International journal of proteomics最新文献

{"title":"Human myocardial protein pattern reveals cardiac diseases.","authors":"Jonas Bergquist,&nbsp;Gökhan Baykut,&nbsp;Maria Bergquist,&nbsp;Matthias Witt,&nbsp;Franz-Josef Mayer,&nbsp;Doan Baykut","doi":"10.1155/2012/342659","DOIUrl":"https://doi.org/10.1155/2012/342659","url":null,"abstract":"<p><p>Proteomic profiles of myocardial tissue in two different etiologies of heart failure were investigated using high performance liquid chromatography (HPLC)/Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS). Right atrial appendages from 10 patients with hemodynamically significant isolated aortic valve disease and from 10 patients with isolated symptomatic coronary heart disease were collected during elective cardiac surgery. As presented in an earlier study by our group (Baykut et al., 2006), both disease forms showed clearly different pattern distribution characteristics. Interesting enough, the classification patterns could be used for correctly sorting unknown test samples in their correct categories. However, in order to fully exploit and also validate these findings there is a definite need for unambiguous identification of the differences between different etiologies at molecular level. In this study, samples representative for the aortic valve disease and coronary heart disease were prepared, tryptically digested, and analyzed using an FT-ICR MS that allowed collision-induced dissociation (CID) of selected classifier masses. By using the fragment spectra, proteins were identified by database searches. For comparison and further validation, classifier masses were also fragmented and analyzed using HPLC-/Matrix-assisted laser desorption ionization (MALDI) time-of-flight/time-of-flight (TOF/TOF) mass spectrometry. Desmin and lumican precursor were examples of proteins found in aortic samples at higher abundances than in coronary samples. Similarly, adenylate kinase isoenzyme was found in coronary samples at a higher abundance. The described methodology could also be feasible in search for specific biomarkers in plasma or serum for diagnostic purposes.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/342659","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30863784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical proteomics.","authors":"Akos Végvári,&nbsp;Tadashi Kondo,&nbsp;John G Marshall","doi":"10.1155/2012/641491","DOIUrl":"https://doi.org/10.1155/2012/641491","url":null,"abstract":"In a rapidly developing technological environment, including advances of mass spectrometric platforms, proteomic applications gain ever-increasing attentions in particularly linked to diseases, offering new means to improve the state-of-the-art in diagnosis and therapy [1]. However, clinical proteomics should not be considered as a collection of studies dealing with analyses of clinical samples but rather studies that can raise clinically relevant questions. As such, clinical proteomics systematically employs proteomic technologies, laboratory medicine, bioinformatics in order to identify protein patterns of diseases comprehensively that can lead to improved patient care and public health for the benefit of better assessment of prevention of disease, detection and diagnosis of disease, selection of personalized therapy, and monitoring of treatment response. In this Special Issue, we present a small set of research and review articles contributing to the field of clinical proteomics. Today, biomarker discovery is certainly one of the most important and widely investigated areas. Although, current routine analyses in clinical chemistry include more than 200 proteins being analyzed in blood samples and an addition number of protein markers that are used for flow cytometry and antigens, none of these biomarkers have been originating from proteomics [2]. Furthermore, quantification of proteins with clinical importance is largely performed by immunoreaction-based assays (e.g., ELISA), where the available methodologies are numerous. However, modern mass spectrometry developments have already brought sufficient power, which are complementary to or even competitors of immunoreaction-based technologies in biomarker research [3]. The essential advantage of the proteomic approach is the potential to identify and quantify multiple biomarkers simultaneously in the large parts of the human proteome, providing an overall view of differential expression of proteins in blood or tissue. Ultimately, this may lead to the distinction of disease phenotypes, which has a growing importance in cancer research, where the personalized treatment of patients offer more sufficient targeted therapy, and thus can ease the burden of healthcare. Tissue samples, well characterized by pathologist, are particularly useful subjects for such comparative proteomic analyses, which may reveal new insights to the heterogeneity of diseases like cancer. Our research experiences indicate that deep proteomic analyses of these clinically valuable