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

abstract：:A role for Src Family Kinases (SFKs) in the dynamics of endocytic and secretory pathways has previously been reported. Identification of low-abundance compartmentalized complexes still remains challenging, highlighting the need for novel tools. Here we describe analysis of SFK-signaling complexes of hepatic Golgi/endo...

journal_title：Journal of proteome research

authors： Bilodeau N,Fiset A,Boulanger MC,Bhardwaj S,Winstall E,Lavoie JN,Faure RL

更新日期：2010-02-05 00:00:00

abstract：:Candida albicans is a commensal microorganism in the oral cavity and gastrointestinal and urogenital tracts of most individuals that acts as an opportunistic pathogen when the host immune response is reduced. Here, we established different immunocompetent murine models to analyze the antibody responses to the C. albic...

journal_title：Journal of proteome research

authors： Huertas B,Prieto D,Pitarch A,Gil C,Pla J,Díez-Orejas R

更新日期：2017-01-06 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：:Workflows in urinary proteomics studies are often complex and require many steps to enrich, purify, deplete, and separate the complex mixture. Many of these methods are laborious, are time-consuming, and have the potential for error. Although individual steps of these methods have been previously studied, their downst...

journal_title：Journal of proteome research

authors： Vaezzadeh AR,Briscoe AC,Steen H,Lee RS

更新日期：2010-11-05 00:00:00

abstract：:As part of the Chromosome-Centric Human Proteome Project (C-HPP) mission, laboratories all over the world have tried to map the entire missing proteins (MPs) since 2012. On the basis of the first and second Chinese Chromosome Proteome Database (CCPD 1.0 and 2.0) studies, we developed systematic enrichment strategies t...

journal_title：Journal of proteome research

authors： Su N,Zhang C,Zhang Y,Wang Z,Fan F,Zhao M,Wu F,Gao Y,Li Y,Chen L,Tian M,Zhang T,Wen B,Sensang N,Xiong Z,Wu S,Liu S,Yang P,Zhen B,Zhu Y,He F,Xu P

更新日期：2015-09-04 00:00:00

abstract：:Glycolysis is the core metabolic pathway supplying energy to cells. Whereas the vast majority of studies focus on specific aspects of the process, global analyses characterizing simultaneously all enzymes involved in the process are scarce. Here, we demonstrate that quantitative label- and standard-free proteomics all...

journal_title：Journal of proteome research

authors： Wiśniewski JR,Gizak A,Rakus D

更新日期：2015-08-07 00:00:00

abstract：:Endothelial cells (ECs) form the inner layer of blood vessels and physically separate the blood from the surrounding tissue. To support tissues with nutrients and oxygen, the endothelial monolayer is semipermeable. When EC permeability is altered, blood vessels are not functional, and this is associated with disease. ...

journal_title：Journal of proteome research

authors： Patella F,Neilson LJ,Athineos D,Erami Z,Anderson KI,Blyth K,Ryan KM,Zanivan S

更新日期：2016-07-01 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：:To gain insights into how TGF-beta regulates epithelial-mesenchymal transition (EMT), we assessed the time course of proteins and mRNAs during EMT by multiplex iTRAQ labeling and 2D-LC-MS/MS, and by hybridization, respectively. Temporal iTRAQ analysis identified 66 proteins as differentially expressed during EMT, incl...

journal_title：Journal of proteome research

authors： Keshamouni VG,Jagtap P,Michailidis G,Strahler JR,Kuick R,Reka AK,Papoulias P,Krishnapuram R,Srirangam A,Standiford TJ,Andrews PC,Omenn GS

更新日期：2009-01-01 00:00:00

abstract：:The world is currently facing the COVID-19 pandemic caused by the SARS-CoV-2 virus. The pandemic is causing the death of people around the world, and public and social health measures to slow or prevent the spread of COVID-19 are being implemented with the involvement of all members of society. Research institutions a...

journal_title：Journal of proteome research

authors： Barros RO,Junior FLCC,Pereira WS,Oliveira NMN,Ramos RM

更新日期：2020-11-06 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：:Ureteral obstruction will lead clinically to hydronephrosis, which may further develop into partial or complete loss of kidney function and even cause permanent histological damage. However, there is little knowledge of metabolic responses during the obstructed process and its recoverability. In this study, a complete...

journal_title：Journal of proteome research

authors： Wang Z,Xu R,Shen G,Feng J

更新日期：2018-09-07 00:00:00

abstract：:The development of systematic proteomic quantification techniques in systems biology research has enabled one to perform an in-depth analysis of cellular systems. We have developed a systematic proteomic approach that encompasses the spectrum from global to targeted analysis on a single platform. We have applied this ...

journal_title：Journal of proteome research

authors： Woo J,Han D,Wang JI,Park J,Kim H,Kim Y

更新日期：2017-09-01 00:00:00

abstract：:A database of nonredundant structures of EF-hand domains--i.e., pairs of helix-loop-helix motifs--has been assembled, and the six angles among the four helices re-determined. A principal component analysis of these angles allows us to use two such components (PC1 and PC2) to describe the system retaining 80% of the to...

journal_title：Journal of proteome research

authors： Babini E,Bertini I,Capozzi F,Luchinat C,Quattrone A,Turano M

更新日期：2005-11-01 00:00:00

abstract：:The coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has impacted a large portion of the world population. From a virus genetic perspective, a recent study described what genomic data revealed about the origin and emergence of SARS-CoV-2, proposing stronger a...

