Selective isolation of lysine-free tryptic peptides delimited by arginine residues: A new tool for proteome analysis.

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 purpose of this study was to evaluate the use of high resolution LC-MS together with metabolomics and D(4)-cholic acid (D(4)-CA) as a metabolic tracer to measure the metabolism and reconjugation of bile acids (BAs) in vitro and in vivo. Metabolic tracers are very important because they allow for the direct detecti...

journal_title：Journal of proteome research

authors： Castro-Perez JM,Roddy TP,Shah V,Wang SP,Ouyang X,Ogawa A,McLaren DG,Tadin-Strapps M,Robinson MJ,Bartz SR,Ason B,Chen Y,Previs SF,Wong KK,Vreeken RJ,Johns DG,Hubbard BK,Hankemeier T,Mitnaul L

更新日期：2011-10-07 00:00:00

abstract：:Prostate cancer (PCa) is the second leading cause of cancer-related mortality in men. The prevalent diagnosis method is based on the serum prostate-specific antigen (PSA) screening test, which suffers from low specificity, overdiagnosis, and overtreatment. In this work, untargeted metabolomic profiling of age-matched ...

journal_title：Journal of proteome research

authors： Zang X,Jones CM,Long TQ,Monge ME,Zhou M,Walker LD,Mezencev R,Gray A,McDonald JF,Fernández FM

更新日期：2014-07-03 00:00:00

abstract：:Extracellular vesicles (EVs) are cell-derived microparticles present in most body fluids, mainly including microvesicles and exosomes. EV-harbored proteins have emerged as novel biomarkers for the diagnosis and prediction of different cancers. We successfully isolated microvesicles and exosomes from human saliva, whic...

journal_title：Journal of proteome research

authors： Sun Y,Huo C,Qiao Z,Shang Z,Uzzaman A,Liu S,Jiang X,Fan LY,Ji L,Guan X,Cao CX,Xiao H

更新日期：2018-03-02 00:00:00

abstract：:Our aim was to analyze the plasma proteome in aspirin (acetylsalicylic acid [ASA])-sensitive and ASA-resistant coronary ischemic patients. Plasma from 19 ASA-sensitive and 19 ASA-resistant patients was analyzed. For the proteomic study, two-dimensional electrophoresis was performed. The expression of one isotype of th...

journal_title：Journal of proteome research

authors： López-Farré AJ,Mateos-Cáceres PJ,Sacristán D,Azcona L,Bernardo E,de Prada TP,Alonso-Orgaz S,Fernández-Arquero M,Fernández-Ortiz A,Macaya C

更新日期：2007-07-01 00:00:00

abstract：:Glycosylation has significant effects on protein function and cell metastasis, which are important in cancer progression. It is of great interest to identify site-specific glycosylation in search of potential cancer biomarkers. However, the abundance of glycopeptides is low compared to that of nonglycopeptides after t...

journal_title：Journal of proteome research

authors： Tan Z,Yin H,Nie S,Lin Z,Zhu J,Ruffin MT,Anderson MA,Simeone DM,Lubman DM

更新日期：2015-04-03 00:00:00

abstract：:Antibiotic-induced microbial perturbations alter host metabolism and affect host physiology. In this study, we aimed to investigate the effects of vancomycin (Vanc) and ciprofloxacin/metronidazole (CiMe) exposures on the gut microbiome and metabolome in the colonic content and tissue samples from advanced-stage type 1...

journal_title：Journal of proteome research

authors： Zheng H,Fan K,Ji H,Jiang Q,Ning J,Xu P,Li C,Gao H

更新日期：2019-11-01 00:00:00

abstract：:Transcription regulation translates static genome information to dynamic cell behaviors, making it central to understand how cells interact with and adapt to their environment. However, only a limited number of transcription regulators and their target genes have been identified in the pathogen Mycobacterium tubercul...

journal_title：Journal of proteome research

authors： Zeng J,Cui T,He ZG

更新日期：2012-09-07 00:00:00

abstract：:We describe Peptoonist, a program that can automatically identify the glycans (sugars) present at each N-glycosylation site of a protein. The input to Peptoonist is a series of mass spectra, both MS and MS/MS, obtained from a liquid chromatography (LC) run of proteolytically digested purified glycoproteins. The progra...

