Integration of mass spectrometry and RNA-Seq data to confirm human ab initio predicted genes and lncRNAs.

abstract：:Gram-negative bacteria release outer membrane vesicles (OMVs) as part of their normal growth that contain a range of cargo from their parent bacterium, including DNA, RNA, and proteins. The protein content of OMVs is suggested to be similar in composition to various sub-cellular locations of their parent bacterium. Ho...

journal_title：Proteomics

authors： Zavan L,Bitto NJ,Johnston EL,Greening DW,Kaparakis-Liaskos M

更新日期：2019-01-01 00:00:00

abstract：:Human embryonic stem cells (hESCs) have received considerable attention due to their therapeutic potential and usefulness in understanding early development and cell fate commitment. In order to appreciate the unique properties of these pluripotent, self-renewing cells, we have performed an in-depth multidimensional f...

journal_title：Proteomics

authors： Zhao P,Schulz TC,Sherrer ES,Weatherly DB,Robins AJ,Wells L

更新日期：2015-01-01 00:00:00

abstract：:To exploit advances in proteomics for drug discovery, high-throughout methods for target validation that directly address the cellular roles of proteins are required. To do this, we have characterized fluorophore-assisted light inactivation (FALI) which uses coherent or diffuse light targeted by fluorescein-labeled pr...

journal_title：Proteomics

authors： Beck S,Sakurai T,Eustace BK,Beste G,Schier R,Rudert F,Jay DG

更新日期：2002-03-01 00:00:00

abstract：:RADARS, a rapid, automated, data archiving and retrieval software system for high-throughput proteomic mass spectral data processing and storage, is described. The majority of mass spectrometer data files are compatible with RADARS, for consistent processing. The system automatically takes unprocessed data files, iden...

journal_title：Proteomics

authors： Field HI,Fenyö D,Beavis RC

更新日期：2002-01-01 00:00:00

abstract：:As an initial screen for novel markers of renal cancer and to minimise background heterogeneity, we have compared the within-patient profiles of serum samples from seven patients pre- and post-nephrectomy. Samples were depleted of six of the most abundant proteins using Agilent's multiple affinity removal system (MARS...

journal_title：Proteomics

authors： Vasudev NS,Ferguson RE,Cairns DA,Stanley AJ,Selby PJ,Banks RE

更新日期：2008-12-01 00:00:00

abstract：:In the post-genomic era, mass spectrometry is destined to fulfil a central role in biomedical research, and it is in the area of protein identification that mass spectrometry is now most rapidly expanding. An important identification method is to subject a protein to proteolysis and determine the resulting peptide mas...

journal_title：Proteomics

authors： Griffiths WJ,Jonsson AP

更新日期：2001-08-01 00:00:00

abstract：:Geobacter sulfurreducens, generally considered to be a strict anaerobe, is a predominant microbe in subsurface environments, where it utilizes available metals as electron acceptors. To better understand the metabolic processes involved in the metal-reduction capability of this microbe, the proteins expressed by cells...

journal_title：Proteomics

authors： Khare T,Esteve-Núñez A,Nevin KP,Zhu W,Yates JR 3rd,Lovley D,Giometti CS

更新日期：2006-01-01 00:00:00

abstract：:Suberoylanilide hydroxamic acid (SAHA) is a potent histone deacetylase (HDAC) inhibitor. Inhibitors of HDACs are used in cancer therapy based on the role HDACs play in transcription by regulating chromatin compaction and non-histone proteins such as transcription factors. Profiling of HDAC expression is of interest in...

journal_title：Proteomics

authors： Fischer JJ,Michaelis S,Schrey AK,Diehl A,Graebner OY,Ungewiss J,Horzowski S,Glinski M,Kroll F,Dreger M,Koester H

更新日期：2011-10-01 00:00:00

abstract：:Using proteomics in tandem with bioinformatics, the secretomes of nonaggressive and aggressive thyroid carcinoma (TC) cell lines were analyzed to detect potential biomarkers for tumor aggressiveness. A panel of nine proteins, activated leukocyte cell adhesion molecule (ALCAM/CD166), tyrosine-protein kinase receptor (A...

journal_title：Proteomics

authors： Chaker S,Kashat L,Voisin S,Kaur J,Kak I,MacMillan C,Ozcelik H,Siu KW,Ralhan R,Walfish PG

更新日期：2013-03-01 00:00:00

abstract：:Basal-like breast cancers are commonly negative for expression of estrogen and progesterone receptors and HER-2 (triple-negative breast cancer), which makes this subtype of breast cancers more aggressive and less responsive to standard treatment. We have applied a small-scale chemical proteomics method using bisindoly...

