Stable Isotope-Assisted Metabolic Profiling Reveals Growth Mode Dependent Differential Metabolism and Multiple Catabolic Pathways of l-Phenylalanine in Rubrivivax benzoatilyticus JA2.

abstract：:Most MALDI instrumentation uses UV lasers. We have designed a MALDI-IM-oTOF-MS which employs both a Nd:YAG laser pumped optical parametric oscillator (OPOTEK, lambda = 2.8-3.2 microm at 20 Hz) to perform IR-LDI or IR-MALDI and a Nd:YLF laser (Crystalaser, lambda = 249 nm at 200 Hz) for the UV. Ion mobility (IM) gives ...

journal_title：Journal of proteome research

authors： Woods AS,Ugarov M,Jackson SN,Egan T,Wang HY,Murray KK,Schultz JA

更新日期：2006-06-01 00:00:00

abstract：:Peptide abundance estimation is generally the first step in protein quantification. In peptide abundance estimation, peptide overlapping and peak intensity variation are two challenges. The main objective of this paper is to estimate peptide abundance by taking advantage of peptide isotopic distribution and smoothness...

journal_title：Journal of proteome research

authors： Yang C,Yang C,Yu W

更新日期：2010-05-07 00:00:00

abstract：:Comparative phosphoproteomics of Mycobacterium tuberculosis (Mtb)- and Mycobacterium bovis BCG (BCG)-infected macrophages could be instrumental in understanding the characteristic post-translational modifications of host proteins and their subsequent involvement in determining Mtb pathogenesis. To identify proteins ac...

journal_title：Journal of proteome research

authors： Choudhary E,Bullen CK,Goel R,Singh AK,Praharaj M,Thakur P,Dhiman R,Bishai WR,Agarwal N

更新日期：2020-06-05 00:00:00

abstract：:In recent years, proteomic data have contributed to genome annotation efforts, most notably in humans and mice, and spawned a field termed "proteogenomics". Yeast, in contrast with higher eukaryotes, has a small genome, which has lent itself to simpler ORF prediction. Despite this, continual advances in mass spectrome...

journal_title：Journal of proteome research

authors： Yagoub D,Tay AP,Chen Z,Hamey JJ,Cai C,Chia SZ,Hart-Smith G,Wilkins MR

更新日期：2015-12-04 00:00:00

abstract：:Type 1 diabetes, in human patients and NOD mice, results from an immune attack on insulin-producing beta-cells of the pancreas by autoreactive T lymphocytes. In NOD mice, genetically controlled perturbations in the signaling pathways downstream of the antigen-specific T cell receptor (TCR) may be instrumental in the a...

journal_title：Journal of proteome research

authors： Iwai LK,Benoist C,Mathis D,White FM

更新日期：2010-06-04 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

authors： Huang Y,Tseng GC,Yuan S,Pasa-Tolic L,Lipton MS,Smith RD,Wysocki VH

更新日期：2008-01-01 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

authors： Chandler JC,Sutherland MD,Harton MR,Molins CR,Anderson RV,Heaslip DG,Bosio CM,Belisle JT

更新日期：2015-02-06 00:00:00

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

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

更新日期：2020-09-04 00:00:00

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

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

更新日期：2007-08-01 00:00:00

abstract：:Mitosis is a highly regulated process in which errors can lead to genomic instability, a hallmark of cancer. During this phase of the cell cycle, transcription is silent and RNA translation is inhibited. Thus, mitosis is largely driven by post-translational modification of proteins, including phosphorylation, methylat...

journal_title：Journal of proteome research

authors： Chuang C,Lin SH,Huang F,Pan J,Josic D,Yu-Lee LY

更新日期：2010-09-03 00:00:00

abstract：:The term "spectral clustering" is sometimes used to refer to the clustering of mass spectrometry data. However, it also classically refers to a family of popular clustering algorithms. To avoid confusion, a more specific term could advantageously be coined. ...

journal_title：Journal of proteome research

authors： Borges H,Guibert R,Permiakova O,Burger T

更新日期：2019-01-04 00:00:00

abstract：:Salt stress is a major abiotic factor limiting maize yield. To characterize the mechanism underlying maize salt tolerance, we compared the seedling root proteomes of salt-tolerant Jing724 and salt-sensitive D9H. The germination rate and growth parameter values (weight and length) were higher for Jing724 than for D9H u...

