Improved membrane proteomics coverage of human embryonic stem cells by peptide IPG-IEF.

abstract：:Liver is unique in its capability to regenerate after an injury. Liver regeneration after a 2/3 partial hepatectomy served as a classical model and is adopted frequently to study the mechanism of liver regeneration. In the present study, semiquantitative analysis of protein expression in mouse liver regeneration follo...

journal_title：Journal of proteome research

authors： Hsieh HC,Chen YT,Li JM,Chou TY,Chang MF,Huang SC,Tseng TL,Liu CC,Chen SF

更新日期：2009-02-01 00:00:00

abstract：:The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analyzed per experiment as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elast...

journal_title：Journal of proteome research

authors： Hulstaert N,Shofstahl J,Sachsenberg T,Walzer M,Barsnes H,Martens L,Perez-Riverol Y

更新日期：2020-01-03 00:00:00

abstract：:In this paper, we describe a method for analyzing large-volume protein samples using capillary electrophoresis in conjunction with laser-induced fluorescence detection (CE-LIF). To improve the stacking and separation efficiencies of proteins, we added either 0.01% sodium dodecyl sulfate (SDS) or 0.01% poly(ethylene ox...

journal_title：Journal of proteome research

authors： Huang YF,Hsieh MM,Tseng WL,Chang HT

更新日期：2006-02-01 00:00:00

abstract：:Protein or peptide sample losses could accompany all steps of the proteomic analysis workflow. We focused on suppression of sample adsorptive losses during sample storage in autosampler vials. We examined suppression capabilities of six different sample injection solutions and seven types of autosampler vial surfaces ...

journal_title：Journal of proteome research

authors： Stejskal K,Potěšil D,Zdráhal Z

更新日期：2013-06-07 00:00:00

abstract：:Epithelial ovarian carcinoma has in general a poor prognosis since the vast majority of tumors are genomically unstable and clinically highly aggressive. This results in rapid progression of malignancy potential while still asymptomatic and thus in late diagnosis. It is therefore of critical importance to develop meth...

journal_title：Journal of proteome research

authors： Waldemarson S,Krogh M,Alaiya A,Kirik U,Schedvins K,Auer G,Hansson KM,Ossola R,Aebersold R,Lee H,Malmström J,James P

更新日期：2012-05-04 00:00:00

abstract：:Glioblastoma (GBM) is the most common adult primary brain tumor. Despite aggressive multimodal therapy, the survival of patients with GBM remains dismal. However, recent evidence has demonstrated the promise of bone marrow-derived mesenchymal stem cells (BM-hMSCs) as a therapeutic delivery vehicle for anti-glioma agen...

journal_title：Journal of proteome research

authors： Wildburger NC,Wood PL,Gumin J,Lichti CF,Emmett MR,Lang FF,Nilsson CL

更新日期：2015-06-05 00:00:00

abstract：:The SwePep database is designed for endogenous peptides and mass spectrometry. It contains information about the peptides such as mass, pl, precursor protein and potential post-translational modifications. Here, we have improved and extended the SwePep database with tandem mass spectra, by adding a locally curated ver...

journal_title：Journal of proteome research

authors： Fälth M,Svensson M,Nilsson A,Sköld K,Fenyö D,Andren PE

更新日期：2008-07-01 00:00:00

abstract：:Crucial metabolites that modulate hosts' metabolome to eliminate bacterial pathogens have been documented, but the metabolic mechanisms are largely unknown. The present study explores the metabolic mechanism for l-leucine-induced metabolome to eliminate Streptococcus iniae in tilapia. GC-MS-based metabolomics was used...

journal_title：Journal of proteome research

authors： Du CC,Yang MJ,Li MY,Yang J,Peng B,Li H,Peng XX

更新日期：2017-05-05 00:00:00

abstract：:Pancreas ductal adenocarcinoma (PDAC) remains a deadly malignancy with poor early diagnostic and no effective therapy. Although several proteomic studies have performed comparative analysis between normal and malignant tissues, there is a lack of clear characterization of proteins that could be of clinical value. Syst...

journal_title：Journal of proteome research

authors： Turtoi A,Musmeci D,Wang Y,Dumont B,Somja J,Bevilacqua G,De Pauw E,Delvenne P,Castronovo V

