Abstract:
:With recent publications of several large-scale protein-protein interaction (PPI) studies, the realization of the full yeast interaction network is getting closer. Here, we have analysed several yeast protein interaction datasets to understand their strengths and weaknesses. In particular, we investigate the effect of experimental biases on some of the protein properties suggested to be enriched in highly connected proteins. Finally, we use support vector machines (SVM) to assess the contribution of these properties to protein interactivity. We find that protein abundance is the most important factor for detecting interactions in tandem affinity purifications (TAP), while it is of less importance for Yeast Two Hybrid (Y2H) screens. Consequently, sequence conservation and/or essentiality of hubs may be related to their high abundance. Further, proteins with disordered structure are over-represented in Y2H screens and in one, but not the other, large-scale TAP assay. Hence, disordered regions may be important both in transient interactions and interactions in complexes. Finally, a few domain families seem to be responsible for a large part of all interactions. Most importantly, we show that there are method-specific biases in PPI experiments. Thus, care should be taken before drawing strong conclusions based on a single dataset.
journal_name
Proteomicsjournal_title
Proteomicsauthors
Björklund AK,Light S,Hedin L,Elofsson Adoi
10.1002/pmic.200800150subject
Has Abstractpub_date
2008-11-01 00:00:00pages
4657-67issue
22eissn
1615-9853issn
1615-9861journal_volume
8pub_type
杂志文章相关文献
PROTEOMICS文献大全abstract::We report on a novel strategy for identification of specific sulfation motifs in chondroitin/dermatan sulfate (CS/DS) chain derived from decorin (Dcn), based on enzyme cleavage and multistage MS (MS(n)). Released CS/DS chains were digested with chondroitin B and in parallel with AC I lyases to obtain oligosaccharides ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800440
更新日期:2009-07-01 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::The nucleus is the organelle where basically all DNA-related processes take place in eukaryotes, such as replication, transcription, and splicing as well as epigenetic regulation. The identification and description of the nuclear proteins is one of the requisites toward a comprehensive understanding of the biological ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201400072
更新日期:2014-10-01 00:00:00
abstract::Induced sputum is a readily accessible biological fluid whose composition may alter as a consequence of disease. To date, however, the proteins that routinely populate this biofluid are largely unknown, in part due to the technical difficulties in processing such mucin-rich samples. To provide a catalogue of sputum pr...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600011
更新日期:2006-08-01 00:00:00
abstract::Tyrosol (TYR, 2-(4-hydroxyphenyl)ethanol), one of the main phenols in olive oil and olive fruit, significantly strengthens resistance to thermal and oxidative stress in the nematode Caenorhabditis elegans and extends its lifespan. To elucidate the cellular functions regulated by TYR, we have used a proteomic procedure...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200579
更新日期:2013-10-01 00:00:00
abstract::With an emphasis on obtaining a multitude of high quality tandem mass spectrometry spectra for protein identification, instrumental parameters are described for the liquid chromatography-tandem mass spectrometry analysis of trypsin digested unfractionated urine using a hybrid quadrupole-time-of-flight (Q-TOF) mass spe...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/1615-9861(200101)1:1<108::AID-PROT108>3.0.
更新日期:2001-01-01 00:00:00
abstract::Carcinoma of the prostate (CaP) is the second leading cause of cancer-related mortality among American men. While high cure rates are associated with localized CaP, no cure exists for advanced recurrent disease. At present there are no known serologic biomarkers specific to this stage of the disease. Several groups ha...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401165
更新日期:2005-07-01 00:00:00
abstract::Autosomal dominant tubulointerstitial kidney disease associated to the MUC1 gene (ADTKD-MUC1; formerly MCKD1) belongs to a heterogeneous group of rare hereditary kidney diseases that is prototypically caused by frameshift mutations in the MUC1 repeat domain. The mutant MUC1 (insC) lacks the transmembrane domaine, exhi...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201700456
更新日期:2018-04-01 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::The PIK3CA gene encodes for the p110 alpha isoform of PI3 kinase and is one of the most frequently mutated oncogenes in human cancers. However, the mechanisms by which PIK3CA mutations activate cell signaling are not fully understood. Here we used a phosphoproteomic approach to compare differential phosphorylation pat...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201400342
更新日期:2015-01-01 00:00:00
abstract::Plant epidermal trichomes are as varied in morphology as they are in function. In the halophyte Mesembryanthemum crystallinum, specialized trichomes called epidermal bladder cells (EBC) line the surface of leaves and stems, and increase dramatically in size and volume upon plant salt-treatment. These cells have been p...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200152
更新日期:2012-09-01 00:00:00
abstract::Multiple-reaction monitoring (MRM) of peptides has been recognized as a promising technology because it is sensitive and robust. Borrowed from stable-isotope dilution (SID) methodologies in the field of small molecules, MRM is now routinely used in proteomics laboratories. While its usefulness validating candidate tar...
