Evaluation of empirical rule of linearly correlated peptide selection (ERLPS) for proteotypic peptide-based quantitative proteomics.

abstract：:SELDI-TOF-MS is rapidly gaining popularity as a screening tool for clinical applications of proteomics. Application of adequate statistical techniques in all the stages from measurement to information is obligatory. One of the statistical methods often used in proteomics is classification: the assignment of subjects t...

journal_title：Proteomics

authors： Hendriks MM,Smit S,Akkermans WL,Reijmers TH,Eilers PH,Hoefsloot HC,Rubingh CM,de Koster CG,Aerts JM,Smilde AK

更新日期：2007-10-01 00:00:00

abstract：:Imbalance in protein homeostasis in specific subcellular organelles is alleviated through organelle-specific stress response pathways. As a canonical example of stress activated pathway, accumulation of misfolded proteins in ER activates unfolded protein response (UPR) in almost all eukaryotic organisms. However, very...

journal_title：Proteomics

authors： Maity S,Basak T,Bhat A,Bhasin N,Ghosh A,Chakraborty K,Sengupta S

更新日期：2014-08-01 00:00:00

abstract：:"Liquid biopsies" have received attention as a complementary tool for traditional tissue biopsies that may enhance the spectrum of analysis for tumor-derived factors. One such factor gaining prominence in the liquid biopsy field is extracellular vesicles (EVs), membrane-bound nanovesicles which are secreted by cells i...

journal_title：Proteomics

authors： Ruhen O,Meehan K

更新日期：2019-01-01 00:00:00

abstract：:Microparticles (MPs) are small membranous particles (100-1000 nm) released under normal steady-state conditions and are thought to provide a communication network between host cells. Previous studies demonstrated that Mycobacterium tuberculosis (M. tb) infection of macrophages increased the release of MPs, and these M...

journal_title：Proteomics

authors： Hare NJ,Chan B,Chan E,Kaufman KL,Britton WJ,Saunders BM

更新日期：2015-09-01 00:00:00

abstract：:Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are an important class of glycoproteins that are tethered to the surface of mammalian cells via the lipid GPI. GPI-APs have been implicated in many important cellular functions including cell adhesion, cell signaling, and immune regulation. Proteomic identificat...

journal_title：Proteomics

authors： Cortes LK,Vainauskas S,Dai N,McClung CM,Shah M,Benner JS,Corrêa IR Jr,VerBerkmoes NC,Taron CH

更新日期：2014-11-01 00:00:00

abstract：:Isolated from Elephantopus scaber L., a Chinese medicinal herb that is widely used to prevent and treat cancers in China, isodeoxyelephantopin (ESI) exerted antitumor effects on several cancer cells. However, its antitumor mechanism is still not clear. In this study, we found that ESI could induce G2/M arrest and subs...

journal_title：Proteomics

authors： Yan GR,Tan Z,Wang Y,Xu ML,Yu G,Li Y,He QY

更新日期：2013-11-01 00:00:00

abstract：:Realistic in vitro models are critical in the drug development process. In this study, a novel in vitro platform is employed to assess drug penetration and metabolism. This platform, which utilizes a 3D printed fluidic device, allows for dynamic dosing of three dimensional cell cultures, also known as spheroids. The p...

journal_title：Proteomics

authors： LaBonia GJ,Lockwood SY,Heller AA,Spence DM,Hummon AB

更新日期：2016-06-01 00:00:00

abstract：:Geobacter species predominate in aquatic sediments and submerged soils where organic carbon sources are oxidized with the reduction of Fe(III). The natural occurrence of Geobacter in some waste sites suggests this microorganism could be useful for bioremediation if growth and metabolic activity can be regulated. 2-DE ...

journal_title：Proteomics

authors： Ahrendt AJ,Tollaksen SL,Lindberg C,Zhu W,Yates JR 3rd,Nevin KP,Babnigg G,Lovley DR,Giometti CS

更新日期：2007-11-01 00:00:00

abstract：:Niemann-Pick disease, type C1 (NPC1) is a fatal, autosomal recessive, neurodegenerative disorder caused by mutations in the NPC1 gene. As a result of the genetic defect, there is accumulation of unesterified cholesterol and sphingolipids in the late endosomal/lysosomal system causing both visceral and neurological def...

