant defense against fungal pathogens. PGIPs exhibit a remarkable degree of specificity in terms of their ability to bind and inhibit their target molecules, the endopolygalacturonases (EPGs). This spe...

journal_title：Journal of proteome research

authors： Lim JM,Aoki K,Angel P,Garrison D,King D,Tiemeyer M,Bergmann C,Wells L

更新日期：2009-02-01 00:00:00