Analysis of PNGase F-Resistant N-Glycopeptides Using SugarQb for Proteome Discoverer 2.1 Reveals Cryptic Substrate Specificities.

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：:The metacestode larval stage of Taenia solium is the causal agent of a zoonotic disease called cysticercosis. The disease has an important impact on pork trade (due to porcine cysticercosis) and public health (due to human neurocysticercosis). In order to improve the current diagnostic tools and to get a better unders...

journal_title：Proteomics

authors： Victor B,Kanobana K,Gabriël S,Polman K,Deckers N,Dorny P,Deelder AM,Palmblad M

更新日期：2012-06-01 00:00:00

abstract：:We have used MALDI-MS imaging (MALDI-MSI) to monitor the time dependent appearance and loss of signals when tissue slices are brought rapidly to room temperature for short to medium periods of time. Sections from mouse brain were cut in a cryostat microtome, placed on a MALDI target and allowed to warm to room tempera...

journal_title：Proteomics

authors： Goodwin RJ,Dungworth JC,Cobb SR,Pitt AR

更新日期：2008-09-01 00:00:00

abstract：:The G-protein complex is a cytoplasmic on-off molecular switch that is set by plasma membrane receptors that activate upon binding of its cognate extracellular agonist. In animals, the default setting is the "off" resting state, while in plants, the default state is constitutively "on" but repressed by a plasma membra...

journal_title：Proteomics

authors： Song G,Brachova L,Nikolau BJ,Jones AM,Walley JW

更新日期：2018-12-01 00:00:00

abstract：:The influenza virus polymerase is formed by the PB1, PB2 and PA subunits and is required for virus transcription and replication in the nucleus of infected cells. Here we present the characterisation of the complexes formed intracellularly by the influenza polymerase in human cells. The virus polymerase was expressed ...

journal_title：Proteomics

authors： Jorba N,Juarez S,Torreira E,Gastaminza P,Zamarreño N,Albar JP,Ortín J

更新日期：2008-05-01 00:00:00

abstract：:During early stages of embryo development, the brain cavity is filled with embryonic cerebrospinal fluid (E-CSF), a complex fluid containing different protein fractions that contributes to the regulation of the survival, proliferation and neurogenesis of the neuroectodermal stem cells. Using 2-DE, protein sequencing a...

journal_title：Proteomics

authors： Parada C,Gato A,Aparicio M,Bueno D

更新日期：2006-01-01 00:00:00

abstract：:Along with unequivocal hits produced by matching multiple MS/MS spectra to database sequences, LC-MS/MS analysis often yields a large number of hits of borderline statistical confidence. To simplify their validation, we propose to use rapid de novo interpretation of all acquired MS/MS spectra and, with the help of a s...

journal_title：Proteomics

authors： Thomas H,Shevchenko A

更新日期：2008-10-01 00:00:00

abstract：:The cancer tissue proteome has enormous potential as a source of novel predictive biomarkers in oncology. Progress in the development of mass spectrometry (MS)-based tissue proteomics now presents an opportunity to exploit this by applying the strategies of comprehensive molecular profiling and big-data analytics that...

journal_title：Proteomics

authors： Tully B,Balleine RL,Hains PG,Zhong Q,Reddel RR,Robinson PJ

更新日期：2019-11-01 00:00:00

abstract：:The oxidation of free and protein-bound methionine into methionine sulfoxide is a frequently occurring modification caused by ROS. Most organisms express methionine sulfoxide reductases (MSR enzymes) to repair this potentially damaging modification. Humans express three different MSRB enzymes which reside in different...

journal_title：Proteomics

authors： Vandermarliere E,Ghesquière B,Jonckheere V,Gevaert K,Martens L

更新日期：2014-09-01 00:00:00

abstract：:A method for quantitative proteomic analysis based on the selective isolation of multiply charged peptides (RH peptides) containing arginine and histidine residues is described. Two pools of proteins are digested in tandem with lysyl-endopeptidase and trypsin and the primary amino groups of proteolytic peptides are se...

journal_title：Proteomics

authors： Sánchez A,González LJ,Betancourt L,Gil J,Besada V,Fernández-de-Cossío J,Rodríguez-Ulloa A,Marrero K,Alvarez F,Fando R,Padrón G

更新日期：2006-08-01 00:00:00

abstract：:A diverse range of proteins are modified by the post-translational covalent attachment of a glycosyl-phosphatidylinositol (GPI) membrane anchor. Hydropathy plots and other computer algorithms can be used to predict the presence of a GPI anchor attachment signal in the nascent polypeptide chain. However, the presence o...