更新日期：2011-09-02 00:00:00

abstract：:The silk gland of the silkworm Bombyx mori undergoes programmed cell death (PCD) during pupal metamorphosis. On the basis of their morphological changes and the occurrence of a DNA ladder, the tissue cells were categorized into three groups: intact, committed, and dying. To identify the proteins involved in this proce...

journal_title：Journal of proteome research

authors： Jia SH,Li MW,Zhou B,Liu WB,Zhang Y,Miao XX,Zeng R,Huang YP

更新日期：2007-08-01 00:00:00

abstract：:As cellular metabolic hubs, mitochondria are the main energy producers for the cell. These organelles host essential energy producing biochemical processes, including the TCA cycle, fatty acid oxidation, and oxidative phosphorylation. An accumulating body of literature has demonstrated that a majority of mitochondrial...

journal_title：Journal of proteome research

authors： Betsinger CN,Cristea IM

更新日期：2019-05-03 00:00:00

abstract：:Several high-throughput statistical methods were evaluated for processing data generated by two-dimensional polyacrylamide gel electrophoresis, including how to handle missing data, normalization, and statistical analysis of data obtained from 2-D gels. Quantile normalization combined with a nonparametric permutation ...

journal_title：Journal of proteome research

authors： Chang J,Van Remmen H,Ward WF,Regnier FE,Richardson A,Cornell J

更新日期：2004-11-01 00:00:00

abstract：:Candida albicans (C. albicans) is a worldwide cause of fungal infectious diseases. As a general post-translational modification (PTM), lysine acetylation of proteins play an important regulatory role in almost every cell. In our research, we used a high-resolution proteomic technique (LC-MS/MS) to present the comprehe...

journal_title：Journal of proteome research

authors： Zhou X,Qian G,Yi X,Li X,Liu W

更新日期：2016-08-05 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：:The zebrafish genome has recently been sequenced and annotated allowing for high-throughput proteomic analysis. Here, we report for the first time a proteomic subset of zebrafish liver, an important organ for metabolizing toxins. Using a newly developed analytical procedure, we have identified 1204 proteins from the c...

journal_title：Journal of proteome research

authors： Wang N,Mackenzie L,De Souza AG,Zhong H,Goss G,Li L

更新日期：2007-01-01 00:00:00

abstract：:A challenge in proteomics is that many observations are missing with the probability of missingness increasing as abundance decreases. Adjusting for this informative missingness is required to assess accurately which proteins are differentially abundant. We propose an empirical Bayesian random censoring threshold (EBR...

journal_title：Journal of proteome research

authors： Koopmans F,Cornelisse LN,Heskes T,Dijkstra TM

更新日期：2014-09-05 00:00:00

abstract：:Post-translational nitration of proteins was analyzed by capillary reversed-phase high-performance liquid chromatography (RP-HPLC) on-line interfaced to electrospray ionization mass spectrometry (ESI--MS) or tandem mass spectrometry (ESI--MS/MS). Both methods were compared using a tryptic digest of bovine serum albumi...

journal_title：Journal of proteome research

authors： Walcher W,Franze T,Weller MG,Pöschl U,Huber CG

更新日期：2003-09-01 00:00:00

abstract：:To decrease the mortality of lung cancer, better screening and diagnostic tools as well as treatment options are needed. Protein glycosylation is one of the major post-translational modifications that is altered in cancer, but it is not exactly clear which glycan structures are affected. A better understanding of the ...

journal_title：Journal of proteome research

authors： Ruhaak LR,Taylor SL,Stroble C,Nguyen UT,Parker EA,Song T,Lebrilla CB,Rom WN,Pass H,Kim K,Kelly K,Miyamoto S

更新日期：2015-11-06 00:00:00

abstract：:Reliable statistical validation of peptide and protein identifications is a top priority in large-scale mass spectrometry based proteomics. PeptideProphet is one of the computational tools commonly used for assessing the statistical confidence in peptide assignments to tandem mass spectra obtained using database searc...

journal_title：Journal of proteome research

authors： Choi H,Ghosh D,Nesvizhskii AI

更新日期：2008-01-01 00:00:00

abstract：:Affinity purification coupled to 1-D gel-free liquid chromatography mass spectrometry (LC-MS) is a well-established and widespread approach for the analyses of noncovalently interacting protein complexes. In this study, two proteins conjugated to a streptavidin-binding peptide and hemagglutinin double tag were express...

journal_title：Journal of proteome research

authors： Huber ML,Sacco R,Parapatics K,Skucha A,Khamina K,Müller AC,Rudashevskaya EL,Bennett KL

