iTRAQ-based quantitative proteomics of developing and ripening muscadine grape berry.

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, changes in the metabolites composition of muscadine grapes have been well documented; however, the molecular changes during berry development and ripening are not fully known. The aim of this study was to investigate changes in the berry proteome during ripening in muscadine grape cv. Noble. Isobaric tags for relative and absolute quantification (iTRAQ) MS/MS was used to detect statistically significant changes in the berry proteome. A total of 674 proteins were detected, and 76 were differentially expressed across four time points in muscadine berry. Proteins obtained were further analyzed to provide information about its potential functions during ripening. Several proteins involved in abiotic and biotic stimuli and sucrose and hexose metabolism were upregulated during berry ripening. Quantitative real-time PCR analysis validated the protein expression results for nine proteins. Identification of vicilin-like antimicrobial peptides indicates additional disease tolerance proteins are present in muscadines for berry protection during ripening. The results provide new information for characterization and understanding muscadine berry proteome and grape ripening.

journal_name

J Proteome Res

authors

Kambiranda D,Katam R,Basha SM,Siebert S

doi

10.1021/pr400731p

subject

Has Abstract

pub_date

2014-02-07 00:00:00

pages

555-69

issue

2

eissn

1535-3893

issn

1535-3907

journal_volume

13

pub_type

杂志文章
  • NopM and NopD are rhizobial nodulation outer proteins: identification using LC-MALDI and LC-ESI with a monolithic capillary column.

    abstract::We have explored the potential of commercial polystyrene-divinylbenzene monolithic capillary nanoLC-MS/MS for identifying Sinorhizobium fredii HH103 nodulation outer proteins. Monolithic nanoLC with off-line MALDI-TOF/TOF and on-line ESI-q-oTOF is fast and robust, generating complementary data and offering high-confid...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr060519f

    authors: Rodrigues JA,López-Baena FJ,Ollero FJ,Vinardell JM,Espuny Mdel R,Bellogín RA,Ruiz-Sainz JE,Thomas JR,Sumpton D,Ault J,Thomas-Oates J

    更新日期:2007-03-01 00:00:00

  • Comparison of the membrane proteome of virulent Mycobacterium tuberculosis and the attenuated Mycobacterium bovis BCG vaccine strain by label-free quantitative proteomics.

    abstract::The Mycobacterium tuberculosis membrane is rich in antigens that are potential targets for diagnostics and the development of new vaccines. To better understand the mechanisms underlying MTB virulence and identify new targets for therapeutic intervention, we investigated the differential composition of membrane proteo...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr400334k

    authors: Gunawardena HP,Feltcher ME,Wrobel JA,Gu S,Braunstein M,Chen X

    更新日期:2013-12-06 00:00:00

  • Mycobacterium tuberculosis-specific phagosome proteome and underlying signaling pathways.

    abstract::The phagosome is very important to host immunity and tissue homeostasis maintenance. The destiny of the phagosome is closely associated with the outcome of the pathogen within. Most pathogens are successfully delivered to the lysosome and destroyed via the fusion of the phagosome with the lysosome. Mycobacterium tube...

    journal_title:Journal of proteome research

    pub_type: 杂志文章,评审

    doi:10.1021/pr300125t

    authors: He Y,Li W,Liao G,Xie J

    更新日期:2012-05-04 00:00:00

  • Cellular responses associated with ROS production and cell fate decision in early stress response to iron limitation in the diatom Thalassiosira pseudonana.

    abstract::Investigation of how diatoms cope with the rapid fluctuations in iron bioavailability in marine environments may facilitate a better understanding of the mechanisms underlying their ecological success, in particular their ability to proliferate rapidly during favorable conditions. In this study, using in vivo biochemi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr5004664

    authors: Luo CS,Liang JR,Lin Q,Li C,Bowler C,Anderson DM,Wang P,Wang XW,Gao YH

    更新日期:2014-12-05 00:00:00

  • Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer.

    abstract::Since 2012, missing proteins (MPs) investigation has been one of the critical missions of Chromosome-Centric Human Proteome Project (C-HPP) through various biochemical strategies. On the basis of our previous testis MPs study, faster scanning and higher resolution mass-spectrometry-based proteomics might be conducive ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.6b00390

    authors: Wei W,Luo W,Wu F,Peng X,Zhang Y,Zhang M,Zhao Y,Su N,Qi Y,Chen L,Zhang Y,Wen B,He F,Xu P

    更新日期:2016-11-04 00:00:00

  • Biomarker discovery for arsenic exposure using functional data. Analysis and feature learning of mass spectrometry proteomic data.

