International journal of proteomics最新文献

{"title":"A survey of computational intelligence techniques in protein function prediction.","authors":"Arvind Kumar Tiwari, Rajeev Srivastava","doi":"10.1155/2014/845479","DOIUrl":"10.1155/2014/845479","url":null,"abstract":"<p><p>During the past, there was a massive growth of knowledge of unknown proteins with the advancement of high throughput microarray technologies. Protein function prediction is the most challenging problem in bioinformatics. In the past, the homology based approaches were used to predict the protein function, but they failed when a new protein was different from the previous one. Therefore, to alleviate the problems associated with homology based traditional approaches, numerous computational intelligence techniques have been proposed in the recent past. This paper presents a state-of-the-art comprehensive review of various computational intelligence techniques for protein function predictions using sequence, structure, protein-protein interaction network, and gene expression data used in wide areas of applications such as prediction of DNA and RNA binding sites, subcellular localization, enzyme functions, signal peptides, catalytic residues, nuclear/G-protein coupled receptors, membrane proteins, and pathway analysis from gene expression datasets. This paper also summarizes the result obtained by many researchers to solve these problems by using computational intelligence techniques with appropriate datasets to improve the prediction performance. The summary shows that ensemble classifiers and integration of multiple heterogeneous data are useful for protein function prediction. </p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/845479","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32963654","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":"Dimerization of peptides by calcium ions: investigation of a calcium-binding motif.","authors":"Azadeh Jamalian,&nbsp;Evert-Jan Sneekes,&nbsp;Lennard J M Dekker,&nbsp;Mario Ursem,&nbsp;Theo M Luider,&nbsp;Peter C Burgers","doi":"10.1155/2014/153712","DOIUrl":"https://doi.org/10.1155/2014/153712","url":null,"abstract":"<p><p>We investigated calcium-binding motifs of peptides and their recognition of active functionalities for coordination. This investigation generates the fundamentals to design carrier material for calcium-bound peptide-peptide interactions. Interactions of different peptides with active calcium domains were investigated. Evaluation of selectivity was performed by electrospray ionization mass spectrometry by infusing solutions containing two different peptides (P1 and P2) in the presence of calcium ions. In addition to signals for monomer species, intense dimer signals are observed for the heterodimer ions (P1 ⋯ Ca(2+) ⋯ P2) (⋯ represents the noncovalent binding of calcium with the peptide) in the positive ion mode and for ions ([P1-2H](2-) ⋯ Ca(2+) ⋯ [P2-2H](2-)) in the negative ion mode. Monitoring of the dissociation from these mass selected dimer ions via the kinetic method provides information on the calcium affinity order of different peptide sequences. </p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/153712","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32728779","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":"Characterisation of the Proteome of Leptospira interrogans Serovar Canicola as a Resource for the Identification of Common Serovar Immunogenic Proteins.","authors":"P C Humphryes,&nbsp;M E Weeks,&nbsp;N G Coldham","doi":"10.1155/2014/572901","DOIUrl":"https://doi.org/10.1155/2014/572901","url":null,"abstract":"<p><p>Over 230 serovars of Leptospira interrogans have been identified; however few have been completely characterised. The aim of this study was to characterise the proteome of serovar Canicola and to compare this against the serovars of Copenhageni and Pomona. 2D-LC/MS analysis identified 1653 Leptospira proteins in serovar Canicola; 60 of these proteins were common to Copenhageni and Pomona, 16 of which are known to be immunogenic. This study provides the first reported proteome for serovar Canicola and suggests that proteomic comparison of different serovars could be used as a tool for identification of novel target molecules for vaccine development. </p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/572901","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32473764","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":"Prediction of spontaneous regression of cervical intraepithelial neoplasia lesions grades 2 and 3 by proteomic analysis.","authors":"Kai-Erik Uleberg,&nbsp;Irene Tveiterås Ovestad,&nbsp;Ane Cecilie Munk,&nbsp;Cato Brede,&nbsp;Bianca van Diermen,&nbsp;Einar Gudlaugsson,&nbsp;Emiel A M Janssen,&nbsp;Anne Hjelle,&nbsp;Jan P A Baak","doi":"10.1155/2014/129064","DOIUrl":"https://doi.org/10.1155/2014/129064","url":null,"abstract":"<p><p>Regression of cervical intraepithelial neoplasia (CIN) 2-3 to CIN 1 or less is associated with immune response as demonstrated by immunohistochemistry in formaldehyde-fixed paraffin-embedded (FFPE) biopsies. Proteomic analysis of water-soluble proteins in supernatants of biopsy samples with LC-MS (LTQ-Orbitrap) was used to identify proteins predictive of CIN2-3 lesions regression. CIN2-3 in the biopsies and persistence (CIN2-3) or regression (≤CIN1) in follow-up cone biopsies was validated histologically by two experienced pathologists. In a learning set of 20 CIN2-3 (10 regressions and 10 persistence cases), supernatants were depleted of seven high abundance proteins prior to unidimensional LC-MS/MS protein analysis. Mean protein concentration was 0.81 mg/mL (range: 0.55-1.14). Multivariate statistical methods were used to identify proteins that were able to discriminate between regressive and persistent CIN2-3. The findings were validated in an independent test