Abstract：
:Natural disasters such as drought, extreme temperatures, and flooding can severely impact crop production. Understanding the metabolic response of crops threatened with these disasters provides insights into biological response mechanisms that can influence survival. In this study, a comparative analysis of GC-MS and (1)H NMR results was conducted for wild-type and tolerant rice varieties stressed by up to 3 days of submergence and allowed 1 day of postsubmergence recovery. Most metabolomics studies are conducted using a single analytical platform. Each platform, however, has inherent advantages and disadvantages that can influence the analytical coverage of the metabolome. In this work, a more thorough analysis of the plant stress response was possible through the use of both (1)H NMR and GC-MS. Several metabolites, such as S-methyl methionine and the dipeptide alanylglycine, were only detected and quantified by (1)H NMR. The high dynamic range of NMR, as compared with that of the GC-TOF-MS used in this study, provided broad coverage of the metabolome in a single experiment. The sensitivity of GC-MS facilitated the quantitation of sugars, organic acids, and amino acids, some of which were not detected by NMR, and provided additional insights into the regulation of the TCA cycle. The combined metabolic information provided by (1)H NMR and GC-MS was essential for understanding the complex biochemical and molecular response of rice plants to submergence.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Barding GA Jr,Béni S,Fukao T,Bailey-Serres J,Larive CKdoi
10.1021/pr300953ksubject
Has Abstractpub_date
2013-02-01 00:00:00pages
898-909issue
2eissn
1535-3893issn
1535-3907journal_volume
12pub_type
杂志文章abstract：:Protein phosphorylation is a reversible post-translational modification that regulates many biological processes in almost all living forms. In the case of the hepatitis C virus (HCV), the nonstructural protein 5A (NS5A) is believed to transit between hypo- and hyper-phosphorylated forms that interact with host protei...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00130
更新日期：2019-07-05 00:00:00
abstract：:Temperature is one of the most critical parameters for yeast growth, and it has deep consequences in many industrial processes where yeast is involved. Nevertheless, the metabolic changes required to accommodate yeast cells at high or low temperatures are still poorly understood. In this work, the ultimate responses o...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00921
更新日期：2018-06-01 00:00:00
abstract：:In the framework of the C-HPP, our Franco-Swiss consortium has adopted chromosomes 2 and 14, coding for a total of 382 missing proteins (proteins for which evidence is lacking at protein level). Over the last 4 years, the French proteomics infrastructure has collected high-quality data sets from 40 human samples, incl...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr5010345
更新日期：2015-09-04 00:00:00
abstract：:In the present study we have used label-free shotgun proteomic analysis to examine the effects of Fe deficiency on the protein profiles of highly pure sugar beet root plasma membrane (PM) preparations and detergent-resistant membranes (DRMs), the latter as an approach to study microdomains. Altogether, 545 proteins we...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00026
更新日期：2016-08-05 00:00:00
abstract：:The impact of low-dose ionizing radiation (IR) on the human brain has recently attracted attention due to the increased use of IR for diagnostic purposes. The aim of this study was to investigate low-dose radiation response in the hippocampus. Female B6C3F1 mice were exposed to total body irradiation with 0 (control),...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00552
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
pub_type： 杂志文章
doi：10.1021/pr050298y
更新日期：2006-02-01 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
pub_type： 杂志文章
doi：10.1021/pr8003024
更新日期：2008-10-01 00:00:00
abstract：:Tomato fruit and seed allergens were detected by IgE-immunoblotting using sera from 18 adult tomato-sensitized patients selected based on a positive history skin prick test (SPT) and specific Immunglobulin (Ig) E-levels. Isolated tomato seed total protein showed high SPT activity comparable or even higher than tomato ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800186d
更新日期：2009-03-01 00:00:00
abstract：:Cytological examination of cells from bronchoalveolar lavage (BAL) is commonly used for the diagnosis of lung cancer. Proteins released from lung cancer cells into BAL may serve as biomarkers for cancer detection. In this study, N-glycoproteins in eight cases of BAL fluid, as well as eight lung adenocarcinoma tissues ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400274w
更新日期：2013-08-02 00:00:00
abstract：:Protein post-translational modification by ubiquitin-fold modifier 1, UFM1, regulates many biological processes such as response to endoplasmic reticulum stress and regulation of tumor progression. A recent study has indicated that the UFM1-binding and PCI domain-containing protein 1 (UFBP1) is required for the conjug...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00843
更新日期：2018-04-06 00:00:00
abstract：:Advances in liquid chromatography tandem mass spectrometry (LC-MS/MS) have permitted phosphoproteomic analysis on a grand scale, but ongoing challenges specifically associated with confident phosphate localization continue to motivate the development of new fragmentation techniques. In the present study, ultraviolet p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00289
更新日期：2016-08-05 00:00:00
abstract：:Russell and colleagues deserve credit for being the first to use a QconCAT standard to simultaneously quantify both the wild-type and mutant peptides of a protein (i.e., CYP2B6) ( J. Proteome Res. 2013, 12 (12), 5934-5942. DOI: 10.1021/pr400279u). However, the rationale of their study was entirely different from ours ...