更新日期：2014-02-07 00:00:00

abstract：:Histone linker proteins H1 and H5 were purified from chicken erythrocyte cell nuclei under nondenaturing conditions. The purified linker histones were analyzed using in-solution enzymatic digestions followed by nanoflow reverse-phase high-performance liquid chromatography tandem mass spectrometry. We have identified a...

journal_title：Journal of proteome research

authors： Snijders AP,Pongdam S,Lambert SJ,Wood CM,Baldwin JP,Dickman MJ

更新日期：2008-10-01 00:00:00

abstract：:The fungal pathogen Fusarium graminearum (telomorph Gibberella zeae) is the causal agent of several destructive crop diseases. Identifying interactions among F. graminearum proteins and understanding their functions can provide insights into pathogenic mechanisms underlying F. graminearum-host interactions. F. gramine...

journal_title：Journal of proteome research

authors： Zhao XM,Zhang XW,Tang WH,Chen L

更新日期：2009-10-01 00:00:00

abstract：:Protein chemical cross-linking combined with mass spectrometry has become an important technique for the analysis of protein structure and protein-protein interactions. A variety of cross-linkers are well developed, but reliable, rapid, and user-friendly tools for large-scale analysis of cross-linked proteins are stil...

journal_title：Journal of proteome research

authors： Lu L,Millikin RJ,Solntsev SK,Rolfs Z,Scalf M,Shortreed MR,Smith LM

更新日期：2018-07-06 00:00:00

abstract：:We developed an ELISA in high-density microarray format to detect hepatocyte growth factor (HGF) in human serum. The microassay can detect HGF at sub-pg/mL concentrations in sample volumes of 100 microL or less. The microassay is also quantitative and was used to detect elevated HGF levels in sera from recurrent breas...

journal_title：Journal of proteome research

authors： Woodbury RL,Varnum SM,Zangar RC

更新日期：2002-05-01 00:00:00

abstract：:Redox regulation plays an important role across a broad spectrum of biology. Accumulating evidence suggests that thioredoxin, a widely distributed redox enzyme, participates in the redox control of numerous target proteins, thus, playing a key role as a signaling intermediate that senses the metabolic state or environ...

journal_title：Journal of proteome research

authors： Yano H,Kuroda S

更新日期：2008-08-01 00:00:00

abstract：:In systemic amyloidosis, accumulation of misfolded proteins as extracellular amyloid fibrils in tissues causes severe organ dysfunction, but the molecular events of tissue damage related to amyloid deposition are still largely unknown. Through the use of the MudPIT proteomic approach, comprehensive protein profiles of...

journal_title：Journal of proteome research

authors： Brambilla F,Lavatelli F,Di Silvestre D,Valentini V,Palladini G,Merlini G,Mauri P

更新日期：2013-12-06 00:00:00

abstract：:Defects in the gene encoding the persulfide dioxygenase ETHE1 are known to cause the severe inherited metabolic disorder ethylmalonic encephalopathy (EE). In spite of known clinical characteristics, the molecular mechanisms underlying the ETHE1 deficiency are still obscure. Herein, to further analyze the molecular phe...

journal_title：Journal of proteome research

authors： Sahebekhtiari N,Nielsen CB,Johannsen M,Palmfeldt J

更新日期：2016-05-06 00:00:00

abstract：:Complicating proteomic analysis of whole tissues is the obvious problem of cell heterogeneity in tissues, which often results in misleading or confusing molecular findings. Thus, the coupling of tissue microdissection for tumor cell enrichment with capillary isotachophoresis-based selective analyte concentration not o...

journal_title：Journal of proteome research

authors： Fang X,Wang C,Balgley BM,Zhao K,Wang W,He F,Weil RJ,Lee CS

更新日期：2012-08-03 00:00:00

abstract：:Charcoal-stripped fetal bovine serum (CS-FBS) is commonly used to study androgen responsiveness and androgen metabolism in cultured prostate cancer (CaP) cells. Switching CaP cells from FBS to CS-FBS may reduce the activity of androgen receptor (AR), inhibit cell proliferation, or modulate intracellular androgen metab...

journal_title：Journal of proteome research

authors： Tu C,Fiandalo MV,Pop E,Stocking JJ,Azabdaftari G,Li J,Wei H,Ma D,Qu J,Mohler JL,Tang L,Wu Y

更新日期：2018-09-07 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