journal_title：Journal of proteome research

authors： Goldberg D,Bern M,Parry S,Sutton-Smith M,Panico M,Morris HR,Dell A

更新日期：2007-10-01 00:00:00

abstract：:The plant cell wall is a dynamic cellular compartment consisting of a complex matrix of components that can change dramatically in response to environmental stresses. During pathogen attack, for instance, a wide spectrum of proteins that participate in various sequential processes involved in plant defense is secreted...

journal_title：Journal of proteome research

authors： Cheng FY,Blackburn K,Lin YM,Goshe MB,Williamson JD

更新日期：2009-01-01 00:00:00

abstract：:Protein phosphorylation is one of the major factors involved in tumor progression and malignancy. We performed exploratory studies aimed at identifying phosphoproteins characteristic to cell lines derived from ovarian clear cell adenocarcinoma (CCA), a highly malignant type of ovarian cancer. Comparative phosphoproteo...

journal_title：Journal of proteome research

authors： Kimura A,Arakawa N,Hirano H

更新日期：2014-11-07 00:00:00

abstract：:Clostridium difficile in recent years has undergone rapid evolution and has emerged as a serious human pathogen. Proteomic approaches can improve the understanding of the diversity of this important pathogen, especially in comparing the adaptive ability of different C. difficile strains. In this study, TMT labeling an...

journal_title：Journal of proteome research

authors： Chen JW,Scaria J,Mao C,Sobral B,Zhang S,Lawley T,Chang YF

更新日期：2013-03-01 00:00:00

abstract：:High density lipoprotein (HDL) particles are blood-borne complexes whose plasma levels have been associated with protection from cardiovascular disease (CVD). Recent studies have demonstrated the existence of distinct HDL subspecies; however, these have been difficult to isolate and characterize biochemically. Here, w...

journal_title：Journal of proteome research

authors： Li H,Gordon SM,Zhu X,Deng J,Swertfeger DK,Davidson WS,Lu LJ

更新日期：2015-08-07 00:00:00

abstract：:Grapes are among the widely cultivated fruit crops in the world. Grape berries like other nonclimacteric fruits undergo a complex set of dynamic, physical, physiological, and biochemical changes during ripening. Muscadine grapes are widely cultivated in the southern United States for fresh fruit and wine. To date, cha...

journal_title：Journal of proteome research

authors： Kambiranda D,Katam R,Basha SM,Siebert S

更新日期：2014-02-07 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：:Two-dimensional differential gel electrophoresis (2-D DIGE) was used to analyze human serum following the removal of albumin and five other high-abundant serum proteins. After protein removal, serum was analyzed by SDS-PAGE as a preliminary screen, and significant differences between four high-abundant protein removal...

journal_title：Journal of proteome research

authors： Chromy BA,Gonzales AD,Perkins J,Choi MW,Corzett MH,Chang BC,Corzett CH,McCutchen-Maloney SL

更新日期：2004-11-01 00:00:00

abstract：:Aberrant protein phosphorylation plays important roles in cancer-related cell signaling. With the goal of achieving multiplexed, comprehensive, and fully automated relative quantitation of site-specific phosphorylation, we present a simple label-free strategy combining an automated pH/acid-controlled IMAC procedure an...

journal_title：Journal of proteome research

authors： Wang YT,Tsai CF,Hong TC,Tsou CC,Lin PY,Pan SH,Hong TM,Yang PC,Sung TY,Hsu WL,Chen YJ

更新日期：2010-11-05 00:00:00

abstract：:Lipolysis involves a number of components including signaling pathways, droplet-associated proteins, and lipases such as hormone-sensitive lipase (HSL). We used surface enhanced laser desorption/ionization time-of-flight mass spectroscopy to identify cellular proteins that might interact with HSL and potentially influ...

journal_title：Journal of proteome research

authors： Shen WJ,Patel S,Eriksson JE,Kraemer FB

更新日期：2010-04-05 00:00:00

abstract：:In this report, we use a proteomic strategy to identify glycoproteins on the surface of exosomes derived from myeloid-derived suppressor cells (MDSCs), and then test if selected glycoproteins contribute to exosome-mediated chemotaxis and migration of MDSCs. We report successful modification of a surface chemistry meth...

journal_title：Journal of proteome research

authors： Chauhan S,Danielson S,Clements V,Edwards N,Ostrand-Rosenberg S,Fenselau C

