Abstract:
:MS-based protein identification is an important part of both gel-based and gel-free proteome studies. The MASCOT search engine (http://www.matrixscience.com) provides one of the most popular automated algorithms for this task. Here we present an open-source software library written in Java that parses raw MASCOT results into an easily accessible and fully functional object model (http://genesis.ugent.be/MascotDatfile). Several scripts based on this library are provided as examples, allowing direct automation of important routine tasks involved in processing peptide identifications.
journal_name
Proteomicsjournal_title
Proteomicsauthors
Helsens K,Martens L,Vandekerckhove J,Gevaert Kdoi
10.1002/pmic.200600682subject
Has Abstractpub_date
2007-02-01 00:00:00pages
364-6issue
3eissn
1615-9853issn
1615-9861journal_volume
7pub_type
杂志文章相关文献
PROTEOMICS文献大全abstract::Knowledge of gender differences is important because nutritional recommendations on the basis of data collected using predominantly male subjects may not be valid for women. In the present study, we performed proteomic analysis in plasma of rats fed a high-fat diet (HFD) using 2-DE combined with MALDI-TOF-MS for analy...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201100127
更新日期:2012-01-01 00:00:00
abstract::In this report we introduce a new concept "proteomic trajectory mapping" for the investigation of a complex phenomenon underlying biological transformation and transition. We define proteomic trajectory to be the kinetic trace of protein expression and present a successful proteomic trajectory mapping of complex molec...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500813
更新日期:2006-06-01 00:00:00
abstract::Currently, most researches on the properties of interacting proteins, hubs in particular, are mainly based on an aggregated network of binary interactions. Here, by projecting a yeast-aggregated cell cycle network into four phase (G1, S, G2 and M) sub-networks, we explored the properties of the hubs of the aggregated ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200900053
更新日期:2009-10-01 00:00:00
abstract::Many cancer cells show unique protein expression patterns. We used proteome technology including MS, free flow isoelectric focusing and Western blotting to determine current concentrations of metabolic enzymes in healthy and malignant human thyroid cells. Three different types of human thyroid cells were investigated ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200070
更新日期:2012-08-01 00:00:00
abstract::A method for the determination of the stoichiometry of protein complexes has been developed, which is based on proteolytic digestion of the complex, labeling with a fluorescent reagent, specific for amino or sulfhydryl groups, and separation by liquid chromatography with fluorescence and mass spectrometric detection. ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200300668
更新日期:2004-03-01 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::Quantitative proteomic analysis using stable isotope labeling with amino acids in cell culture (SILAC), as metabolic labeling with MS, has been used as an excellent technique to measure relative abundance change in proteins and post-transitional modifications. Since its development in 2002, SILAC has proven to have un...
journal_title:Proteomics
pub_type: 评论,杂志文章
doi:10.1002/pmic.201700458
更新日期:2018-03-01 00:00:00
abstract::Selective activation of T helper subsets 1 (Th1) and 2 (Th2) plays a crucial role in different pathological conditions. Th1 cell response is involved in pathogenesis of autoimmune diseases, such as type II diabetes and multiple sclerosis, and Th2 cell response in pathogenesis of allergy and asthma. Cytokine interleuki...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401151
更新日期:2005-08-01 00:00:00
abstract::Since detergent-resistant lipid rafts play important roles in the signal transduction for myogenesis, their comprehensive proteomic analysis could provide new insights to understand their function in myotubes. Here, the detergent-resistant lipid rafts were isolated from C2C12 myotubes and analyzed by capillary RPLC/MS...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200900826
更新日期:2010-07-01 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::Ibuprofen is a member of the proprionic acid group of nonsteroidal anti-inflammatory drugs (NSAID), with the S-enantiomer being more active than the R-enantiomer. It has been shown to display protective effects against neuroinflammation, which is linked to the pathogenesis of several neurodegenerative disorders, inclu...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200700556
更新日期:2008-04-01 00:00:00
abstract::Proteins undergo PTM, which modulates their structure and regulates their function. Estimates of the PTM occurrence vary but it is safe to assume that there is an important gap between what is currently known and what remains to be discovered. The highest throughput and most comprehensive efforts to catalogue protein ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200900502
更新日期:2010-02-01 00:00:00
abstract::Modification through beta-elimination has proven to be a reliable first step in the approach for enrichment of serine/threonine-phopshorylated (Ser-/Thr) peptides. However, under harsh basic conditions, Ser-/Thr-glycosylated peptides are susceptible to beta-elimination as well. Therefore, we have optimized these condi...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600373
更新日期:2006-12-01 00:00:00
abstract::GlycoMod (http://www.expasy.ch/tools/glycomod/) is a software tool designed to find all possible compositions of a glycan structure from its experimentally determined mass. The program can be used to predict the composition of any glycoprotein-derived oligosaccharide comprised of either underivatised, methylated or ac...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/1615-9861(200102)1:2<340::AID-PROT340>3.0.
更新日期:2001-02-01 00:00:00
abstract::The field of biochemistry is currently faced with the enormous challenge of assigning functional significance to more than thirty thousand predicted protein products encoded by the human genome. In order to accomplish this daunting task, methods will be required that facilitate the global analysis of proteins in compl...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/1615-9861(200109)1:9<1067::AID-PROT1067>3.
