Multiplexed Quantitative Proteomic Analysis of HEK293 Provides Insights into Molecular Changes Associated with the Cell Density Effect, Transient Transfection, and Virus-Like Particle Production.

abstract：:As spectral library searching has received increasing attention for peptide identification, constructing good decoy spectra from the target spectra is the key to correctly estimating the false discovery rate in searching against the concatenated target-decoy spectral library. Several methods have been proposed to cons...

journal_title：Journal of proteome research

authors： Cheng CY,Tsai CF,Chen YJ,Sung TY,Hsu WL

更新日期：2013-05-03 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：:Clematis terniflora DC. has potential pharmaceutical value; on the contrary, high-level UV-B irradiation with dark treatment led to the accumulation of secondary metabolites. Metabolomic and proteomic analyses of leaf of C. terniflora were performed to investigate the systematic response mechanisms to high-level UV-B ...

journal_title：Journal of proteome research

authors： Yang B,Wang X,Gao C,Chen M,Guan Q,Tian J,Komatsu S

更新日期：2016-08-05 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：:Natural disasters such as drought, extreme temperatures, and flooding can severely impact crop production. Understanding the metabolic response of crops threatened with these disasters provides insights into biological response mechanisms that can influence survival. In this study, a comparative analysis of GC-MS and ...

journal_title：Journal of proteome research

authors： Barding GA Jr,Béni S,Fukao T,Bailey-Serres J,Larive CK

更新日期：2013-02-01 00:00:00

abstract：:Glycosylation is one of the most common post-translational modifications in proteins, existing in ~50% of mammalian proteins. Several research groups have demonstrated that mass spectrometry is an efficient technique for glycopeptide identification; however, this problem is still challenging because of the enormous di...

journal_title：Journal of proteome research

authors： Zhang Y,Yu CY,Song E,Li SC,Mechref Y,Tang H,Liu X

更新日期：2015-12-04 00:00:00

abstract：:Sexual dimorphism is initialed by the components of the sex determination pathway and is most evident in gonads and germ cells. Although striking dimorphic expressions have been detected at the transcriptional level between the silkworm larval testis and the ovary, the sex-dimorphic expressions at the protein level ha...

journal_title：Journal of proteome research

authors： Chen JE,Li JY,You ZY,Liu LL,Liang JS,Ma YY,Chen M,Zhang HR,Jiang ZD,Zhong BX

更新日期：2013-06-07 00:00:00

abstract：:Butyrate, a fermentation product of the large bowel microflora, is potentially protective against the development of colorectal cancer. In vitro, butyrate has been shown to induce apoptosis and inhibit proliferation in numerous cancer cell lines, including colorectal cancer. Although these tumor suppressing properties...

journal_title：Journal of proteome research

authors： Fung KY,Lewanowitsch T,Henderson ST,Priebe I,Hoffmann P,McColl SR,Lockett T,Head R,Cosgrove LJ

更新日期：2009-03-01 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：:Cannabinoid 2 receptor (CB2R), a Class-A G-protein coupled receptor (GPCR), is a promising drug target under a wide array of pathological conditions. Rational drug design has been hindered due to our poor understanding of the structural features involved in ligand binding. Binding of a high-affinity biarylpyrazole inv...

journal_title：Journal of proteome research

authors： Mallipeddi S,Kreimer S,Zvonok N,Vemuri K,Karger BL,Ivanov AR,Makriyannis A

更新日期：2017-07-07 00:00:00

abstract：:In humans, the olfactory epithelium is located in two narrow passages, the olfactory clefts, at the upper part of the nasal cavities. The olfactory epithelium is covered by a mucus layer which is essential for the function of the olfactory neurons that are directly connected with the brain through the cribriform plate...

journal_title：Journal of proteome research

authors： Débat H,Eloit C,Blon F,Sarazin B,Henry C,Huet JC,Trotier D,Pernollet JC

更新日期：2007-05-01 00:00:00

abstract：:We undertook an unbiased metabolite profiling of fibroblasts from schizophrenia patients and healthy controls to identify metabolites and pathways that are dysregulated in disease, seeking to gain new insights into the disease biology of schizophrenia and to discover potential disease-related biomarkers. We measured p...