journal_title:Proteomics
pub_type: 评论,杂志文章
doi:10.1002/pmic.201500090
更新日期:2015-04-01 00:00:00
abstract::A brief period of ischemia followed by timely reperfusion may lead to prolonged, yet reversible, contractile dysfunction (myocardial stunning). Damage to the myocardium occurs not only during ischemia, but also during reperfusion, where a massive release of oxygen-free radicals (OFR) occurs. We have previously utilize...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600219
更新日期:2006-12-01 00:00:00
abstract::The presence of high-abundance proteins in complex protein mixtures often masks low-abundance proteins and causes loss of resolution of 2DE. Protein fractionation steps conducted prior to 2DE can enhance the detection of low-abundance proteins and improve the resolution of 2DE. Here, we report a method to prefractiona...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201100475
更新日期:2012-04-01 00:00:00
abstract::CD28 delivers a co-stimulatory signal for T cell antigen receptor induced activation of T cells through a mechanism which remains mostly elusive to date. In order to try and gain insight into CD28 function, we therefore applied state-of-the-art mass spectrometric protein identification technology to the analysis of CD...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/1615-9861(200101)1:1<70::AID-PROT70>3.0.CO
更新日期:2001-01-01 00:00:00
abstract::Prostate cancer is one of the leading cancers in men. Taking dietary supplements, such as fish oil (FO), which is rich in n-3 polyunsaturated fatty acids (PUFAs), has been employed as a strategy to lower prostate cancer risk and control disease progression. In this study, we investigated the global phosphoproteomic ch...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201600166
更新日期:2016-09-01 00:00:00
abstract::A large repertoire of immunological methods permits monitoring the interaction of antibodies with their specific antigen. However, recognition of a protein by a conformation-specific antibody represents a challenge because native conditions must be kept throughout the assay. Native immunoblotting of blue native gels c...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200900468
更新日期:2010-01-01 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::Pancreatic cancer is the most lethal of all the common malignancies. Markers for early detection of this disease are urgently needed. Here, we optimized and applied a proteome analysis of human pancreatic juice to identify biomarkers for pancreatic cancer. Pancreatic juice samples, devoid of blood or bile contaminatio...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600086
更新日期:2007-04-01 00:00:00
abstract::A proteome wide analysis was performed in Escherichia coli to identify the impact on protein N-termini of actinonin, an antibiotic specifically inhibiting peptide deformylase (PDF). A strategy and tool suite (SILProNaQ) was employed to provide large-scale quantitation of N-terminal modifications. In control conditions...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201500027
更新日期:2015-07-01 00:00:00
abstract::In-gel peptide digestion has become a widely used technique for characterizing proteins resolved by two-dimensional gel electrophoresis. Peptides generated from gel pieces are frequently contaminated with detergent and salts. Prior to matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysi...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/1615-9861(200202)2:2<145::aid-prot145>3.0.
更新日期:2002-02-01 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::The monitoring of gene expression via the technologies encompassed under the term 'proteomics' allows proteins of significance to be related to phenotypes associated with strain variability, environmental influences and the effects of genetic manipulation. The characterizations of these molecules are routinely perform...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/1615-9861(200104)1:4<461::AID-PROT461>3.0.
更新日期:2001-04-01 00:00:00
abstract::The accurate and precise absolute abundance of proteins can be determined using mass spectrometry by spiking the sample with stable isotope-labeled standards. In this study, we developed a strategy of hierarchical use of peptide-concatenated standards (PCSs) to quantify more proteins over a wider dynamic range. Multip...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201500414
更新日期:2016-05-01 00:00:00
abstract::Bottom-up proteomics is a mass spectrometric (MS)-based approach for the characterization of peptides obtained from in-solution protein digestion. MS is favored over other methods for peptide and protein analysis because of its better sensitivity and high throughput. Inorganic ions and surfactants present in the sampl...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201700011
更新日期:2017-10-01 00:00:00
abstract::Daphnia pulex is a keystone species for aquatic habitats and an ecological/evolution model organism. Although significant progress has been made on characterizing its genome, the D. pulex proteome remains largely uncharacterized partially due to abnormally high protein degradation during homogenization and emphasis on...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201700460
更新日期:2018-08-01 00:00:00
abstract::Puccinia triticina causes leaf rust, a disease that causes annual yield losses in wheat. It is an obligate parasite that invades the host leaf and forms intracellular structures called haustoria, which obtain nutrients and suppress host immunity using secreted proteins called effectors. Since effector proteins act at ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201400241
更新日期:2015-04-01 00:00:00
abstract::Plant cell walls (CWs) contain a large proportion of polysaccharides (90-95% of CW mass) and proteins (5-10%) that play major roles in CW plasticity during development and in response to environmental cues. Here, we present CW proteomics data of Arabidopsis thaliana roots. Plants were cultivated in hydroponic conditio...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201500129
更新日期:2016-02-01 00:00:00
abstract::PROTICdb is a web-based application, mainly designed to store and analyze plant proteome data obtained by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and mass spectrometry (MS). The purposes of PROTICdb are (i) to store, track, and query information related to proteomic experiments, i.e., from tissue...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401111
更新日期:2005-05-01 00:00:00
abstract::In the era of quantitative proteomics, where mass spectrometry plays a pivotal role, in particular associated with the use of data-independent acquisition, it is time to perform an overview of this growing field with special focus on one of the most promising approaches: SWATH-MS, and to present future perspectives fo...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201600278
更新日期:2017-02-01 00:00:00