journal_title：Proteomics

authors： Dolai S,Xu Q,Liu F,Molloy MP

更新日期：2011-07-01 00:00:00

abstract：:Mulberry dwarf (MD) is a serious infectious disease of mulberry caused by phytoplasma. Infection with MD phytoplasma results in stress phenotypes of yellowing, phyllody, stunting, proliferation, and witches' broom. Physiological and biochemical analysis has shown that infection with MD phytoplasma causes an increase i...

journal_title：Proteomics

authors： Ji X,Gai Y,Zheng C,Mu Z

更新日期：2009-12-01 00:00:00

abstract：:Collision-activated dissociation and electron-transfer dissociation (ETD) each produce spectra containing unique features. Though several database search algorithms (e.g. SEQUEST, MASCOT, and Open Mass Spectrometry Search Algorithm) have been modified to search ETD data, this consists chiefly of the ability to search ...

journal_title：Proteomics

authors： Good DM,Wenger CD,Coon JJ

更新日期：2010-01-01 00:00:00

abstract：:With advances in liquid chromatography coupled to tandem mass spectrometry technologies combined with the continued goals of biomarker discovery, clinical applications of established biomarkers, and integrating large multiomic datasets (i.e. "big data"), there remains an urgent need for robust tools to assess instrume...

journal_title：Proteomics

authors： Bereman MS

更新日期：2015-03-01 00:00:00

abstract：:Recombinant human growth hormone (rhGH) is used for the treatment of several disorders. Structural integrity of rhGH is of critical importance for its clinical use and modifications thereof may act as markers in situations such as rhGH doping, as illegal rhGH-abuse in sports is of increasing interest. In the current s...

journal_title：Proteomics

authors： Hepner F,Csaszar E,Roitinger E,Pollak A,Lubec G

更新日期：2006-02-01 00:00:00

abstract：:Low root temperature causes a decrease in water uptake, which leads to mineral and nutrient deficiencies with potentially decreased root and shoot growth. Differential temperature effects in plants have been studied extensively, however, the effect of root chilling on the global protein expression in shoots has not be...

journal_title：Proteomics

authors： Neilson KA,Scafaro AP,Chick JM,George IS,Van Sluyter SC,Gygi SP,Atwell BJ,Haynes PA

更新日期：2013-06-01 00:00:00

abstract：:Deciphering a complete landscape of protein-RNA interactions in the human proteome remains an elusive challenge. We computationally elucidate RNA binding proteins (RBPs) using an approach that complements previous efforts. We employ two modern complementary sequence-based methods that provide accurate predictions from...

journal_title：Proteomics

authors： Chowdhury S,Zhang J,Kurgan L

更新日期：2018-11-01 00:00:00

abstract：:Staphylococcus aureus, a bacterial, food-borne pathogen of humans, can contaminate raw fruits and vegetables. While physical and chemical methods are available to control S. aureus, scientists are searching for inhibitory phytochemicals from plants. One promising compound from pomegranate is punicalagin, a natural ant...

journal_title：Proteomics

authors： Cooper B,Islam N,Xu Y,Beard HS,Garrett WM,Gu G,Nou X

更新日期：2018-05-01 00:00:00

abstract：:Affinity purification coupled to mass spectrometry (AP-MS) is gaining widespread use for the identification of protein-protein interactions. It is unclear, however, whether typical AP sample complexity is limiting for the identification of all protein components using standard one-dimensional LC-MS/MS. Multidimensiona...

journal_title：Proteomics

authors： Dunham WH,Larsen B,Tate S,Badillo BG,Goudreault M,Tehami Y,Kislinger T,Gingras AC

更新日期：2011-07-01 00:00:00

abstract：:Although the importance of the extracellular signal-regulated kinase (ERK) pathway in regulating the transition from G1 to S has been extensively studied, its role during the G2/M transition is less well understood. Previous reports have shown that inhibition of the ERK pathway in mammalian cells delays entry as well ...

journal_title：Proteomics

authors： Roberts EC,Hammond K,Traish AM,Resing KA,Ahn NG

更新日期：2006-08-01 00:00:00

abstract：:The function of a protein is modulated by its abundance and its degree of specific post-translational modifications such as phosphorylation, glycosylation or truncation. Consequently, changes of protein concentration and the extent of their post-translational modifications has a great influence on the activity of intr...