    abstract::Plasma biomarkers of exposure to environmental contaminants play an important role in early detection of disease. The emerging field of proteomics presents an attractive opportunity for candidate biomarker discovery, as it simultaneously measures and analyzes a large number of proteins. This article presents a case st...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070491n

    authors: Harezlak J,Wu MC,Wang M,Schwartzman A,Christiani DC,Lin X

    更新日期:2008-01-01 00:00:00

  • Identification of Novel N-Glycosylation Sites at Noncanonical Protein Consensus Motifs.

    abstract::N-glycosylation of proteins is well known to occur at asparagine residues that fall within the canonical consensus sequence N-X-S/T but has also been identified at a small number of asparagine residues within N-X-C motifs, including the N491 residue of human serotransferrin. Here we report novel glycosylation sites wi...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.5b00733

    authors: Lowenthal MS,Davis KS,Formolo T,Kilpatrick LE,Phinney KW

    更新日期:2016-07-01 00:00:00

  • Protein biomarkers for in vitro testing of embryotoxicity.

    abstract::There are new challenges for hazard and risk assessment in the chemical industry with regard to REACH legislation in Europe and related activities in the U.S. and Japan, which require the development of novel in vitro models for the molecular characterization of drug- or chemical-related effects replacing conventional...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100514e

    authors: Groebe K,Hayess K,Klemm-Manns M,Schwall G,Wozny W,Steemans M,Peters AK,Sastri C,Jaeckel P,Stegmann W,Zengerling H,Schopf R,Poznanovic S,Stummann TC,Seiler A,Spielmann H,Schrattenholz A

    更新日期:2010-11-05 00:00:00

  • Screening of Chemical Modifications in Human Skin Keratins by Mass Spectrometry-Based Proteomic Analysis via Noninvasive Sampling and On-Tape Digestion.

    abstract::Proteins are continuously exposed to diverse chemical stresses, and the resulting chemical modifications can provide significant information on biological events. Keratins are the main constituent of human skin and are the major target proteins of various chemical modifications. We have previously developed a mass spe...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00406

    authors: Lee SH,Kawase J,Hiroshima Y,Oe T

    更新日期:2020-09-04 00:00:00

  • Online microwave D-cleavage LC-ESI-MS/MS of intact proteins: site-specific cleavages at aspartic acid residues and disulfide bonds.

    abstract::An online nonenzymatic digestion method utilizing a microwave-heated flow cell and mild acid hydrolysis at aspartic acid (D) for rapid protein identification is described. This methodology, here termed microwave D-cleavage, was tested with proteins ranging in size from 5 kDa (insulin) to 67 kDa (bovine serum albumin) ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr700596e

    authors: Hauser NJ,Basile F

    更新日期:2008-03-01 00:00:00

  • Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

    abstract::The Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO) has now been developing and promoting open community standards and software tools in the field of proteomics for 15 years. Under the guidance of the chair, cochairs, and other leadership positions, the PSI working groups are tasked wit...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00370

    authors: Deutsch EW,Orchard S,Binz PA,Bittremieux W,Eisenacher M,Hermjakob H,Kawano S,Lam H,Mayer G,Menschaert G,Perez-Riverol Y,Salek RM,Tabb DL,Tenzer S,Vizcaíno JA,Walzer M,Jones AR

    更新日期:2017-12-01 00:00:00

  • Phosphoproteomics reveals the effect of ethylene in soybean root under flooding stress.

    abstract::Flooding has severe negative effects on soybean growth. To explore the flooding-responsive mechanisms in early-stage soybean, a phosphoproteomic approach was used. Two-day-old soybean plants were treated without or with flooding for 3, 6, 12, and 24 h, and root tip proteins were then extracted and analyzed at each tim...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500621c

    authors: Yin X,Sakata K,Komatsu S

    更新日期:2014-12-05 00:00:00

  • Param-Medic: A Tool for Improving MS/MS Database Search Yield by Optimizing Parameter Settings.

    abstract::In shotgun proteomics analysis, user-specified parameters are critical to database search performance and therefore to the yield of confident peptide-spectrum matches (PSMs). Two of the most important parameters are related to the accuracy of the mass spectrometer. Precursor mass tolerance defines the peptide candidat...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00028

    authors: May DH,Tamura K,Noble WS

    更新日期:2017-04-07 00:00:00

  • Differential expression of defense/stress-related marker proteins in leaves of a unique rice blast lesion mimic mutant (blm).

    abstract::We analyzed a unique rice (Oryza sativa L.) blast lesion mimic (blm) mutant for differentially expressed proteins in leaves of one- and two-week-old seedlings manifesting the lesion mimic phenotype. Gel-based one- and two-dimensional electrophoresis (1- and 2-DGE) was performed using leaves (blm and wild-type, WT) bef...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr060092c

    authors: Jung YH,Rakwal R,Agrawal GK,Shibato J,Kim JA,Lee MO,Choi PK,Jung SH,Kim SH,Koh HJ,Yonekura M,Iwahashi H,Jwa NS

    更新日期:2006-10-01 00:00:00

  • Proteomic analysis of human serum by two-dimensional differential gel electrophoresis after depletion of high-abundant proteins.