journal_title：Journal of proteome research

authors： Huang JH,Park H,Iaconelli J,Berkovitch SS,Watmuff B,McPhie D,Öngür D,Cohen BM,Clish CB,Karmacharya R

更新日期：2017-02-03 00:00:00

abstract：:To further our understanding of the biology of the thermophilic bacterium Geobacillus thermoleovorans T80, we now report the first proteomic analysis of the insoluble subproteome of this isolate. A combination of both shotgun and multidimensional methodologies were utilized, and a total of 8628 peptides was initially ...

journal_title：Journal of proteome research

authors： Graham RL,O'Loughlin SN,Pollock CE,Ternan NG,Weatherly DB,Jackson PJ,Tarleton RL,McMullan G

更新日期：2006-09-01 00:00:00

abstract：:The insulin/insulin-like growth factor-1 (IGF-1) signaling system is a public regulator of aging in the model animals Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus. For the first time, proteomic analyses of the environmentally resistant and 'nonaging' C. elegans dauer stage and long-lived daf-2 mut...

journal_title：Journal of proteome research

authors： Jones LM,Staffa K,Perally S,LaCourse EJ,Brophy PM,Hamilton JV

更新日期：2010-06-04 00:00:00

abstract：:The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyse...

journal_title：Journal of proteome research

authors： Ortea I,Cañas B,Gallardo JM

更新日期：2009-11-01 00:00:00

abstract：:Human embryonic stem cells (hESCs) are promising in regenerative medicine (RM) due to their differentiation plasticity and proliferation potential. However, a major challenge in RM is the generation of a vascular system to support nutrient flow to newly synthesized tissues. Here we refined an existing method to genera...

journal_title：Journal of proteome research

authors： Tsolis KC,Bagli E,Kanaki K,Zografou S,Carpentier S,Bei ES,Christoforidis S,Zervakis M,Murphy C,Fotsis T,Economou A

更新日期：2016-06-03 00:00:00

abstract：:The secreted proteins of bacteria are usually accompanied by virulence factors, which can cause inflammation and damage host cells. Identifying the secretomes arising from the interactions of bacteria and host cells could therefore increase understanding of the mechanisms during initial pathogenesis. The present study...

journal_title：Journal of proteome research

authors： Chiu KH,Wang LH,Tsai TT,Lei HY,Liao PC

更新日期：2017-01-06 00:00:00

abstract：:During vertebrate central nervous system development, the apical neuroepithelium is bathed with embryonic Cerebrospinal Fluid (e-CSF) which plays regulatory roles in cortical cell proliferation and maintenance. Here, we report the first proteomic analysis of human e-CSF and compare it to an extensive proteomic analysi...

journal_title：Journal of proteome research

authors： Zappaterra MD,Lisgo SN,Lindsay S,Gygi SP,Walsh CA,Ballif BA

更新日期：2007-09-01 00:00:00

abstract：:Hundreds of ribosomally synthesized cyclopeptides have been isolated from all domains of life, the vast majority having been reported in the last 15 years. Studies of cyclic peptides have highlighted their exceptional potential both as stable drug scaffolds and as biomedicines in their own right. Despite this, computa...

journal_title：Journal of proteome research

authors： Mohimani H,Liu WT,Mylne JS,Poth AG,Colgrave ML,Tran D,Selsted ME,Dorrestein PC,Pevzner PA

更新日期：2011-10-07 00:00:00

abstract：:Ricin is a type II ribosome-inactivating protein toxin consisting of A and B chains linked by one interchain disulfide bond. Because of its high toxicity depending on both chains together, confirming the presence of both A and B chains of intact ricin is required during the investigation of the illegal production and ...

journal_title：Journal of proteome research

authors： Liu CC,Liang LH,Yang Y,Yu HL,Yan L,Li XS,Chen B,Liu SL,Xi HL

更新日期：2021-01-01 00:00:00

abstract：:The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked wit...