journal_title：Proteomics

authors： Moritz B,Meyer HE

更新日期：2003-11-01 00:00:00

abstract：:Human galectin-3 (hGal-3) is a mammalian lectin involved in regulation of RNA splicing, apoptosis, cell differentiation, and proliferation. Multimerized extracellular hGal-3 is thought to crosslink cells by binding to glycoproteins and glycosylated cancer antigens on the cell surface or extracellular matrix. Fluoresce...

journal_title：Proteomics

authors： Bogoeva VP,Varriale A,John CM,D'Auria S

更新日期：2010-05-01 00:00:00

abstract：:Most of the energy that is introduced into the oceans by photosynthetic primary producers is in the form of organic matter that then sustains the rest of the food web, from micro to macro-organisms. However, it is the interactions between phototrophs and heterotrophs that are vital to maintaining the nutrient balance ...

journal_title：Proteomics

authors： Christie-Oleza JA,Scanlan DJ,Armengaud J

更新日期：2015-10-01 00:00:00

abstract：:Among the group of lactic acid bacteria, Streptococcus thermophilus has found a wide application in industrial processes used for the manufacture of dairy products. Taking advantage of different proteome extraction and subfractionation protocols, bacterial cytosolic and membrane proteins were isolated and resolved by ...

journal_title：Proteomics

authors： Salzano AM,Arena S,Renzone G,D'Ambrosio C,Rullo R,Bruschi M,Ledda L,Maglione G,Candiano G,Ferrara L,Scaloni A

更新日期：2007-05-01 00:00:00

abstract：:CREC proteins constitute a family of EF-hand calcium binding proteins localized to the secretory pathway. Calumenin is the only member known to be secreted. Recently, it was shown that thrombin-activated thrombocytes liberate calumenin, which also is found in atherosclerotic lesions but not in normal vasculature. To s...

journal_title：Proteomics

authors： Ostergaard M,Hansen GA,Vorum H,Honoré B

更新日期：2006-06-01 00:00:00

abstract：:Post-translational methylation of the epsilon-amino group of lysine residues regulates a number of protein functions. Calmodulin, a key modulator of intracellular calcium signaling, is methylated on lysine 115 in many species. Although the amino acid sequence of calmodulin is highly conserved in eukaryotes, it has bee...

journal_title：Proteomics

authors： Takemori N,Komori N,Thompson JN Jr,Yamamoto MT,Matsumoto H

更新日期：2007-08-01 00:00:00

abstract：:Separation or prefractionation of proteins by gel electrophoresis, followed by in-gel proteolytic digest and analysis by MS is a typical standard application in proteomics. For many laboratories, it is not cost-effective to use a robot with all its drawbacks. On the other hand, manual digest is time consuming and not ...

journal_title：Proteomics

authors： Franz T,Li X

更新日期：2012-08-01 00:00:00

abstract：:Renal cell carcinoma (RCC) originates in the renal cortex. It accounts for 2-3 percent of all cancers occurring in adults and it is characterised by lack of early clinical manifestations, unpredictable outcome, and absence of effective treatment modalities except early surgery. RCC comprises a heterogeneous group of t...

journal_title：Proteomics

authors： Sarto C,Déon C,Doro G,Hochstrasser DF,Mocarelli P,Sanchez JC

更新日期：2001-10-01 00:00:00

abstract：:Spatial organisation of proteins according to their function plays an important role in the specificity of their molecular interactions. Emerging proteomics methods seek to assign proteins to sub-cellular locations by partial separation of organelles and computational analysis of protein abundance distributions among ...

journal_title：Proteomics

authors： Trotter MW,Sadowski PG,Dunkley TP,Groen AJ,Lilley KS

更新日期：2010-12-01 00:00:00

abstract：:The existence of a gamma-glutamyl cycle consisting of intracellular GSH synthesis, extrusion to the apoplastic space and recovery by gamma-glutamyl transferase (GGT)-assisted degradation into its constituent amino acids, has been demonstrated in plants. To address the significance of this cycle in plant cells, we perf...

journal_title：Proteomics

authors： Tolin S,Arrigoni G,Trentin AR,Veljovic-Jovanovic S,Pivato M,Zechman B,Masi A

更新日期：2013-06-01 00:00:00

abstract：:Somatic embryogenesis is a biotechnological approach mainly used for the clonal propagation of different plants worldwide. In somatic embryogenesis, embryos arise from somatic cells under appropriate culture conditions. This plasticity in plants is a demonstration of true cellular totipotency and is the best approach ...

journal_title：Proteomics

authors： Heringer AS,Santa-Catarina C,Silveira V

更新日期：2018-03-01 00:00:00