journal_title：Proteomics

authors： Pergande MR,Serna-Perez F,Mohsin SB,Hanek J,Cologna SM

更新日期：2019-09-01 00:00:00

abstract：:Immune proteomics is an increasingly powerful tool for the investigation of the adaptive immune response to natural encounters between micro-organisms and their hosts. The versatile species Staphylococcus aureus serves to illustrate how these techniques can be employed to appreciate the complexity and diversity of the...

journal_title：Proteomics

authors： Bröker BM,van Belkum A

更新日期：2011-08-01 00:00:00

abstract：:The hypothalamus is the central regulatory unit that balances a number of body functions including metabolic rate, hunger, and satiety signals. Hypothalamic neurons monitor and respond to alterations of circulating nutrients and hormones that reflect the peripheral energy status. These extracellular signals are integr...

journal_title：Proteomics

authors： Kuhla B,Kuhla S,Rudolph PE,Albrecht D,Metges CC

更新日期：2007-10-01 00:00:00

abstract：:In the era of quantitative proteomics, where mass spectrometry plays a pivotal role, in particular associated with the use of data-independent acquisition, it is time to perform an overview of this growing field with special focus on one of the most promising approaches: SWATH-MS, and to present future perspectives fo...

journal_title：Proteomics

authors： Anjo SI,Santa C,Manadas B

更新日期：2017-02-01 00:00:00

abstract：:The eukaryotic chromatin/chromosome stores genomic information, controls genetic material distribution, and plays an essential role in the establishment and maintenance of spatial and temporal gene expression profile. Despite over a century of research, the protein composition and higher level structure of chromatin s...

journal_title：Proteomics

authors： Tan F,Li G,Chitteti BR,Peng Z

更新日期：2007-12-01 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：: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：:Top-down proteomics have recently started to gain attention as a novel method to provide insight into the structure of proteins in their native state, specifically the number and location of disulfide bridges. However, previous techniques still relied on complex and time-consuming protein purification and reduction re...

journal_title：Proteomics

authors： Khairallah RJ,Sadayappan S

更新日期：2013-11-01 00:00:00

abstract：:As one of the most important post-translational modifications, the discovery, isolation, and identification of glycoproteins are becoming increasingly important. In this study, a Con A-magnetic particle conjugate-based method was utilized to selectively isolate the glycoproteins and their glycomes from the healthy don...

journal_title：Proteomics

authors： Yang G,Cui T,Wang Y,Sun S,Ma T,Wang T,Chen Q,Li Z

更新日期：2013-05-01 00:00:00

abstract：:High-affinity molecular pairs provide a convenient and flexible modular base for the design of molecular probes and protein/antigen assays. Specificity and sensitivity performance indicators of a bioassay critically depend on the dissociation constant (K(D)) of the molecular pair, with avidin:biotin being the state-of...

journal_title：Proteomics

authors： Sreenivasan VK,Kelf TA,Grebenik EA,Stremovskiy OA,Say JM,Rabeau JR,Zvyagin AV,Deyev SM

更新日期：2013-05-01 00:00:00

abstract：:In an accompanying study (in this issue, DOI 10.1002/pmic.200402044), we have characterised the proteome of Sca-1(+) progenitor cells, which may function as precursors of vascular smooth muscle cells (SMCs). In the present study, we have analysed and mapped protein expression in aortic SMCs of mice, using 2-DE, MALDI-...

journal_title：Proteomics

authors： Mayr U,Mayr M,Yin X,Begum S,Tarelli E,Wait R,Xu Q

更新日期：2005-11-01 00:00:00

abstract：:The use of isobaric tags such as iTRAQ allows the relative and absolute quantification of hundreds of proteins in a single experiment for up to eight different samples. More classical techniques such as 2-DE can offer a complimentary approach for the analysis of complex protein samples. In this study, the proteomes of...

journal_title：Proteomics

authors： Mehaffy C,Hess A,Prenni JE,Mathema B,Kreiswirth B,Dobos KM

更新日期：2010-05-01 00:00:00

abstract：:Advances in gel-based nonradioactive protein expression and PTM detection using fluorophores has served as the impetus for developing analytical instrumentation with improved imaging capabilities. We describe a CCD camera-based imaging instrument, equipped with both a high-pressure Xenon arc lamp and a UV transillumin...

journal_title：Proteomics

authors： Scrivener E,Boghigian BA,Golenko E,Bogdanova A,Jackson P,Mikulskis A,Denoyer E,Courtney P,Lopez MF,Patton WF

