Abstract:
:In shotgun proteomics, proteins can be fractionated by 1-D gel electrophoresis and digested into peptides, followed by liquid chromatography to separate the peptide mixture. Mass spectrometry generates hundreds of thousands of tandem mass spectra from these fractions, and proteins are identified by database searching. However, the search scores are usually not sufficient to distinguish the correct peptides. In this study, we propose a confident protein identification method for high-throughput analysis of human proteome. To build a filtering protocol in database search, we chose Pseudomonas putida KT2440 as a reference because this bacterial proteome contains fewer modifications and is simpler than the human proteome. First, the P. putida KT2440 proteome was filtered by reversed sequence database search and correlated by the molecular weight in 1-D-gel band positions. The characterization protocol was then applied to determine the criteria for clustering of the human plasma proteome into three different groups. This protein filtering method, based on bacterial proteome data analysis, represents a rapid way to generate higher confidence protein list of the human proteome, which includes some of heavily modified and cleaved proteins.
journal_name
Proteomicsjournal_title
Proteomicsauthors
Park GW,Kwon KH,Kim JY,Lee JH,Yun SH,Kim SI,Park YM,Cho SY,Paik YK,Yoo JSdoi
10.1002/pmic.200500318subject
Has Abstractpub_date
2006-02-01 00:00:00pages
1121-32issue
4eissn
1615-9853issn
1615-9861journal_volume
6pub_type
杂志文章相关文献
PROTEOMICS文献大全abstract::Imbalance in protein homeostasis in specific subcellular organelles is alleviated through organelle-specific stress response pathways. As a canonical example of stress activated pathway, accumulation of misfolded proteins in ER activates unfolded protein response (UPR) in almost all eukaryotic organisms. However, very...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300449
更新日期:2014-08-01 00:00:00
abstract::Most cancers consist of heterogeneous populations of cells with substantial differences in tumorigenicity. Cells that possess self-renewal and tumor-initiating properties are often called cancer stem cells (CSCs). Since CSCs underlie tumor recurrence and metastasis and are resistant to current anti-cancer therapies, n...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201500472
更新日期:2016-12-01 00:00:00
abstract::A monolithic enzymatic microreactor was prepared in a fused-silica capillary by in situ polymerization of acrylamide, glycidyl methacrylate (GMA) and ethylene dimethacrylate (EDMA) in the presence of a binary porogenic mixture of dodecanol and cyclohexanol, followed by ammonia solution treatment, glutaraldehyde activa...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500234
更新日期:2006-01-01 00:00:00
abstract::In this work, for the first time, perfluorinated magnetic mesoporous microspheres were designed and synthesized for the highly specific enrichment of fluorous-derivatized phosphopeptides through the unique fluorine-fluorine interactions. The perfluorinated magnetic mesoporous microspheres were prepared through a surfa...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201500323
更新日期:2016-04-01 00:00:00
abstract::Scab, caused by Fusarium graminearum, is a serious spike disease in wheat. To identify proteins in resistant wheat cultivar Wangshuibai induced by F. graminearum infection, proteins extracted from spikes 6, 12 and 24 h after inoculation were separated by 2-DE. Thirty protein spots showing 3-fold change in abundance wh...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401317
更新日期:2005-11-01 00:00:00
abstract::The present review deals with the use of combinatorial ligand libraries, composed by hexapeptides, in the capture and concentration of the low-abundance proteome. This method, first reported in 2005, is compared with other current methodologies aimed at exploring the "deep proteome", such as: depletion of high-abundan...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.200800389
更新日期:2009-03-01 00:00:00
abstract::A proteomic analysis of a wild-type and of a phoB mutant showed that Vibrio cholerae expresses genes of two major regulons in response to phosphate starvation. The Pho regulon, expressed by the wild-type, allowed the cells to adapt to the new environment. Induction of the general stress regulon was mainly observed in ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500238
更新日期:2006-03-01 00:00:00
abstract::Atopic dermatitis (AD) is a chronic relapsing inflammatory skin disease typically characterized by a distribution of eczematous skin lesions with lichenification, pruritic excoriations, and dry skin with wide varieties of pathophysiologic aspects. Recently, AD was divided into extrinsic and intrinsic forms according t...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200400998
更新日期:2004-11-01 00:00:00
abstract::Oviductal fluid (ODF) proteins modulate and support reproductive processes in the oviduct. In the present study, proteins involved in the biological events that precede fertilization have been identified in the rabbit ODF proteome, isolated from the ampulla and isthmus of the oviduct at different time points within 8 ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201800319
更新日期:2019-03-01 00:00:00
abstract::Aspergillus fumigatus faces abrupt changes in oxygen concentrations at the site of infection. An increasing number of studies has demonstrated that elevated production of intracellular reactive oxygen species (ROS) under low oxygen conditions plays a regulatory role in modulating cellular responses for adaptation to h...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201800339
更新日期:2019-03-01 00:00:00
abstract::Protein arrays permit the parallel analysis of many different markers in a small sample volume. However, the problem of cross-reactivity limits the degree of multiplexing in parallel sandwich immunoassays (using monoclonal antibodies (mAbs)), meaning antibodies must be prescreened in order to reduce false positives. I...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200300736
更新日期:2004-05-01 00:00:00
abstract::Leukaemic transformation is frequently associated with the aberrant activity of a protein tyrosine kinase (PTK). As such it is of clinical relevance to be able to map the effects of these leukaemogenic PTKs on haemopoietic cells at the level of phosphorylation modulation. In this paradigm study we have employed a rang...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000176
更新日期:2010-09-01 00:00:00
abstract::Quantitative proteomics technology based on isobaric tags is playing an important role in proteomic investigation. In this paper, we present an automated software, named IQuant, which integrates a postprocessing tool of protein identification and advanced statistical algorithms to process the MS/MS signals generated f...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300361