journal_title：Proteomics

authors： Hooper NM

更新日期：2001-06-01 00:00:00

abstract：:Proteins extracted from leaf blades of rice plants infected with blast fungus, Magnaporthe grisea, were separated by two-dimensional polyacrylamide gel electrophoresis. The separated proteins were electroblotted onto a polyvinylidene difluoride membrane, and 63 proteins were analyzed by a gas-phase protein sequencer. ...

journal_title：Proteomics

authors： Konishi H,Ishiguro K,Komatsu S

更新日期：2001-09-01 00:00:00

abstract：:The Asia Oceania Human Proteome Organisation (AOHUPO) has embarked on a Membrane Proteomics Initiative with goals of systematic comparison of strategies for analysis of membrane proteomes and discovery of membrane proteins. This multilaboratory project is based on the analysis of a subcellular fraction from mouse live...

journal_title：Proteomics

authors： Peng L,Kapp EA,Fenyö D,Kwon MS,Jiang P,Wu S,Jiang Y,Aguilar MI,Ahmed N,Baker MS,Cai Z,Chen YJ,Van Chi P,Chung MC,He F,Len AC,Liao PC,Nakamura K,Ngai SM,Paik YK,Pan TL,Poon TC,Salekdeh GH,Simpson RJ,Sirdesh

更新日期：2010-11-01 00:00:00

abstract：:Legume symbiosis with rhizobia results in the formation of a specialized organ, the root nodule, where atmospheric dinitrogen is reduced to ammonia. In Lotus japonicus (Lotus), several genes involved in nodule development or nodule function have been defined using biochemistry, genetic approaches, and high-throughput ...

journal_title：Proteomics

authors： Dam S,Dyrlund TF,Ussatjuk A,Jochimsen B,Nielsen K,Goffard N,Ventosa M,Lorentzen A,Gupta V,Andersen SU,Enghild JJ,Ronson CW,Roepstorff P,Stougaard J

更新日期：2014-02-01 00:00:00

abstract：:This review provides a brief overview of the development of data-independent acquisition (DIA) mass spectrometry-based proteomics and selected DIA data analysis tools. Various DIA acquisition schemes for proteomics are summarized first including Shotgun-CID, DIA, MSE , PAcIFIC, AIF, SWATH, MSX, SONAR, WiSIM, BoxCar, S...

journal_title：Proteomics

authors： Zhang F,Ge W,Ruan G,Cai X,Guo T

更新日期：2020-09-01 00:00:00

abstract：:Seed coat color is an important attribute determining consumption of soybean seeds. Soybean cultivar Mallikong (M) has yellow seed coat while its naturally mutated cultivar Mallikong mutant (MM), has brown colored seed coat. We used integrated proteomics and metabolomics approach to investigate the differences between...

journal_title：Proteomics

authors： Gupta R,Min CW,Kim SW,Wang Y,Agrawal GK,Rakwal R,Kim SG,Lee BW,Ko JM,Baek IY,Bae DW,Kim ST

更新日期：2015-05-01 00:00:00

abstract：:The explosion of site- and context-specific in vivo phosphorylation events presents a potentially rich source of biological knowledge and calls for novel data analysis and modeling paradigms. Perhaps the most immediate challenge is delineating detected phosphorylation sites to their effector kinases. This is important...

journal_title：Proteomics

authors： Tan CS,Linding R

更新日期：2009-12-01 00:00:00

abstract：:We here present the jmzReader library: a collection of Java application programming interfaces (APIs) to parse the most commonly used peak list and XML-based mass spectrometry (MS) data formats: DTA, MS2, MGF, PKL, mzXML, mzData, and mzML (based on the already existing API jmzML). The library is optimized to be used i...

journal_title：Proteomics

authors： Griss J,Reisinger F,Hermjakob H,Vizcaíno JA

更新日期：2012-03-01 00:00:00

abstract：:Here, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3-D structures. The tool has been designed to display very complex networks of up to 40 000 proteins or 6000 multiprotein com...

journal_title：Proteomics

authors： Widjaja YY,Pang CN,Li SS,Wilkins MR,Lambert TD

更新日期：2009-12-01 00:00:00

abstract：:Intracellular serine protease-1 (Isp-1) is a major intracellular serine protease of Bacillus subtilis, whose functions still remain largely unknown. Furthermore, physiological substrates are yet to be determined. To identify Isp-1 substrates, we digested extract obtained from an Isp-1 deficient Bacillus mutant with pu...

journal_title：Proteomics

authors： Lee AY,Goo Park S,Kho CW,Young Park S,Cho S,Lee SC,Lee DH,Myung PK,Park BC