samples require thorough preparation procedures, which are currently a major focus of developments. Novel and effective preparation methods in combination with archived biobanking material, such as formalin-fixed and paraffinembedded tissues, will be beneficial for future improvements [4]. Lastly, we would like to express our appreciation to the authors of this Special Issue for their contributions and the staff of International Journal of Proteomics f","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/641491","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30868918","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Seven-signal proteomic signature for detection of operable pancreatic ductal adenocarcinoma and their discrimination from autoimmune pancreatitis.","authors":"Kiyoshi Yanagisawa,&nbsp;Shuta Tomida,&nbsp;Keitaro Matsuo,&nbsp;Chinatsu Arima,&nbsp;Miyoko Kusumegi,&nbsp;Yukihiro Yokoyama,&nbsp;Shigeru B H Ko,&nbsp;Nobumasa Mizuno,&nbsp;Takeo Kawahara,&nbsp;Yoko Kuroyanagi,&nbsp;Toshiyuki Takeuchi,&nbsp;Hidemi Goto,&nbsp;Kenji Yamao,&nbsp;Masato Nagino,&nbsp;Kazuo Tajima,&nbsp;Takashi Takahashi","doi":"10.1155/2012/510397","DOIUrl":"https://doi.org/10.1155/2012/510397","url":null,"abstract":"<p><p>There is urgent need for biomarkers that provide early detection of pancreatic ductal adenocarcinoma (PDAC) as well as discrimination of autoimmune pancreatitis, as current clinical approaches are not suitably accurate for precise diagnosis. We used mass spectrometry to analyze protein profiles of more than 300 plasma specimens obtained from PDAC, noncancerous pancreatic diseases including autoimmune pancreatitis patients and healthy subjects. We obtained 1063 proteomic signals from 160 plasma samples in the training cohort. A proteomic signature consisting of 7 mass spectrometry signals was used for construction of a proteomic model for detection of PDAC patients. Using the test cohort, we confirmed that this proteomic model had discrimination power equal to that observed with the training cohort. The overall sensitivity and specificity for detection of cancer patients were 82.6% and 90.9%, respectively. Notably, 62.5% of the stage I and II cases were detected by our proteomic model. We also found that 100% of autoimmune pancreatitis patients were correctly assigned as noncancerous individuals. In the present paper, we developed a proteomic model that was shown able to detect early-stage PDAC patients. In addition, our model appeared capable of discriminating patients with autoimmune pancreatitis from those with PDAC.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/510397","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30674635","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Comprehensive Subcellular Proteomic Survey of Salmonella Grown under Phagosome-Mimicking versus Standard Laboratory Conditions.","authors":"Roslyn N Brown,&nbsp;James A Sanford,&nbsp;Jea H Park,&nbsp;Brooke L Deatherage,&nbsp;Boyd L Champion,&nbsp;Richard D Smith,&nbsp;Fred Heffron,&nbsp;Joshua N Adkins","doi":"10.1155/2012/123076","DOIUrl":"https://doi.org/10.1155/2012/123076","url":null,"abstract":"<p><p>Towards developing a systems-level pathobiological understanding of Salmonella enterica, we performed a subcellular proteomic analysis of this pathogen grown under standard laboratory and phagosome-mimicking conditions in vitro. Analysis of proteins from cytoplasmic, inner membrane, periplasmic, and outer membrane fractions yielded coverage of 25% of the theoretical proteome. Confident subcellular location could be assigned to over 1000 proteins, with good agreement between experimentally observed location and predicted/known protein properties. Comparison of protein location under the different environmental conditions provided insight into dynamic protein localization and possible moonlighting (multiple function) activities. Notable examples of dynamic localization were the response regulators of two-component regulatory systems (e.g., ArcB and PhoQ). The DNA-binding protein Dps that is generally regarded as cytoplasmic was significantly enriched in the outer membrane for all growth conditions examined, suggestive of moonlighting activities. These observations imply the existence of unknown transport mechanisms and novel functions for a subset of Salmonella proteins. Overall, this work provides a catalog of experimentally verified subcellular protein locations for Salmonella and a framework for further investigations using computational modeling.