Abstract:
:Two-dimensional electrophoresis is a widely used method for separating a large number of proteins from complex protein mixtures and for revealing differential patterns of protein expressions. In the computer-assisted proteome research, the comparison of protein separation profiles involves several heuristic steps, ranging from protein spot detection to matching of unknown spots. An important prerequisite for efficient protein spot matching is the image warping step, where the geometric relationship between the gel profiles is modeled on the basis of a given set of known corresponding spots, so-called landmarks, and the locations of unknown spots are predicted using the optimized model. Traditionally, polynomial functions together with least squares optimization has been used, even though this approach is known to be incapable of modeling all the complex distortions inherent in electrophoretic data. To satisfy the need of more flexible gel distortion correction, a hierarchical grid transformation method with stochastic optimization is presented. The method provides an adaptive multiresolution model between the gels, and good correction performance in the practical cross-validation tests suggests that automatic warping of gel images could be based on this approach. We believe that the proposed model also has significance in the ultimate comparison of corresponding protein spots since the matching process should benefit from the closeness of the true spot pairs.
journal_name
Proteomicsjournal_title
Proteomicsauthors
Salmi J,Aittokallio T,Westerholm J,Griese M,Rosengren A,Nyman TA,Lahesmaa R,Nevalainen Odoi
10.1002/1615-9861(200211)2:11<1504::AID-PROT1504>3subject
Has Abstractpub_date
2002-11-01 00:00:00pages
1504-15issue
11eissn
1615-9853issn
1615-9861journal_volume
2pub_type
杂志文章相关文献
PROTEOMICS文献大全abstract::The determination of possible biomarkers in nasal secretion of healthy subjects can have a role in early diagnosis of diseases such as rhinosinusitis. For this purpose, nasal lavage fluids (NLFs) from ten volunteers, collected before and after they had been submitted to nasal provocations, were investigated. Separatio...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401172
更新日期:2005-07-01 00:00:00
abstract::Many tumors arising from epithelial tissues produce mucins, which readily come into contact with infiltrating cells in cancer tissues. MUC2 mucins were purified from the conditioned medium of a colorectal cancer cell line, LS180 cells. It is known that in cancer patients, the number of dendritic cells (DCs) is reduced...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800039
更新日期:2008-08-01 00:00:00
abstract::Helicobacter pylori is one of the most common bacterial pathogens and causes a variety of diseases, such as peptic ulcer or gastric cancer. Despite intensive study of this human pathogen in the last decades, knowledge about its membrane proteins and, in particular, those which are putative components of the type IV se...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200401019
更新日期:2005-04-01 00:00:00
abstract::The computational simulation of complete proteomic data sets and their utility to validate detection and interpretation algorithms, to aid in the design of experiments and to assess protein and peptide false discovery rates is presented. The simulation software has been developed for emulating data originating from da...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201000576
更新日期:2011-03-01 00:00:00
abstract::Plant tissues contain large amounts of secondary compounds that significantly interfere with protein extraction and 2DE analysis. Thus, sample preparation is a crucial step prior to 2DE in plant proteomics. This tutorial highlights the guidelines that need to be followed to perform an adequate total protein extraction...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300239
更新日期:2014-03-01 00:00:00
abstract::MDM2 is a multidomain protein that functions as an E3 ubiquitin ligase, transcription repressor, mRNA-binding protein, translation factor, and molecular chaperone. The small molecule Nutlin-3 has been engineered to bind to the N-terminal hydrophobic pocket domain of MDM2. This binding of Nutlin-3 has two consequences:...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300029
更新日期:2013-08-01 00:00:00
abstract::The ubiquitin-proteasome system allows the targeted degradation of proteins and plays a critical role in the regulation of many cellular processes. Proteasome inhibition is a recent antitumor therapeutic strategy and bortezomib was the first proteasome inhibitor approved for clinical use. In this study, we used the NB...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200233
更新日期:2013-01-01 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::In 2001, the German Federal Ministry of Education and Research (BMBF) initiated the National Genome Research Network (NGFN; www.ngfn.de) as a nation-wide multidisciplinary networking platform aiming at the analysis of common human diseases and aging. Within the NGFN the Human Brain Proteome Project (HBPP; www.smp-prot...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.200700980
更新日期:2008-03-01 00:00:00
abstract::Glycan-binding proteins (GBPs) play an important role in cell adhesion, bacterial/viral infection, and cellular signaling pathways. However, little is known about the precision alteration of GBPs referred to pathological changes in hepatic stellate cells (HSCs) during liver fibrosis. Here, the carbohydrate microarrays...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201500030
更新日期:2015-10-01 00:00:00
abstract::Identification of mucin-type O-glycosylated proteins with known functions in model organisms like Drosophila could provide keys to elucidate functions of the O-glycan moiety and proteomic analyses of O-glycoproteins in higher eukaryotes remain a challenge due to structural heterogeneity and a lack of efficient tools f...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200600793
更新日期:2007-09-01 00:00:00