journal_title：Journal of proteome research

authors： Deutsch EW,Orchard S,Binz PA,Bittremieux W,Eisenacher M,Hermjakob H,Kawano S,Lam H,Mayer G,Menschaert G,Perez-Riverol Y,Salek RM,Tabb DL,Tenzer S,Vizcaíno JA,Walzer M,Jones AR

更新日期：2017-12-01 00:00:00

abstract：:Recombinant virus-like particles (VLPs) have been shown to induce protective immunity. Despite their potential significance as promising vaccine candidates, the protein composition of VLPs produced in insect cells has not been well characterized. Here we report a proteomic analysis of influenza VLPs containing hemaggl...

journal_title：Journal of proteome research

authors： Song JM,Choi CW,Kwon SO,Compans RW,Kang SM,Kim SI

更新日期：2011-08-05 00:00:00

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：:Although tandem mass spectrometry (MS/MS) has become an integral part of proteomics, intensity patterns in MS/MS spectra are rarely weighted heavily in most widely used algorithms because they are not yet fully understood. Here a knowledge mining approach is demonstrated to discover fragmentation intensity patterns an...

journal_title：Journal of proteome research

authors： Huang Y,Tseng GC,Yuan S,Pasa-Tolic L,Lipton MS,Smith RD,Wysocki VH

更新日期：2008-01-01 00:00:00

abstract：:We have developed a high-throughput system for generating baculoviruses and testing the expression, solubility, and affinity column purification of encoded proteins. We have used this system to generate baculoviruses for and analyze the expression of 337 proteins from three different herpesviruses (HSV-1, EBV, and CMV...

journal_title：Journal of proteome research

authors： Gao M,Brufatto N,Chen T,Murley LL,Thalakada R,Domagala M,Beattie B,Mamelak D,Athanasopoulos V,Johnson D,McFadden G,Burks C,Frappier L

更新日期：2005-11-01 00:00:00

abstract：:Protein microarrays consist of known proteins spotted onto solid substrates and are used to perform highly multivariate assessments of protein-binding interactions. Human protein arrays are routinely applied to pathogen detection, immune response biomarker profiling, and antibody specificity profiling. Here, we descri...

journal_title：Journal of proteome research

authors： Feng F,Ataca ST,Ran M,Wang Y,Breen M,Kepler TB

更新日期：2020-07-02 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：:Populations around the world are aging rapidly. Age-related loss of physiological functions negatively affects quality of life. A major contributor to the frailty syndrome of aging is loss of skeletal muscle. In this study we assessed the skeletal muscle biopsy metabolome of healthy young, healthy older and frail olde...

journal_title：Journal of proteome research

authors： Fazelzadeh P,Hangelbroek RW,Tieland M,de Groot LC,Verdijk LB,van Loon LJ,Smilde AK,Alves RD,Vervoort J,Müller M,van Duynhoven JP,Boekschoten MV

更新日期：2016-02-05 00:00:00

abstract：:Sperm proteomes have emerged for several species; however, the extent of species similarity is unknown. Sheep are an important agricultural species for which a comprehensive sperm proteome has not been produced. In addition, potential proteomic factors from seminal plasma that may contribute to improved fertility afte...

journal_title：Journal of proteome research

authors： Pini T,Leahy T,Soleilhavoup C,Tsikis G,Labas V,Combes-Soia L,Harichaux G,Rickard JP,Druart X,de Graaf SP

更新日期：2016-10-07 00:00:00

abstract：:Profiling of tissues and cell types through systematic characterization of expressed genes or proteins shows promise as a basic research tool, and has potential applications in disease diagnosis and classification. We used multidimensional protein identification protein identification technology (MudPIT) to analyze pr...

journal_title：Journal of proteome research

authors： Cagney G,Park S,Chung C,Tong B,O'Dushlaine C,Shields DC,Emili A

更新日期：2005-09-01 00:00:00