journal_title：Journal of proteome research

authors： Luo M,Zhao Y,Wang Y,Shi Z,Zhang P,Zhang Y,Song W,Zhao J

更新日期：2018-01-05 00:00:00

abstract：:Histones are subjected to extensive post-translational modifications (PTMs) that are known to play key roles in many biological processes. In this study, we report a fast, efficient, highly reproducible, and easily automated method involving ultra-high performance liquid chromatography (UHPLC) coupled to a high resolu...

journal_title：Journal of proteome research

authors： Contrepois K,Ezan E,Mann C,Fenaille F

更新日期：2010-10-01 00:00:00

abstract：:The peptide toxins in the venoms of small invertebrates such as stinging ants have rarely been studied due to the limited amount of venom available per individual. We used a venomics strategy to identify the molecular diversity of the venom peptidome for the myrmicine ant Tetramorium bicarinatum. The methodology inclu...

journal_title：Journal of proteome research

authors： Touchard A,Téné N,Song PCT,Lefranc B,Leprince J,Treilhou M,Bonnafé E

更新日期：2018-10-05 00:00:00

abstract：:Hydrogen peroxide (H(2)O(2)) and nitric oxide ((•)NO) elicit numerous processes in plants. However, our knowledge of H(2)O(2) and (•)NO-responsive proteins is limited. The present study aimed to identify proteins whose accumulation levels were regulated by these signaling molecules in citrus leaves. To address this qu...

journal_title：Journal of proteome research

authors： Tanou G,Job C,Belghazi M,Molassiotis A,Diamantidis G,Job D

更新日期：2010-11-05 00:00:00

abstract：:In an attempt to identify prostate cancer biomarkers with greater diagnostic and prognostic capabilities, we have developed an integrative proteomic discovery workflow focused on N-linked glycoproteins that refines the target selection process. In this work, hydrazide-based chemistry was used to identify N-linked glyc...

journal_title：Journal of proteome research

authors： Whitmore TE,Peterson A,Holzman T,Eastham A,Amon L,McIntosh M,Ozinsky A,Nelson PS,Martin DB

更新日期：2012-05-04 00:00:00

abstract：:Partially folded conformations are important players in protein self-organization, function, and misfolding, thus attracting the intensive and constant attention of researchers. Different conformational states of proteins can be easily discriminated from one another using the multiparametric approach, which usually in...

journal_title：Journal of proteome research

authors： Kuznetsova IM,Turoverov KK,Uversky VN

更新日期：2004-05-01 00:00:00

abstract：:Plant secretory (Class III) peroxidases are redox enzymes that rely on N-glycosylation for full enzyme activity and stability. Peroxidases from palm tree leaves comprise the most stable and active plant peroxidases characterized to date. Herein, site-specific glycosylation and microheterogeneity of windmill palm tree ...

journal_title：Journal of proteome research

authors： Baker MR,Tabb DL,Ching T,Zimmerman LJ,Sakharov IY,Li QX

更新日期：2016-06-03 00:00:00

abstract：:The development of computational strategies for the quantitative characterization of the functional mechanisms of SARS-CoV-2 spike proteins is of paramount importance in efforts to accelerate the discovery of novel therapeutic agents and vaccines combating the COVID-19 pandemic. Structural and biophysical studies have...

journal_title：Journal of proteome research

authors： Verkhivker GM

更新日期：2020-11-06 00:00:00

abstract：:RelA (NF-kappaB) is a transcription factor inducible by distinct stimuli in many different cell types. To find new cell type specific cofactors of NF-kappaB dependent transcription, we isolated RelA transcription activation domain binding proteins from the nuclear extracts of three different cell types. Analysis by el...

journal_title：Journal of proteome research

authors： Owen HR,Quadroni M,Bienvenut W,Buerki C,Hottiger MO

更新日期：2005-07-01 00:00:00

abstract：:Proteomics methods are being increasingly used to study archaeological and palaeontological bone, assisting in species identification and phylogenetic studies as well as improving our understanding of bone diagenesis. More recently, there are developing interests in the study of post-translational modifications, some ...

journal_title：Journal of proteome research

authors： Procopio N,Buckley M

更新日期：2017-02-03 00:00:00

abstract：:We performed systematic evaluation of 38 protocols to concentrate normal human urinary proteins prior to 2D-PAGE analysis. Recovery yield and pattern of resolved protein spots were compared among different methods and intra-/inter-individual variabilities were examined. Precipitation with 90% ethanol provided the grea...