abstract::Ruminants make large contributions to sustainable agriculture by converting crop by-products into agricultural food. Multi-omics integrative analysis helps to uncover the underlying molecular mechanisms. The liver metabolome-transcriptome interface (LMTI) in dairy cows, including 3938 significant correlations (p < 0.0...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201800122
更新日期:2018-08-01 00:00:00
abstract::The von Hippel-Lindau (VHL) tumour suppressor gene plays a central role in development of clear cell renal cell carcinoma (RCC). Using a cell line pair generated from the VHL-defective RCC cell line UMRC2 by transfection with vector control or VHL (-/+VHL) and stable isotope labelling with amino acids in cell culture ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800756
更新日期:2009-04-01 00:00:00
abstract::Helicobacter pylori is one of the most prevalent human pathogens in the world and is the aetiological agent of gastritis, peptic ulcer disease and gastric malignancies. In addition H. pylori and other novel members of the genus are capable of successfully colonising the bile-rich niche of the upper intestine and are a...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200390040
更新日期:2003-03-01 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::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::Quantitative proteomic studies are contributing greatly to the understanding of the spermatozoon through the provision of detailed information on the proteins spermatozoa acquire and shed in the acquisition of fertility. Extracellular vesicles (EVs) are thought to aid in the delivery of proteins to spermatozoa in the ...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201900289
更新日期:2020-06-01 00:00:00
abstract::SDS interferes with both bottom-up and top-down MS analysis, requiring removal prior to detection. Filter-aided sample preparation (FASP) is favored for bottom-up proteomics (BUP) while acetone precipitation is popular for top-down proteomics (TDP). We recently demonstrated acetone precipitation in a membrane filter c...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201700025
更新日期:2018-05-01 00:00:00
abstract::Liquid Chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS) is a powerful analytical technique for the identification and mass analysis of complex protein mixtures. Here, we present a combination of methods developed for the extensive/deep proteomic analysis of purified ribosome/mRNA particles assembled i...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201400628
更新日期:2015-07-01 00:00:00
abstract::LTQ Orbitrap data analyzed with ProteinPilot can be further improved by MaxQuant raw data processing, which utilizes precursor-level high mass accuracy data for peak processing and MGF creation. In particular, ProteinPilot results from MaxQuant-processed peaklists for Orbitrap data sets resulted in improved spectral u...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201100097
更新日期:2012-06-01 00:00:00
abstract::The ascomycete Botrytis cinerea is a phytopathogenic fungus infecting and causing significant yield losses in a number of crops. Moreover, in the last few years, B. cinerea has been adopted as an important model system in molecular phytopathology. In spite of these contributions, the molecular basis of the infection c...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200800540
更新日期:2009-05-01 00:00:00
abstract::Protein arginine methylation is a PTM catalyzed by an evolutionarily conserved family of enzymes called protein arginine methyltransferases (PRMTs), with PRMT1 being the most conserved member of this enzyme family. This modification has emerged to be an important regulator of protein functions. To better understand th...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201200132
更新日期:2012-11-01 00:00:00
abstract::This review provides a brief overview of the development of data-independent acquisition (DIA) mass spectrometry-based proteomics and selected DIA data analysis tools. Various DIA acquisition schemes for proteomics are summarized first including Shotgun-CID, DIA, MSE , PAcIFIC, AIF, SWATH, MSX, SONAR, WiSIM, BoxCar, S...
journal_title:Proteomics
pub_type: 杂志文章,评审
doi:10.1002/pmic.201900276
更新日期:2020-09-01 00:00:00
abstract::The hair follicle dermal papilla is composed primarily of extracellular matrix (ECM) proteins secreted by resident fibroblasts. Dermal papilla is endowed with hair morphogenic properties, yet its composition is poorly characterized. In an attempt to understand its specificity better, we compared the protein compositio...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200402040
更新日期:2006-11-01 00:00:00
abstract::CREC proteins constitute a family of EF-hand calcium binding proteins localized to the secretory pathway. Calumenin is the only member known to be secreted. Recently, it was shown that thrombin-activated thrombocytes liberate calumenin, which also is found in atherosclerotic lesions but not in normal vasculature. To s...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.200500686
更新日期:2006-06-01 00:00:00
abstract::Several lines of evidence suggest that hnRNPs A/B (hnRNPs A1, A2/B1, and A3) play an important role in proliferation, although the functional overlap among members of hnRNPs A/B remains largely unknown. In this study, we have employed RNAi knockdown and proteomic approaches to investigate the biological functions of h...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/pmic.201300549
更新日期:2014-06-01 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::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::In proteomic research, two-dimensional electrophoresis (2-D) is an important tool for investigating differential patterns of qualitative and quantitative protein expression. The strength of the technique is due to its unrivalled power of being able to separate simultaneously thousands of proteins. The key to the compa...
journal_title:Proteomics
pub_type: 杂志文章
doi:10.1002/1615-9861(200107)1:7<856::AID-PROT856>3.0.
更新日期:2001-07-01 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