Abstract:
:The explosion of site- and context-specific in vivo phosphorylation events presents a potentially rich source of biological knowledge and calls for novel data analysis and modeling paradigms. Perhaps the most immediate challenge is delineating detected phosphorylation sites to their effector kinases. This is important for (re)constructing transient kinase-substrate interaction networks that are essential for mechanistic understanding of cellular behaviors and therapeutic intervention, but has largely eluded high-throughput protein-interaction studies due to their transient nature and strong dependencies on cellular context. Here, we surveyed some of the computational approaches developed to dissect phosphorylation data detected in systematic proteomic experiments and reviewed some experimental and computational approaches used to map phosphorylation sites to their effector kinases in efforts aimed at reconstructing biological signaling networks.
journal_name
Proteomicsjournal_title
Proteomicsauthors
Tan CS,Linding Rdoi
10.1002/pmic.200900266subject
Has Abstractpub_date
2009-12-01 00:00:00pages
5233-42issue
23eissn
1615-9853issn
1615-9861journal_volume
9pub_type
杂志文章,评审相关文献
PROTEOMICS文献大全abstract::The Asia Oceania Human Proteome Organisation (AOHUPO) has embarked on a Membrane Proteomics Initiative with goals of systematic comparison of strategies for analysis of membrane proteomes and discovery of membrane proteins. This multilaboratory project is based on the analysis of a subcellular fraction from mouse live...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000126
更新日期:2010-11-01 00:00:00
abstract::We introduce a new methodology named ligand profiling and identification for effective discovery of bioactive ligands such as peptide hormones. This technology was developed from a new concept of parallel column chromatography and active fraction profiling by nano-LC MS. Traditional methods use sequential column chrom...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500511
更新日期:2006-03-01 00:00:00
abstract::In mass spectrometry-based proteomics, protein identification results usually consist of peptide sequences and database-dependent accession identifiers of the matching proteins. Often certain annotations are only available in particular databases that in turn must be queried by a certain identifier. In order to simpli...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600018
更新日期:2006-08-01 00:00:00
abstract::In higher plants many different genes encode Lhcb proteins that belong to a highly conserved protein family. Evolutionary conservation of this genetic redundancy suggests that individual gene products play different roles in light harvesting and photoprotection depending on environmental conditions. We have tested the...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200402008
更新日期:2005-02-01 00:00:00
abstract::High hydrostatic pressure (HHP) exerts diverse effects on microorganisms, leading to stress response and cell death. While inactivation of microorganisms by lethal HHP is well investigated in the context of food preservation and the hygienic safety of minimal food processes, sublethal HHP stress response and its effec...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200402086
更新日期:2006-03-01 00:00:00
abstract::Biotherapeutics, molecules produced from biological systems, require rigorous purification steps to remove impurities including host cell proteins (HCPs). Regulatory guidelines require manufacturers to monitor process-related impurities along the purification workflow. Mass spectrometry (MS) has recently been consider...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.202000152
更新日期:2021-01-18 00:00:00
abstract::In this study, we generated 40 somatic cell cloned (scNT) piglets. Of these, five piglets were stillborn, 22 scNT piglets died suddenly within the first week of life, and 1 piglet died after 40 days. Twelve scNT piglets are still healthy. The birth weights of compromised scNT piglets in comparison with those of normal...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401079
更新日期:2005-05-01 00:00:00
abstract::ProDaC (Proteomics Data Collection), a "Coordination Action" within the 6(th) EU framework programme, was created to support the collection, distribution and public availability of data from proteomics experiments. Within the consortium standards are created and maintained enabling an extensive data collection within ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800732
更新日期:2009-01-01 00:00:00
abstract::Lipid particles (LP) of all types of cells are a depot of neutral lipids. The present investigation deals with the isolation of LP from the yeast Yarrowia lipolytica and the characterization of their lipid and protein composition. Properties of LP varied depending on the carbon source. LP from glucose-grown cells reve...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500339
更新日期:2006-03-01 00:00:00
abstract::The skin provides protection against environmental stress. However, intrinsic and extrinsic aging causes significant alteration to skin structure and components, which subsequently impairs molecular characteristics and biochemical processes. Here, we have conducted an immunohistological investigation and established t...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201600141
更新日期:2016-10-01 00:00:00
abstract::Gram-negative bacteria release outer membrane vesicles (OMVs) as part of their normal growth that contain a range of cargo from their parent bacterium, including DNA, RNA, and proteins. The protein content of OMVs is suggested to be similar in composition to various sub-cellular locations of their parent bacterium. Ho...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201800209
更新日期:2019-01-01 00:00:00
abstract::The hepatitis B virus X-protein (HBx), a multifunctional viral regulator, participates in the viral life cycle and in the development of hepatocellular carcinoma (HCC). We previously reported a high incidence of HCC in transgenic mice expressing HBx. In this study, proteomic analysis was performed to identify proteins...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800779
更新日期:2009-11-01 00:00:00
abstract::Long-lived conifer trees depend on both constitutive and induced defenses for resistance against a myriad of potential pathogens and herbivores. In species of spruce (Picea spp.), several of the late events of pathogen-, insect-, or elicitor-induced defense responses have previously been characterized at the anatomica...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800252
更新日期:2009-01-01 00:00:00
abstract::Plant cell wall-degrading enzymes produced by microorganisms possess important biotechnological applications, including biofuel production. Some anaerobic bacteria are able to produce multienzymatic complexes called cellulosomes while filamentous fungi normally secrete individual hydrolytic enzymes that act synergisti...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200048