更新日期：2005-11-01 00:00:00

abstract：:Glycan-binding proteins (GBPs) play an important role in cell adhesion, bacterial/viral infection, and cellular signaling pathways. However, little is known about the precision alteration of GBPs referred to pathological changes in hepatic stellate cells (HSCs) during liver fibrosis. Here, the carbohydrate microarrays...

journal_title：Proteomics

authors： Zhong Y,Qin Y,Dang L,Jia L,Zhang Z,Wu H,Cui J,Bian H,Li Z

更新日期：2015-10-01 00:00:00

abstract：:In the present study, changes in protein synthesis patterns after salt shock visualized by 35S-methionine labeling and the changed protein composition in salt-acclimated cells of the cyanobacterium Synechocystis sp. strain PCC 6803 were analyzed by a combination of 2-DE for protein separation and PMF for protein ident...

journal_title：Proteomics

authors： Fulda S,Mikkat S,Huang F,Huckauf J,Marin K,Norling B,Hagemann M

更新日期：2006-05-01 00:00:00

abstract：:Protein quantification at proteome-wide scale is an important aim, enabling insights into fundamental cellular biology and serving to constrain experiments and theoretical models. While proteome-wide quantification is not yet fully routine, many datasets approaching proteome-wide coverage are becoming available throug...

journal_title：Proteomics

authors： Wang M,Herrmann CJ,Simonovic M,Szklarczyk D,von Mering C

更新日期：2015-09-01 00:00:00

abstract：:The Annual Spring workshop of the HUPO-PSI was this year held at the EMBL International Centre for Advanced Training (EICAT) in Heidelberg, Germany. Delegates briefly reviewed the successes of the group to date. These include the wide spread implementation of the molecular interaction data exchange formats, PSI-MI XML...

journal_title：Proteomics

authors： Orchard S,Albar JP,Deutsch EW,Eisenacher M,Vizcaíno JA,Hermjakob H

更新日期：2011-11-01 00:00:00

abstract：:Protein phosphorylation on serine, threonine, and tyrosine is known to be involved in a wide variety of cellular processes, signal transduction, and bacterial virulence. We characterized, for the first time, the extracellular phosphoproteins of the Pseudomonas aeruginosa PA14 strain. We identified 28 phosphoproteins (...

journal_title：Proteomics

authors： Ouidir T,Jarnier F,Cosette P,Jouenne T,Hardouin J

更新日期：2014-09-01 00:00:00

abstract：:Treatment of patients with malignant melanoma with interferon-alpha achieves a response in a small but significant subset of patients. Currently, although much is known about interferon biology, little is known about either the particular mechanisms of interferon-alpha activity that are crucial for response or why onl...

journal_title：Proteomics

authors： Craven RA,Stanley AJ,Hanrahan S,Totty N,Jackson DP,Popescu R,Taylor A,Frey J,Selby PJ,Patel PM,Banks RE

更新日期：2004-12-01 00:00:00

abstract：:The pilot phase of the Human Brain Proteome Project as a part of the Human Proteome Organisation has just been started. In two pilot studies, 18 different laboratories are analyzing mouse brains of three age stages and human brain autopsy versus biopsy material, respectively. The overall aim is to elucidate the portfo...

journal_title：Proteomics

authors： Blüggel M,Bailey S,Körting G,Stephan C,Reidegeld KA,Thiele H,Apweiler R,Hamacher M,Meyer HE

更新日期：2004-08-01 00:00:00

abstract：:This paper proposes a novel profiling method for SELDI-TOF and MALDI-TOF MS data that integrates a novel peak detection method based on modified smoothed non-linear energy operator, correlation-based peak selection and Bayesian additive regression trees. The peak detection and classification performance of the propose...

journal_title：Proteomics

authors： He S,Li X,Viant MR,Yao X

更新日期：2009-09-01 00:00:00

abstract：:As we transition from genomics to the challenges of the functional proteome, new tools to explore the expression of proteins within tissue are essential. We have developed a method of transferring proteins from a formalin fixed, paraffin embedded tissues section to a stack of membranes which is then probed with antibo...

journal_title：Proteomics

authors： Chung JY,Braunschweig T,Baibakov G,Galperin M,Ramesh A,Skacel M,Gannot G,Knezevic V,Hewitt SM

更新日期：2006-02-01 00:00:00