更新日期:2014-10-01 00:00:00
abstract::Large-scale interaction studies contribute the largest fraction of protein interactions information in databases. However, co-purification of non-specific or indirect ligands, often results in data sets that are affected by a considerable number of false positives. For the fraction of interactions mediated by short li...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000030
更新日期:2011-01-01 00:00:00
abstract::The effects of di(2-ethylhexyl) phthalate (DEHP) on proteins secreted by HepG2 cells were studied using a proteomic approach. HepG2 cells were exposed to various concentrations of DEHP (0, 2.5, 5, 10, 25, 50, 100, and 250 microM) for 24 or 48 h. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and c...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200900674
更新日期:2010-05-01 00:00:00
abstract::Exosomes are deliverers of critically functional proteins, capable of transforming target cells in numerous cancers, including hepatocellular carcinoma (HCC). We hypothesize that the motility of HCC cells can be featured by comparative proteome of exosomes. Hence, we performed the super-SILAC-based MS analysis on the ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201700103
更新日期:2017-07-01 00:00:00
abstract::Sepsis is an extreme host response to infection that leads to loss of organ function and cardiovascular integrity. Mortality from sepsis is on the rise. Despite more than three decades of research and clinical trials, specific diagnostic and therapeutic strategies for sepsis are still absent. The use of LFQ- and TMT-b...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201800389
更新日期:2019-03-01 00:00:00
abstract::Shewanella inhabit a wide variety of niches in nature and can utilize a broad spectrum of electron acceptors under anaerobic conditions. How they modulate their gene expression to adapt is poorly understood. ArcA, homologue of a global regulator controlling hundreds of genes involved in aerobic and anaerobic respirati...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201100651
更新日期:2012-06-01 00:00:00
abstract::Data-independent acquisition (DIA) offers several advantages over data-dependent acquisition (DDA) schemes for characterizing complex protein digests analyzed by LC-MS/MS. In contrast to the sequential detection, selection, and analysis of individual ions during DDA, DIA systematically parallelizes the fragmentation o...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201400323
更新日期:2015-03-01 00:00:00
abstract::Progress in MS-based methods for veterinary research and diagnostics is lagging behind compared to the human research, and proteome data of domestic animals is still not well represented in open source data repositories. This is particularly true for the equine species. Here we present a first Equine PeptideAtlas enco...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300398
更新日期:2014-03-01 00:00:00
abstract::Sequencing of the human genome opened the way to the exploration of the proteome and this has lead to the identification of large numbers of proteins in complex biological samples. The identification of diagnostic patterns in samples taken from patients to aid diagnosis is in the early stages of development. The solut...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.200700665
更新日期:2008-02-01 00:00:00
abstract::The sodium (Na+ )-calcium (Ca2+ ) exchanger 1 (NCX1) is an antiporter membrane protein encoded by the SLC8A1 gene. In the heart, it maintains cytosolic Ca2+ homeostasis, serving as the primary mechanism for Ca2+ extrusion during relaxation. Dysregulation of NCX1 is observed in end-stage human heart failure. In this st...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201600417
更新日期:2017-09-01 00:00:00
abstract::Staphylococcus aureus Clp ATPases (molecular chaperones) alter normal physiological functions including an aconitase-mediated effect on post-stationary growth, acetate catabolism, and entry into death phase (Chatterjee et al., J. Bacteriol. 2005, 187, 4488-4496). In the present study, the global function of ClpC in ph...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800586
更新日期:2009-03-01 00:00:00
abstract::The aim of the study was to evaluate the SELDI-TOF MS technique for pancreatic islet research. Mouse islets were cultured at low or high glucose levels in the absence or presence of oleate and characterized by measuring insulin secretion and oxygen tension. Subsequently, the islets were protein profiled. Up to 200 dif...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200601019
更新日期:2007-09-01 00:00:00
abstract::Each postnatal hair follicle (HF) perpetually goes through three phases: anagen, catagen, and telogen. The molecular signals that orchestrate the follicular transition between phases are still largely unknown. Our previous study shows that the keratinocyte specific Smad4 knockout mice exhibit progressive alopecia due ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200700760
更新日期:2008-06-01 00:00:00
abstract::Hpn is a small histidine-rich cytoplasmic protein from Helicobacter pylori and has been recognized as a high-risk factor for several cancers including gastric cancer, colorectal cancer, and MALT lymphoma. However, the relationship between Hpn and cancers remains elusive. In this study, we discovered that Hpn protein e...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201600350
更新日期:2017-06-01 00:00:00
abstract::Protein arginine methyltransferase 5 (PRMT5) is a major enzyme responsible for generating monomethyl and symmetric dimethyl arginine in proteins. PRMT5 is essential for cell viability and development, and its overexpression is observed in a variety of cancers. In the present study, it is found that levels of PRMT5 pro...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201900367
更新日期:2020-05-28 00:00:00
abstract::In this article, we provide a comprehensive study of the content of the Universal Protein Resource (UniProt) protein data sets for human and mouse. The tryptic search spaces of the UniProtKB (UniProt knowledgebase) complete proteome sets were compared with other data sets from UniProtKB and with the corresponding Inte...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201400227
更新日期:2015-01-01 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::Human embryonic stem cells (hESCs) have received considerable attention due to their therapeutic potential and usefulness in understanding early development and cell fate commitment. In order to appreciate the unique properties of these pluripotent, self-renewing cells, we have performed an in-depth multidimensional f...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201400132
更新日期:2015-01-01 00:00:00