更新日期:2012-08-01 00:00:00
abstract::Two-dimensional difference gel electrophoresis (2-D DIGE) allows for reliable quantification of global protein abundance changes. The threshold of significance for protein abundance changes depends on the experimental variation (biological and technical). This study estimates biological, technical and total variation ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201100071
更新日期:2011-08-01 00:00:00
abstract::Lipid rafts are membrane microdomains of unique lipid composition that segregate proteins with poorly understood consequences for membrane organization. Identification of raft associated proteins could therefore provide novel insight into raft-dependent functions. Monocytes process antigens for presentation to T cells...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200390067
更新日期:2003-04-01 00:00:00
abstract::Many proteomic studies focus on quantitative aspects, using different stable isotope labeling techniques that require specialized software to analyze the generated data. Here we present jTraqX, an easy-to-use tool for processing and visualizing protein quantification data. jTraqX is platform independent and is compati...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200900374
更新日期:2010-03-01 00:00:00
abstract::The CpG motif of bacterial DNA (CpG-DNA) is a potent immunostimulating agent whose mechanism of action is not yet clear. Here, we used both DNA microarray and proteomic approaches to investigate the effects of oligodeoxynucleotides containing the CpG motif (CpG-ODN) on gene transcription and protein expression profile...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401144
更新日期:2005-03-01 00:00:00
abstract::Sandwich ELISA microarrays have great potential for validating disease biomarkers. Each ELISA relies on robust-affinity reagents that retain activity when immobilized on a solid surface or when labeled for detection. Single-chain antibodies (scFv) are affinity reagents that have greater potential for high-throughput p...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200701036
更新日期:2008-06-01 00:00:00
abstract::Total parenteral nutrition (TPN) is provided as the primary nitrogen source to manage patients with intestinal failure who were not able to sustain themselves on enteral feeds. The most common complication of long-term TPN use is hepatitis. A proteomic approach was used to identify proteins that are differentially exp...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201500128
更新日期:2015-11-01 00:00:00
abstract::Acute kidney injury (AKI) is one of the more frequent and lethal pathological conditions seen in intensive care units. Currently available treatments are not totally effective but stem cell-based therapies are emerging as promising alternatives, especially the use of mesenchymal stromal cells (MSC), although the signa...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300084
更新日期:2014-06-01 00:00:00
abstract::Prevotella intermedia binds and invades a variety of host cells. This binding is most probably mediated through cell surface proteins termed adhesins. To identify proteins binding to the host extracellular matrix (ECM) component, fibronectin, and study the molecular mechanism underlying bacterial colonization, we appl...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600177
更新日期:2006-11-01 00:00:00
abstract::During clinical mastitis in dairy cows, the quantity of milk produced decreases and the composition of the milk is altered. As the severity of inflammation associated with the disease increases, the chemical composition of milk approaches that of blood as a consequence of increased permeability of the blood mammary ba...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200300723
更新日期:2004-07-01 00:00:00
abstract::Most proteins execute their functions through interacting with other proteins. Thus, understanding protein-protein interactions (PPIs) is essential to decipher biological functions in a living cell. To predict large-scale PPIs, effective and efficient computational approaches are desirable to integrate heterogeneous d...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200326
更新日期:2013-01-01 00:00:00
abstract::We have developed a proteome database (DB), BiomarkerDigger (http://biomarkerdigger.org) that automates data analysis, searching, and metadata-gathering function. The metadata-gathering function searches proteome DBs for protein-protein interaction, Gene Ontology, protein domain, Online Mendelian Inheritance in Man, a...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800593
更新日期:2009-07-01 00:00:00
abstract::Despite affecting up to 70% of HIV-positive patients and being the leading cause of dementia in patients under 40 years, the molecular mechanisms involved in the onset of HIV-associated neurocognitive disorders (HAND) are not well understood. To address this, we performed SILAC-based quantitative proteomic analysis on...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201600236
更新日期:2017-03-01 00:00:00
abstract::Panax ginseng is an important herb that has clear effects on the treatment of diverse diseases. Until now, the natural peptide constitution of this herb remains unclear. Here, we conduct an extensive characterization of Ginseng peptidome using MS-based data mining and sequencing. The screen on the charge states of pre...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201600183
更新日期:2016-11-01 00:00:00
abstract::The use of anthrax spores as a bioweapon has spurred efforts aimed at identifying key proteins expressed in Bacillus anthracis. Because spore germination and outgrowth occur prior to and are required for disease manifestations, blocking germination and early outgrowth with novel vaccines or inhibitors targeting critic...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200400831
更新日期:2004-09-01 00:00:00
abstract::A curated set of 81 proven and 44 predicted lipoproteins of Escherichia coli K-12 was defined with the combined use of a literature survey, a variety of predictive tools and human expertise. The well-documented Gram-negative proteome of E. coli K-12 was chosen to assess how the different approaches complement each oth...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200300749
更新日期:2004-06-01 00:00:00
abstract::Neurons present a highly polarized morphology, often displaying a significantly imbalanced distribution of the cytoplasm between the somatic and axonal domains. This imbalance requires cell-specific mechanisms for the maintenance of the axoplasmic mass during development, neuronal homeostasis, and recovery after injur...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201900054
更新日期:2019-08-01 00:00:00