    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

    pub_type: 杂志文章

    doi:10.1021/pr049921p

    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

  • 'Signature sets', minimal fragment sets for identifying protein disulfide structures with cyanylation-based mass mapping methodology.

    abstract::Our cyanylation (CN)-based methodology for determining disulfide structure of cystinyl proteins overcomes the limitations of conventional proteolytic methods. However, the CN-based method has the potential drawback that occasionally some CN-induced cleavage fragments may not be detected. We show that CN-based methods ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr049961t

    authors: Wu W,Huang W,Qi J,Chou YT,Torng E,Watson JT

    更新日期:2004-07-01 00:00:00

  • Elucidation of glycoprotein structures by unspecific proteolysis and direct nanoESI mass spectrometric analysis of ZIC-HILIC-enriched glycopeptides.

    abstract::Protein glycosylation was explored by direct nanoESI MS and MS/MS analysis of ZIC-HILIC-enriched proteolytic glycopeptides without further separation or purification. In a previous publication, we demonstrated that a direct MS-based analysis of proteolytic glycopeptides is feasible for a number of proteins (Henning , ...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr101082c

    authors: Neue K,Mormann M,Peter-Katalinić J,Pohlentz G

    更新日期:2011-05-06 00:00:00

  • Tryptic Peptides Bearing C-Terminal Dimethyllysine Need to Be Considered during the Analysis of Lysine Dimethylation in Proteomic Study.

    abstract::Lysine methylation plays important roles in structural and functional regulation of chromatin. Although trypsin is the most widely used protease in mass spectrometry-based proteomic analysis for lysine methylation substrates, the proteolytic activity of trypsin on dimethylated lysine residues remains an arguable issue...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.7b00373

    authors: Chen M,Zhang M,Zhai L,Hu H,Liu P,Tan M

    更新日期:2017-09-01 00:00:00

  • Novel proteomic strategy reveal combined alpha1 antitrypsin and cathepsin D as biomarkers for colorectal cancer early screening.

    abstract::Biomarkers for colorectal cancer (CRC) early diagnosis are currently lacking. The purpose of this study was to interpret molecular events in the early stage of CRC that may bring about new biomarkers for early diagnosis. Methylation isotope labeling assistant gel-enhanced liquid chromatography-mass spectrometry (GeLC-...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr100406z

    authors: Xie LQ,Zhao C,Cai SJ,Xu Y,Huang LY,Bian JS,Shen CP,Lu HJ,Yang PY

    更新日期:2010-09-03 00:00:00

  • Gain-Scanning for Protein Microarray Assays.

    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

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.9b00892

    authors: Feng F,Ataca ST,Ran M,Wang Y,Breen M,Kepler TB

    更新日期:2020-07-02 00:00:00

  • Subtractive proteomic approach to the endometrial carcinoma invasion front.

    abstract::Tumor invasion defines the transition between tissue-restricted carcinomas, related to good outcome as optimal surgery becomes possible, and metastatic tumors associated with poor prognosis and a dramatic decrease in survival. In endometrial cancer, myometrial infiltration represents a determinant parameter highly val...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr900390t

    authors: Monge M,Doll A,Colas E,Gil-Moreno A,Castellvi J,Garcia A,Colome N,Perez-Benavente A,Pedrola N,Lopez-Lopez R,Dolcet X,Ramon y Cajal S,Xercavins J,Matias-Guiu X,Canals F,Reventos J,Abal M

    更新日期:2009-10-01 00:00:00

  • Proteomic evidence for roles for nucleolin and poly[ADP-ribosyl] transferase in drug resistance.

    abstract::One-hundred twenty-four proteins have been identified in the soluble nuclear protein mixture from MCF-7 human breast cancer cells, of which more than 90% are classically categorized as nuclear proteins. Proteins were also studied from three drug resistant MDF-7 lines, selected previously from the same parent line by e...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr0501158

    authors: Fu Z,Fenselau C

    更新日期:2005-09-01 00:00:00

  • In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions.