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/123076","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30840377","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rapid Screening of the Epidermal Growth Factor Receptor Phosphosignaling Pathway via Microplate-Based Dot Blot Assays.","authors":"Amedeo Cappione,&nbsp;Janet Smith,&nbsp;Masaharu Mabuchi,&nbsp;Timothy Nadler","doi":"10.1155/2012/473843","DOIUrl":"https://doi.org/10.1155/2012/473843","url":null,"abstract":"<p><p>Expression profiling on a large scale, as is the case in drug discovery, is often accomplished through use of sophisticated solid-phase protein microarrays or multiplex bead technologies. While offering both high-throughput and high-content analysis, these platforms are often too cost prohibitive or technically challenging for many research settings. Capitalizing on the favorable attributes of the standard ELISA and slot blotting techniques, we developed a modified dot blot assay that provides a simple cost-effective alternative for semiquantitative expression analysis of multiple proteins across multiple samples. Similar in protocol to an ELISA, but based in a membrane bound 96-well microplate, the assay takes advantage of vacuum filtration to expedite the tedious process of washing in between binding steps. We report on the optimization of the assay and demonstrate its use in profiling temporal changes in phosphorylation events in the well-characterized EGF-induced signaling cascade of A431 cells.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/473843","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30868917","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Proteomic and bioinformatics analyses of mouse liver microsomes.","authors":"Fang Peng,&nbsp;Xianquan Zhan,&nbsp;Mao-Yu Li,&nbsp;Fan Fang,&nbsp;Guoqing Li,&nbsp;Cui Li,&nbsp;Peng-Fei Zhang,&nbsp;Zhuchu Chen","doi":"10.1155/2012/832569","DOIUrl":"https://doi.org/10.1155/2012/832569","url":null,"abstract":"<p><p>Microsomes are derived mostly from endoplasmic reticulum and are an ideal target to investigate compound metabolism, membrane-bound enzyme functions, lipid-protein interactions, and drug-drug interactions. To better understand the molecular mechanisms of the liver and its diseases, mouse liver microsomes were isolated and enriched with differential centrifugation and sucrose gradient centrifugation, and microsome membrane proteins were further extracted from isolated microsomal fractions by the carbonate method. The enriched microsome proteins were arrayed with two-dimensional gel electrophoresis (2DE) and carbonate-extracted microsome membrane proteins with one-dimensional gel electrophoresis (1DE). A total of 183 2DE-arrayed proteins and 99 1DE-separated proteins were identified with tandem mass spectrometry. A total of 259 nonredundant microsomal proteins were obtained and represent the proteomic profile of mouse liver microsomes, including 62 definite microsome membrane proteins. The comprehensive bioinformatics analyses revealed the functional categories of those microsome proteins and provided clues into biological functions of the liver. The systematic analyses of the proteomic profile of mouse liver microsomes not only reveal essential, valuable information about the biological function of the liver, but they also provide important reference data to analyze liver disease-related microsome proteins for biomarker discovery and mechanism clarification of liver disease.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/832569","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30573186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of the phosphoproteome in human bronchoalveolar lavage fluid.","authors":"Francesco Giorgianni,&nbsp;Valentina Mileo,&nbsp;Dominic M Desiderio,&nbsp;Silvia Catinella,&nbsp;Sarka Beranova-Giorgianni","doi":"10.1155/2012/460261","DOIUrl":"https://doi.org/10.1155/2012/460261","url":null,"abstract":"<p><p>Global-scale examination of protein phosphorylation in human biological fluids by phosphoproteomics approaches is an emerging area of research with potential for significant contributions towards discovery of novel biomarkers. In this pilot work, we analyzed the phosphoproteome in human bronchoalveolar lavage fluid (BAL) from nondiseased subjects. The main objectives were to assess the feasibility to probe phosphorylated proteins in human BAL and to obtain the initial catalog of BAL phosphoproteins, including protein identities and exact description of their phosphorylation sites. We used a gel-free bioanalytical workflow that included whole-proteome digestion of depleted BAL proteins, enrichment of phosphopeptides by immobilized metal ion affinity chromatography (IMAC), LC-MS/MS analyses with a linear ion trap mass spectrometer, and searches of a protein sequence database to generate a panel of BAL phosphoproteins and their sites of phosphorylation. Based on sequence-diagnostic MS/MS fragmentation patterns, we identified a collection of 36 phosphopeptides that contained 26 different phosphorylation sites. These phosphopeptides mapped to 21 phosphoproteins including, for example, vimentin, plastin-2, ferritin heavy chain, kininogen-1, and others. The characterized phosphoproteins have diverse characteristics in terms of cellular origin and biological function. To the best of our knowledge, results of this study represent the first description of the human BAL phosphoproteome.