更新日期:2001-09-01 00:00:00
abstract::Site-specific isomerization of uridines into pseudouridines in RNAs is catalyzed either by stand-alone enzymes or by box H/ACA ribonucleoprotein particles (sno/sRNPs). The archaeal box H/ACA sRNPs are five-component complexes that consist of a guide RNA and the aCBF5, aNOP10, L7Ae, and aGAR1 proteins. In this study, w...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201400529
更新日期:2015-08-01 00:00:00
abstract::Aging is associated with a progressive loss of skeletal muscular function that often leads to progressive disability and loss of independence. Although muscle aging is well documented, the molecular mechanisms of this condition still remain unclear. To gain greater insight into the changes associated with aging of ske...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200497
更新日期:2014-01-01 00:00:00
abstract::A protein chip has been developed that allows the simultaneous detection of a multitude of different biowarfare agents. The chip was developed for the ArrayTube platform providing a cheap and easy to handle technology solution that combines a microtube-integrated protein chip with the classical procedure of a sandwich...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500721
更新日期:2006-05-01 00:00:00
abstract::Trichomonas vaginalis, a sexually transmitted parasite, has many cysteine proteinases (CPs); some are involved in trichomonal pathogenesis, express during infection, and antibodies against CPs have been detected in patient sera. The goal of this study was to identify the antigenic proteinases of T. vaginalis as potent...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200900479
更新日期:2010-02-01 00:00:00
abstract::The Ser/Thr/Tyr phosphoproteome of Bacillus subtilis was analyzed by a 2-D gel-based approach combining Pro-Q Diamond staining and [(33)P]-labeling. In exponentially growing B. subtilis cells 27 proteins could be identified after staining with Pro-Q Diamond and/or [(33)P]-labeling and one additional protein was labele...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200700232
更新日期:2007-10-01 00:00:00
abstract::Antibodies that recognize PTMs of histones play a central role in epigenetic proteomic research. Modification-specific antibodies are employed in chromatin immunoprecipitation, for Western blotting and during the immunoprecipitation steps for MS-based global proteomic analyses. Knowledge about the antibodies' off-targ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200383
更新日期:2013-03-01 00:00:00
abstract::We performed phosphoproteome analysis of proteins from the extremely thermophilic Gram-negative eubacterium Thermus thermophilus HB8 using gel-free mass spectrometric method. We identified 52 phosphopeptides from 48 proteins and determined 46 phosphorylation sites: 30 on serine, 12 on threonine, and 4 on tyrosine. The...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201100573
更新日期:2012-05-01 00:00:00
abstract::Cyanobacteria are oxygenic photosynthetic prokaryotes and play a crucial role in the Earth's carbon and nitrogen cycles. The photoautotrophic cyanobacterium Anabaena sp. PCC 7120 has the ability to fix atmospheric nitrogen in heterocysts and produce hydrogen as a byproduct through a nitrogenase. In order to improve hy...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201800332
更新日期:2019-10-01 00:00:00
abstract::Thirteen proteins (identified with 2-D gels and MALDI-TOF MS) are significantly altered during staurosporine-induced apoptosis in SH-SY5Y cells. To gain further insight into the integrated cellular response to apoptosis, we have investigated whether a network can be generated of direct and indirect interactions betwee...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200900112
更新日期:2010-03-01 00:00:00
abstract::Elite rice hybrids, when compared to their parental lines, exhibit increased yield and other favorable agronomical traits, such as pathogen- and water-stress resistances, which are described as heterosis, and the molecular mechanism of heterosis remains to be elucidated. Since genomic sequences of the paternal (9311) ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200701164
更新日期:2008-11-01 00:00:00
abstract::In order to investigate the unique contribution of individual wine grape (Vitis vinifera) berry tissues and water-deficit to wine quality traits, a survey of tissue-specific differences in protein and selected metabolites was conducted using pericarp (skin and pulp) and seeds of berries from vines grown under well-wat...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800158
更新日期:2009-05-01 00:00:00
abstract::The oxidation of free and protein-bound methionine into methionine sulfoxide is a frequently occurring modification caused by ROS. Most organisms express methionine sulfoxide reductases (MSR enzymes) to repair this potentially damaging modification. Humans express three different MSRB enzymes which reside in different...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300357
更新日期:2014-09-01 00:00:00
abstract::A method is introduced to evaluate protein concentrations using the height sum of all MALDI-MS peaks that unambiguously match theoretic tryptic peptide masses of the protein sought after. The method uses native chromatographic protein fractionation prior to digestion but does not require any depletion, labeling, deriv...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500747
更新日期:2006-07-01 00:00:00
abstract::The Annual Spring workshop of the HUPO-PSI was this year held at the EMBL International Centre for Advanced Training (EICAT) in Heidelberg, Germany. Delegates briefly reviewed the successes of the group to date. These include the wide spread implementation of the molecular interaction data exchange formats, PSI-MI XML...
journal_title:Proteomics
pub_type:
doi:10.1002/pmic.201190117
更新日期:2011-11-01 00:00:00
abstract::The characterization of peptides bound to human leukocyte antigen (HLA) class I is of fundamental importance for understanding CD8+ T cell-driven immunological processes and for the development of immunomodulatory therapeutic strategies. However, until now, the mass spectrometric analysis of HLA-bound peptides has typ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201500445
更新日期:2016-05-01 00:00:00