journal_title：Journal of proteome research

authors： Zhang YM,Wang L,Liu XZ,Zhang H

更新日期：2020-11-06 00:00:00

abstract：:TGFBR2 serves as an initial regulator of the TGF-β signaling pathway, and loss or reduction of its expression can lead to uncontrolled cell growth. This study was conducted to further explore the mechanism of TGFBR2/SMAD4 on the migration and proliferation of CC cells. Here, TGFBR2 and SMAD4 expressions in CC cells an...

journal_title：Journal of proteome research

authors： Yuan J,Yi K,Yang L

更新日期：2020-08-07 00:00:00

abstract：:Nanobacteria may cause peripheral neuropathy by adhesion to the perineurium. This hypothesis receives support from five independent observations: (1) identification of perineurial apatite in diabetic patients with peripheral neuropathy, (2) massive presence of nanobacteria in a diabetic patient, (3) beneficial effect ...

journal_title：Journal of proteome research

authors： Sommer AP

更新日期：2004-09-01 00:00:00

abstract：:Dysregulated protein phosphorylation is a primary culprit in multiple physiopathological states. Hence, although analysis of signaling cascades on a proteome-wide scale would provide significant insight into both normal and aberrant cellular function, such studies are simultaneously limited by sheer biological complex...

journal_title：Journal of proteome research

authors： Ndassa YM,Orsi C,Marto JA,Chen S,Ross MM

更新日期：2006-10-01 00:00:00

abstract：:Geobacter sulfurreducens is a dissimilatory metal-reducing bacterium capable of forming thick electron-conducting biofilms on solid electrodes. Here, we employ for the first time comparative proteomics to identify key physiological changes involved in G. sulfurreducens adaptation from fumarate-respiring planktonic cel...

journal_title：Journal of proteome research

authors： Kavanagh P,Botting CH,Jana PS,Leech D,Abram F

更新日期：2016-01-01 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：:Pancreatic cancer is a devastating disease and early diagnosis and treatment are essential to improve the prognosis. We previously showed that α-fibrinogen containing hydroxylated proline residues at positions 530 and 565 is increased in plasma of pancreatic cancer patients. However, no antibody specific for hydroxyla...

journal_title：Journal of proteome research

authors： Yoneyama T,Ohtsuki S,Ono M,Ohmine K,Uchida Y,Yamada T,Tachikawa M,Terasaki T

更新日期：2013-02-01 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：:Stroke remains a major public health problem worldwide; it causes severe disability and is associated with high mortality rates. However, early diagnosis of stroke is difficult, and no reliable biomarkers are currently established. In this study, mass-spectrometry-based metabolomics was utilized to characterize the me...

journal_title：Journal of proteome research

authors： Liu P,Li R,Antonov AA,Wang L,Li W,Hua Y,Guo H,Wang L,Liu P,Chen L,Tian Y,Xu F,Zhang Z,Zhu Y,Huang Y

更新日期：2017-02-03 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：:Multiple reaction monitoring (MRM)-based mass spectrometric quantification of peptides and their corresponding proteins has been successfully applied for biomarker validation in serum. The option of multiplexing offers the chance to analyze various proteins in parallel, which is especially important in obesity researc...

journal_title：Journal of proteome research

authors： Oberbach A,Schlichting N,Neuhaus J,Kullnick Y,Lehmann S,Heinrich M,Dietrich A,Mohr FW,von Bergen M,Baumann S

更新日期：2014-12-05 00:00:00

abstract：:"Omics" studies reported to date have dealt with either thoroughly characterized single species or poorly explored meta-microbial communities. However, these techniques are capable of producing highly informative data for the analysis of interactions between two organisms. We examined the bacterial interaction between...

journal_title：Journal of proteome research

authors： Nakanishi Y,Fukuda S,Chikayama E,Kimura Y,Ohno H,Kikuchi J

更新日期：2011-02-04 00:00:00

abstract：:The Lewis x (Le(x)) structure (Galβ1-4(Fucα1-3)GlcNAc-R) is a carbohydrate epitope comprising the stage-specific embryonic antigen-1 (SSEA-1) and CD15, and it is synthesized by α1,3-fucosyltransferase 9 (Fut9). Fut9 is expressed specifically in the stomach, kidney, brain, and in leukocytes, suggesting a specific funct...

journal_title：Journal of proteome research

authors： Noro E,Togayachi A,Sato T,Tomioka A,Fujita M,Sukegawa M,Suzuki N,Kaji H,Narimatsu H

更新日期：2015-09-04 00:00:00

abstract：:While the proteome defines the expressed gene products, the metabolome results from reactions controlled by such gene products. Plasma represents an accessible "window" to the metabolome both in regard of availability and content. The wide range of the plasma metabolome, in terms of molecular diversity and abundance, ...

journal_title：Journal of proteome research

authors： Griffiths WJ,Hornshaw M,Woffendin G,Baker SF,Lockhart A,Heidelberger S,Gustafsson M,Sjövall J,Wang Y

更新日期：2008-08-01 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

authors： Zhu Y,Lei Q,Li D,Zhang Y,Jiang X,Hu Z,Xu G

更新日期：2018-04-06 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