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/460261","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30921949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An economical high-throughput protocol for multidimensional fractionation of proteins.","authors":"David John Tooth,&nbsp;Varun Gopala Krishna,&nbsp;Robert Layfield","doi":"10.1155/2012/735132","DOIUrl":"https://doi.org/10.1155/2012/735132","url":null,"abstract":"<p><p>A sequential protocol of multidimensional fractionation was optimised to enable the comparative profiling of fractions of proteomes from cultured human cells. Differential detergent fractionation was employed as a first step to obtain fractions enriched for cytosolic, membrane/organelle, nuclear, and cytoskeletal proteins. Following buffer exchange using gel-permeation chromatography, cytosolic proteins were further fractionated by 2-dimensional chromatography employing anion-exchange followed by reversed-phase steps. Chromatographic fractions were shown to be readily compatible with 1- and 2-dimensional gel electrophoresis or with direct analysis by mass spectrometry using linear-MALDI-TOF-MS. Precision of extraction was confirmed by reproducible SDS-PAGE profiles, MALDI-TOF-MS spectra, and quantitation of trypsinolytic peptides using LC-MS/MS (MRM) analyses. Solid phases were immobilised in disposable cartridges and mobile-phase flow was achieved using a combination of centrifugation and vacuum pumping. These approaches yielded parallel sample handling which was limited only by the capacities of the employed devices and which enabled both high-throughput and experimentally precise procedures, as demonstrated by the processing of experimental replicates. Protocols were employed at 10 mg scale of extracted cell protein, but these approaches would be directly applicable to both smaller and larger quantities merely by adjusting the employed solid- and mobile-phase volumes. Additional potential applications of the fractionation protocol are briefly described.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/735132","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30930825","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Miniaturized Ligand Binding Assay for EGFR.","authors":"Jochen M Schwenk, Oliver Poetz, Robert Zeillinger, Thomas O Joos","doi":"10.1155/2012/247059","DOIUrl":"10.1155/2012/247059","url":null,"abstract":"<p><p>In order to study receptor abundance and its function in solutions or in homogenates from clinical specimen, methods such as sandwich or radioimmunoassays are most commonly employed. For the determination of epidermal growth factor receptor (EGFR), we describe the development of a miniaturized bead-based ligand binding assay using its ligand EGF as immobilized capture reagent. This assay was used to analyze lysates from cell lines, and the ligand-bound EGFR was detected using an EGFR-specific antibody combined with a fluorescence-based reporter system. In a proof-of concept study with lysates from breast biopsies, the assay allowed to classify breast cancer samples in accordance to clinically the relevant EGFR cut-off level. The study suggests that such a ligand binding receptor assay could become an integral part of protein profiling procedures to provide additional information about receptor functionality in addition to its abundance.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3332193/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30611963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cancer Phenotype Diagnosis and Drug Efficacy within Japanese Health Care.","authors":"Toshihide Nishimura,&nbsp;Harubumi Kato,&nbsp;Norihiko Ikeda,&nbsp;Makoto Kihara,&nbsp;Masaharu Nomura,&nbsp;Yasufumi Kato,&nbsp;György Marko-Varga","doi":"10.1155/2012/921901","DOIUrl":"https://doi.org/10.1155/2012/921901","url":null,"abstract":"<p><p>An overview on targeted personalized medicine is given describing the developments in Japan of lung cancer patients. These new targeted therapies with novel personalized medicine drugs require new implementations, in order to follow and monitor drug efficacy and outcome. Examples from IRESSA (Gefitinib) and TARCEVA (Erlotinib) treatments used in medication of lung cancer patients are presented. Lung cancer is one of the most common causes of cancer mortality in the world. The importance of both the quantification of disease progression, where diagnostic-related biomarkers are being implemented, in addition to the actual measurement of disease-specific mechanisms relating to pathway signalling activation of disease-progressive protein targets is summarised. An outline is also presented, describing changes and adaptations in Japan, meeting the rising costs and challenges. Today, urgent implementation of programs to address these needs has led to a rebuilding of the entire approach of medical evaluation and clinical care.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2012/921901","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30680109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}