更新日期：2017-01-06 00:00:00

abstract：:A rate-limiting and costly step in many proteomics analyses is the cloning of all of the ORFs for an organism into technique-specific vectors. Here, we describe the generation of a Campylobacter jejuni expression clone set using a high-throughput cloning approach based on recombination in E. coli. The approach uses na...

journal_title：Journal of proteome research

authors： Parrish JR,Limjindaporn T,Hines JA,Liu J,Liu G,Finley RL Jr

更新日期：2004-05-01 00:00:00

abstract：:We report the structural analysis of cap-binding proteins using a chemical probe/ultraviolet photodissociation (UVPD) mass spectrometry strategy for evaluating solvent accessibility of proteins. Our methodology utilized a chromogenic probe (NN) to probe the exposed amine residues of wheat eukaryotic translation initia...

journal_title：Journal of proteome research

authors： O'Brien JP,Mayberry LK,Murphy PA,Browning KS,Brodbelt JS

更新日期：2013-12-06 00:00:00

abstract：:Staphylococcus aureus with spa-type t437 has been identified as a predominant community-associated methicillin-resistant S. aureus clone from Asia, which is also encountered in Europe. Molecular typing has previously shown that t437 isolates are highly similar regardless of geographical regions or host environments. T...

journal_title：Journal of proteome research

authors： Zhao X,Palma Medina LM,Stobernack T,Glasner C,de Jong A,Utari P,Setroikromo R,Quax WJ,Otto A,Becher D,Buist G,van Dijl JM

更新日期：2019-07-05 00:00:00

abstract：:Hepatocellular carcinoma (HCC) remains as the fifth most common cancer in the world and accounts for more than 700,000 deaths annually. Changes in serum glycosylation have long been associated with this cancer but the source of that material is unknown and direct glycan analysis of HCC tissues has been limited. Our la...

journal_title：Journal of proteome research

authors： West CA,Wang M,Herrera H,Liang H,Black A,Angel PM,Drake RR,Mehta AS

更新日期：2018-10-05 00:00:00

abstract：:Protein tyrosine nitration by oxidative and nitrate stress is important in the pathogenesis of many inflammatory or aging-related diseases. Mass spectrometry analysis of protein nitrotyrosine is very challenging because the non-nitrated peptides suppress the signals of the low-abundance nitrotyrosine (NT) peptides. No...

journal_title：Journal of proteome research

authors： Zhao Y,Zhang Y,Sun H,Maroto R,Brasier AR

更新日期：2017-08-04 00:00:00

abstract：:We have developed herein a quantitative mass spectrometry-based approach to analyze the etiology-related alterations in fucosylation degree of serum haptoglobin in patients with liver cirrhosis and hepatocellular carcinoma (HCC). The three most common etiologies, including infection with hepatitis B virus (HBV), infec...

journal_title：Journal of proteome research

authors： Zhu J,Lin Z,Wu J,Yin H,Dai J,Feng Z,Marrero J,Lubman DM

更新日期：2014-06-06 00:00:00

abstract：:Manassantin A is a natural product that has been shown to have anticancer activity in cell-based assays, but has a largely unknown mode-of-action. Described here is the use of two different energetics-based approaches to identify protein targets of manassantin A. Using the stability of proteins from rates of oxidation...

journal_title：Journal of proteome research

authors： Geer Wallace MA,Kwon DY,Weitzel DH,Lee CT,Stephenson TN,Chi JT,Mook RA Jr,Dewhirst MW,Hong J,Fitzgerald MC

更新日期：2016-08-05 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：: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：:In the past few years, the focus of phosphoproteomics has shifted from merely qualitative to quantitative and targeted studies. Tryptic digestion is a critical step that directly affects quantification and that can be impaired by phosphorylation. Therefore, we systematically characterized the digestion efficiency of 1...

journal_title：Journal of proteome research

authors： Dickhut C,Feldmann I,Lambert J,Zahedi RP

更新日期：2014-06-06 00:00:00

abstract：:Large-scale identification of protein-protein interactions (PPIs) in functional complexes represents an efficient route to elucidate the regulatory rules of cellular functions. Whereas many methods have been developed to identify the PPIs associated with particular target/bait protein in complexes, little information ...

journal_title：Journal of proteome research

authors： Du Y,Zhou J,Fan J,Shen Z,Chen X

更新日期：2009-05-01 00:00:00