更新日期：2004-11-01 00:00:00

abstract：:Cancer cells maintain their intracellular ROS concentrations at required levels for their survival. Changes in ROS concentrations can regulate biochemical signaling mechanisms that control cell function. It has been demonstrated that ROS regulate the cellular events through redox regulation of redox-sensitive proteins...

journal_title：Proteomics

authors： Yuan K,Liu Y,Chen HN,Zhang L,Lan J,Gao W,Dou Q,Nice EC,Huang C

更新日期：2015-01-01 00:00:00

abstract：:In this article, we provide a comprehensive study of the content of the Universal Protein Resource (UniProt) protein data sets for human and mouse. The tryptic search spaces of the UniProtKB (UniProt knowledgebase) complete proteome sets were compared with other data sets from UniProtKB and with the corresponding Inte...

journal_title：Proteomics

authors： Alpi E,Griss J,da Silva AW,Bely B,Antunes R,Zellner H,Ríos D,O'Donovan C,Vizcaíno JA,Martin MJ

更新日期：2015-01-01 00:00:00

abstract：:Surface-enhanced laser desorption/ionization (SELDI) time of flight (TOF) is a mass spectrometry technology for measuring the composition of a sampled protein mixture. A mass spectrum contains peaks corresponding to proteins in the sample. The peak areas are proportional to the measured concentrations of the correspon...

journal_title：Proteomics

authors： Dijkstra M,Roelofsen H,Vonk RJ,Jansen RC

更新日期：2006-10-01 00:00:00

abstract：:It becomes increasingly clear that separation of pure cell populations provides a uniquely sensitive and accurate approach to protein profiling in biological systems and opens up a new area for proteomic analysis. The method we described could simultaneously isolate population of hepatocytes (HCs), hepatic stellate ce...

journal_title：Proteomics

authors： Liu W,Hou Y,Chen H,Wei H,Lin W,Li J,Zhang M,He F,Jiang Y

更新日期：2011-09-01 00:00:00

abstract：:A classical proteomic analysis was used to establish a reference map of proteins associated with healthy human erythrocyte ghosts. Following osmotic lysis and differential centrifugation, ghost proteins were separated by either one-dimensional gel electrophoresis (1-DE) or two-dimensional gel electrophoresis (2-DE). S...

journal_title：Proteomics

authors： Low TY,Seow TK,Chung MC

更新日期：2002-09-01 00:00:00

abstract：:The prediction of adverse drug reactions (ADRs) has become increasingly important, due to the rising concern on serious ADRs that can cause drugs to fail to reach or stay in the market. We proposed a framework for predicting ADR profiles by integrating protein-protein interaction (PPI) networks with drug structures. W...

journal_title：Proteomics

authors： Huang LC,Wu X,Chen JY

更新日期：2013-01-01 00:00:00

abstract：:In this study we investigated the cellular response to the application of high hydrostatic pressure. High pressure is increasingly used for food preservation. With high resolution 2-D electrophoresis we compared the protein patterns of atmospherically grown Lactobacillus sanfranciscensis with those pressure treated up...

journal_title：Proteomics

authors： Drews O,Weiss W,Reil G,Parlar H,Wait R,Görg A

更新日期：2002-06-01 00:00:00

abstract：:High-density lipoprotein (HDL) is the most abundant lipoprotein particle in the plasma and a negative risk factor of atherosclerosis. By using a proteomic approach it is possible to obtain detailed information about its protein content and protein modifications that may give new information about the physiological rol...

journal_title：Proteomics

authors： Karlsson H,Leanderson P,Tagesson C,Lindahl M

更新日期：2005-04-01 00:00:00

abstract：:Lipid rafts are membrane microdomains of unique lipid composition that segregate proteins with poorly understood consequences for membrane organization. Identification of raft associated proteins could therefore provide novel insight into raft-dependent functions. Monocytes process antigens for presentation to T cells...

journal_title：Proteomics

authors： Li N,Mak A,Richards DP,Naber C,Keller BO,Li L,Shaw AR

更新日期：2003-04-01 00:00:00

abstract：:A method is introduced to evaluate protein concentrations using the height sum of all MALDI-MS peaks that unambiguously match theoretic tryptic peptide masses of the protein sought after. The method uses native chromatographic protein fractionation prior to digestion but does not require any depletion, labeling, deriv...

journal_title：Proteomics

authors： Bublitz R,Kreusch S,Ditze G,Schulze M,Cumme GA,Fischer C,Winter A,Hoppe H,Rhode H

更新日期：2006-07-01 00:00:00