journal_title：Journal of proteome research

authors： Thongboonkerd V,Chutipongtanate S,Kanlaya R

更新日期：2006-01-01 00:00:00

abstract：:Yellow fever virus (YFV) replication is highly dependent on host cell factors. YFV NS4B is reported to be involved in viral replication and immune evasion. Here interactions between NS4B and human proteins were determined using a GST pull-down assay and analyzed using 1-DE and LC-MS/MS. We present a total of 207 prote...

journal_title：Journal of proteome research

authors： Vidotto A,Morais AT,Ribeiro MR,Pacca CC,Terzian AC,Gil LH,Mohana-Borges R,Gallay P,Nogueira ML

更新日期：2017-04-07 00:00:00

abstract：:A steady increase in the incidence of osteoarthritis and other rheumatic diseases has been observed in recent decades, including autoimmune conditions such as rheumatoid arthritis, spondyloarthropathies, systemic lupus erythematosus, systemic sclerosis, and Sjögren's syndrome. Rheumatic and autoimmune diseases (RADs) ...

journal_title：Journal of proteome research

authors： Ruiz-Romero C,Lam MPY,Nilsson P,Önnerfjord P,Utz PJ,Van Eyk JE,Venkatraman V,Fert-Bober J,Watt FE,Blanco FJ

更新日期：2019-12-06 00:00:00

abstract：:Reversed-phase gradient LC-MS was used to perform untargeted metabonomic analysis on extracts of human colorectal cancer (CRC) cell lines (COLO 205, HT-29, HCT 116 and SW620) subcutaneously implanted into age-matched athymic nude male mice to study small molecule metabolic profiles and examine possible correlations wi...

journal_title：Journal of proteome research

authors： Loftus NJ,Lai L,Wilkinson RW,Odedra R,Wilson ID,Barnes AJ

更新日期：2013-06-07 00:00:00

abstract：:Mutagenesis through fast neutron (FN) radiation of soybean resulted in a mutant with a 15% increase in seed protein content. A comparative genomic hybridization analysis confirmed that the mutant is lacking 24 genes located at chromosomes 5 and 10. A tandem mass tag-based proteomic profiling of the wild type and the F...

journal_title：Journal of proteome research

authors： Islam N,Krishnan HB,Natarajan S

更新日期：2020-10-02 00:00:00

abstract：:Serum protein profiling by mass spectrometry is a promising method for early detection of cancer. We have implemented a combined strategy based on matrix-assisted laser desorption ionization mass spectrometry (MALDI MS) and statistical data analysis for serum protein profiling and applied it in a well-described breast...

journal_title：Journal of proteome research

authors： Callesen AK,Vach W,Jørgensen PE,Cold S,Tan Q,Depont Christensen R,Mogensen O,Kruse TA,Jensen ON,Madsen JS

更新日期：2008-04-01 00:00:00

abstract：:Energy imbalance is a primary cause of obesity. While the classical approach to attenuate weight gain includes an increase in energy expenditure through exercise, dietary manipulation such as the inclusion of dairy products has also been proven effective. In the present study, we explored the potential mechanisms by w...

journal_title：Journal of proteome research

authors： Mayengbam S,Mickiewicz B,Trottier SK,Mu C,Wright DC,Reimer RA,Vogel HJ,Shearer J

更新日期：2019-11-01 00:00:00

abstract：:Mixed lineage leukemia results from chromosomal rearrangements of the gene mixed lineage leukemia (MLL). MLL-AF9 is one such rearrangement that recruits the lysine methyltransferase, human disruptor of telomere silencing 1-like (DOT1L) and lysine specific demethylase 1 (LSD1), resulting in elevated expression of the H...

journal_title：Journal of proteome research

authors： Lillico R,Lawrence CK,Lakowski TM

更新日期：2018-08-03 00:00:00

abstract：:Arctic ground squirrels provide a unique model to investigate metabolic responses to hibernation in mammals. During winter months these rodents are exposed to severe hypothermia, prolonged fasting, and hypoxemia. In the light of their role in oxygen transport/off-loading and owing to the absence of nuclei and organell...

journal_title：Journal of proteome research

authors： Gehrke S,Rice S,Stefanoni D,Wilkerson RB,Nemkov T,Reisz JA,Hansen KC,Lucas A,Cabrales P,Drew K,D'Alessandro A

更新日期：2019-04-05 00:00:00