    abstract::Accurate and sensitive detection of protein-protein and protein-RNA interactions is key to understanding their biological functions. Traditional methods to identify these interactions require cell lysis and biochemical manipulations that exclude cellular compartments that cannot be solubilized under mild conditions. H...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr500196b

    authors: Beck DB,Narendra V,Drury WJ 3rd,Casey R,Jansen PW,Yuan ZF,Garcia BA,Vermeulen M,Bonasio R

    更新日期:2014-12-05 00:00:00

  • NMR-based metabolomic analysis of the molecular pathogenesis of therapy-related myelodysplasia/acute myeloid leukemia.

    abstract::Hematopoietic stem cell transplantation is the oldest and most successful form of stem cell therapy. High dose therapy (HDT) followed by hematopoietic stem cell transplantation allows physicians to administer increased amounts of chemotherapy and/or radiation while minimizing negative side effects such as damage to bl...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr200200y

    authors: Cano KE,Li L,Bhatia S,Bhatia R,Forman SJ,Chen Y

    更新日期:2011-06-03 00:00:00

  • A Two-Way Interaction between Methotrexate and the Gut Microbiota of Male Sprague-Dawley Rats.

    abstract::Methotrexate (MTX) is a chemotherapeutic agent that can cause a range of toxic side effects including gastrointestinal damage, hepatotoxicity, myelosuppression, and nephrotoxicity and has potentially complex interactions with the gut microbiome. Following untargeted UPLC-qtof-MS analysis of urine and fecal samples fro...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/acs.jproteome.0c00230

    authors: Letertre MPM,Munjoma N,Wolfer K,Pechlivanis A,McDonald JAK,Hardwick RN,Cherrington NJ,Coen M,Nicholson JK,Hoyles L,Swann JR,Wilson ID

    更新日期:2020-08-07 00:00:00

  • Comprehensive appraisal of the extracellular proteins from a monoderm bacterium: theoretical and empirical exoproteomes of Listeria monocytogenes EGD-e by secretomics.

    abstract::Defined as proteins actively transported via secretion systems, secreted proteins can have radically different subcellular destinations in monoderm (Gram-positive) bacteria. From degradative enzymes in saprophytes to virulence factors in pathogens, secreted proteins are the main tools used by bacteria to interact with...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr1003642

    authors: Desvaux M,Dumas E,Chafsey I,Chambon C,Hébraud M

    更新日期:2010-10-01 00:00:00

  • Prediction of membrane protein types in a hybrid space.

    abstract::Prediction of the types of membrane proteins is of great importance both for genome-wide annotation and for experimental researchers to understand proteins' functions. We describe a new strategy for the prediction of the types of membrane proteins using the Nearest Neighbor Algorithm. We introduced a bipartite feature...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr700715c

    authors: Jia P,Qian Z,Feng K,Lu W,Li Y,Cai Y

    更新日期:2008-03-01 00:00:00

  • Proteomic analysis of near-isogenic sunflower varieties differing in seed oil traits.

    abstract::Near-isogenic sunflower lines containing 25% (inbred RHA280) and 48% (RHA801) oil by seed dry mass were comparatively analyzed in biological triplicate at 18 days after flowering using two-dimensional (both pI 3-10 and 4-7) Difference Gel Electrophoresis. Additionally, two inbred lines varying in oleic acid content, H...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr070149a

    authors: Hajduch M,Casteel JE,Tang S,Hearne LB,Knapp S,Thelen JJ

    更新日期:2007-08-01 00:00:00

  • Mass spectrometry characterization of species-specific peptides from arginine kinase for the identification of commercially relevant shrimp species.

    abstract::The identification of commercial shrimp species is a relevant issue to ensure correct labeling, maintain consumer confidence and enhance the knowledge of the captured species, benefiting both, fisheries and manufacturers. A proteomic approach, based on 2DE, tryptic in-gel digestion, MALDI-TOF MS, and ESI-MS/MS analyse...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr900663d

    authors: Ortea I,Cañas B,Gallardo JM

    更新日期:2009-11-01 00:00:00

  • Serum metabolic signatures of fulminant type 1 diabetes.

    abstract::Fulminant type 1 diabetes (FT1DM) is a relatively new clinical entity featured by acute destruction of pancreatic beta cells. Clinical consequences of FT1DM could be fatal when timely medications are not provided, suggesting the particular importance of rapid and accurate diagnosis. Here we report a serum metabonomics...

    journal_title:Journal of proteome research

    pub_type: 杂志文章

    doi:10.1021/pr300523x

    authors: Lu J,Zhou J,Bao Y,Chen T,Zhang Y,Zhao A,Qiu Y,Xie G,Wang C,Jia W,Jia W

    更新日期:2012-09-07 00:00:00