journal_title：Journal of proteome research
pub_type： 评论,杂志文章
doi：10.1021/acs.jproteome.8b00940
更新日期：2019-03-01 00:00:00
abstract：:Glycosylation is one of the most common post-translational modifications in proteins, existing in ~50% of mammalian proteins. Several research groups have demonstrated that mass spectrometry is an efficient technique for glycopeptide identification; however, this problem is still challenging because of the enormous di...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00299
更新日期：2015-12-04 00:00:00
abstract：:Campylobacter jejuni is the most common cause of bacterial gastroenteritis in the developed world. Immunoproteomics highlighted a 42-45 kDa antigen that comigrated on two-dimensional (2-DE) gels with the C. jejuni major outer membrane protein (MOMP). Predictive analysis revealed two candidates for the identity of the ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900544x
更新日期：2009-10-01 00:00:00
abstract：:Stress in the form of moderate periods of maternal separation of newborn rats has been postulated to cause permanent changes in the central nervous system and diseases in later life. It is also considered that dietary supplementation with long chain polyunsaturated fatty acids (LC-PUFAs) can potentially ameliorate the...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0504182
更新日期：2006-07-01 00:00:00
abstract：:Detergents are indispensable solubilizing agents in the purification and analysis of membrane proteins. For mass spectrometric identification of proteins, it is essential that detergents are removed prior to analysis, necessitating an in-gel digestion step. Here, we report a procedure that allows use of detergents and...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800412j
更新日期：2008-11-01 00:00:00
abstract：:We undertook an unbiased metabolite profiling of fibroblasts from schizophrenia patients and healthy controls to identify metabolites and pathways that are dysregulated in disease, seeking to gain new insights into the disease biology of schizophrenia and to discover potential disease-related biomarkers. We measured p...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00628
更新日期：2017-02-03 00:00:00
abstract：:The current technique used for microbial identification in hospitals is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, it suffers from important limitations, in particular, for closely related species or when the database used for the identification lacks the appr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00351
更新日期：2021-01-01 00:00:00
abstract：:Quantitative analysis of protein biomarkers in plasma is typically done by ELISA, but this method is limited by the availability of high-quality antibodies. An alternative approach is protein immunoprecipitation combined with multiple reaction monitoring mass spectrometry (IP-MRM). We compared IP-MRM to ELISA for the ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400877e
更新日期：2013-12-06 00:00:00
abstract：:Correct phosphorylation site assignment is a critical aspect of phosphoproteomic analysis. Large-scale phosphopeptide data sets that are generated through liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) analysis often contain hundreds or thousands of phosphorylation sites that require validation. To ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr800169k
更新日期：2008-07-01 00:00:00
abstract：:Although tandem mass spectrometry (MS/MS) has become an integral part of proteomics, intensity patterns in MS/MS spectra are rarely weighted heavily in most widely used algorithms because they are not yet fully understood. Here a knowledge mining approach is demonstrated to discover fragmentation intensity patterns an...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070106u
更新日期：2008-01-01 00:00:00
abstract：:The neurodegenerative disorder Alzheimer's disease (AD) is the most common cause of dementia in the elderly. The presence of neurofibrillary tangles, consisting of hyperphosphorylated tau protein, is one of the major neuropathologic characteristics of the disease, making this protein an attractive biomarker for AD and...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr7008669
更新日期：2008-05-01 00:00:00
abstract：:Francisella tularensis causes disease (tularemia) in a large number of mammals, including man. We previously demonstrated enhanced efficacy of conventional antibiotic therapy for tularemia by postexposure passive transfer of immune sera developed against a F. tularensis LVS membrane protein fraction (MPF). However, th...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500628k
更新日期：2015-02-06 00:00:00
abstract：:Antibody reagents have been remained as a standard approach to characterize blood group (BG) antigens in clinic. The specificity and cross-reactivity of these BG antibodies are routine detected using the gel microcolumn assay (GMA). However, the GMA is neither specific nor sensitive, thus increasing the risk of improp...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00370
更新日期：2018-09-07 00:00:00
abstract：:Ion mobility-mass spectrometry (IM-MS) is a useful technique for determining information about analyte ion conformation in addition to mass/charge ratio. The physical principles that govern the mobility of an ion through a gas in the presence of a uniform electric field are well understood, enabling rotationally avera...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3005327
更新日期：2012-11-02 00:00:00
abstract：:We report here using a novel technology-electrospray-assisted laser desorption ionization (ELDI)/mass spectrometry-for the rapid and sensitive detection of the major proteins that exist in dried biological fluids (e.g., blood, tears, saliva, serum), bacterial cultures, and tissues (e.g., porcine liver and heart) under...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050442f
更新日期：2006-05-01 00:00:00
abstract：:Colorectal cancer (CRC) is the third most common cancer worldwide and has poor prognosis. To identify the proteins involved in colorectal carcinogenesis, we employed 2-DE and MALDI-TOF/TOF-based proteomics approach to study the differentially expressed proteins in tumor and adjacent nontumor tissue samples. Samples fr...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr900365e
更新日期：2009-10-01 00:00:00
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
更新日期：2016-07-01 00:00:00
abstract：:A "one-pot" alternative method for processing proteins and isolating peptide mixtures from bacterial samples is presented for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and data reduction. The conventional in-solution digestion of the protein contents of bacteria is compared to a small disposab...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101086a
更新日期：2011-02-04 00:00:00
abstract：:Skeletal muscle has emerged as an important secretory organ that produces so-called myokines, regulating energy metabolism via autocrine, paracrine, and endocrine actions; however, the nature and extent of the muscle secretome has not been fully elucidated. Mass spectrometry (MS)-based proteomics, in principle, allows...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00720
更新日期：2015-11-06 00:00:00