set of 20 CIN2-3 (10 regressions and 10 persistence cases). Multistep identification criteria identified 165 proteins. In the learning set, zinc finger protein 441 and phospholipase D6 independently discriminated between regressive and persistent CIN2-3 lesions and correctly classified all 20 patients. Nine regression and all persistence cases were correctly classified in the validation set. Zinc finger protein 441 and phospholipase D6 in supernatant samples detected by LTQ-Orbitrap can predict regression of CIN2-3. </p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/129064","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32501674","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":"Comparison of Heavy Labeled (SIL) Peptide versus SILAC Protein Internal Standards for LC-MS/MS Quantification of Hepatic Drug Transporters.","authors":"Bhagwat Prasad,&nbsp;Jashvant D Unadkat","doi":"10.1155/2014/451510","DOIUrl":"https://doi.org/10.1155/2014/451510","url":null,"abstract":"<p><p>We studied the precision of quantification of organic anion-transporting polypeptide 1B1 (OATP1B1), OATP1B3, OATP2B1, and P-glycoprotein (P-gp) in human livers by surrogate peptide based LC-MS/MS approach using two different internal standards: stable isotope labeled peptide (SIL) versus stable isotope labeled protein (SILAC). The SIL peptides were procured commercially and the SILAC proteins were generated in-house by labeling arginine and/or lysine residues in cells expressing these transporters. Liver tissue (n = 20) was homogenized and the membrane fraction was isolated. The membranes were trypsin digested and the peptides were analyzed using LC-MS/MS under optimized conditions. The precision in the quantification of proteins in three independently trypsin digested samples from each liver was calculated as the standard deviation of the log transformed protein concentration. The precision of the SIL internal standard method was either slightly (P < 0.05, paired t-test) better than that of the SILAC method (OATP1B1, OATP1B3, and P-gp) or not different (OATP2B1). Trypsin digestion, as measured by the response of the labeled peptide derived from the SILAC protein, was consistent across liver samples. These results indicate that when maximum trypsin digestion is ensured, the SIL internal standard method can be used with confidence for quantification of drug transporters. </p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/451510","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32251508","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":"The effect of alendronate on proteome of hepatocellular carcinoma cell lines.","authors":"Amber Ilyas,&nbsp;Zehra Hashim,&nbsp;Nadia Naeem,&nbsp;Kanwal Haneef,&nbsp;Shamshad Zarina","doi":"10.1155/2014/532953","DOIUrl":"https://doi.org/10.1155/2014/532953","url":null,"abstract":"<p><p>Cancer is a life threatening disorder effecting 11 million people worldwide annually. Among various types of cancers, Hepatocellular carcinoma (HCC) has a higher rate of mortality and is the fifth leading cause of cancer related deaths around the world. Many chemotherapeutic drugs have been used for the treatment of HCC with many side effects. These drugs are inhibitors of different cell regulatory pathways. Mevalonate (MVA) pathway is an important cellular cascade vital for cell growth. A variety of inhibitors of MVA pathway have been reported for their anticancerous activity. Bisphosphonates (BPs) are members of a family involved in the treatment of skeletal complications. In recent years, their anticancer potential has been highlighted. Current study focuses on exploring the effects of alendronate (ALN), a nitrogen containing BP, on hepatocellular carcinoma cell line using genomic and proteomics approach. Our results identified ten differentially expressed proteins, of which five were up regulated and five were down regulated in ALN treated cells. Furthermore, we also performed gene expression analysis in treated and control cell lines. The study may help in understanding the molecular mechanism involved in antitumor activity of ALN, identification of possible novel drug targets, and designing new therapeutic strategies for HCC. </p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/532953","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32197027","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 colorimetric method for monitoring tryptic digestion prior to shotgun proteomics.","authors":"Richard I Somiari,&nbsp;Kutralanathan Renganathan,&nbsp;Stephen Russell,&nbsp;Steven Wolfe,&nbsp;Florentina Mayko,&nbsp;Stella B Somiari","doi":"10.1155/2014/125482","DOIUrl":"https://doi.org/10.1155/2014/125482","url":null,"abstract":"<p><p>Tryptic digestion is an important preanalytical step in shotgun proteomics because inadequate or excessive digestion can result in a failed or incomplete experiment. Unfortunately, this step is not routinely monitored before mass spectrometry because methods available for protein digestion monitoring either are time/sample consuming or require expensive equipment. To determine if a colorimetric method (ProDM Kit) can be used to identify the extent of tryptic digestion that yields the best proteomics outcome, plasma and serum digested for 8 h and 24 h were screened with ProDM, Bioanalyzer, and LC/MS/MS, and the effect of digestion on the number of proteins identified and sequence coverage was compared. About 6% and 16% less proteins were identified when >50% of proteins were digested in plasma and serum, respectively, compared to when ~46% of proteins were digested. Average sequence coverage for albumin, haptoglobin, and serotransferrin after 2 h, 8 h, and 24 h digestion was 52%, 45%, and 45% for serum and 54%, 47%, and 42% for plasma, respectively. This paper reiterates the importance of optimizing the tryptic digestion step and demonstrates the extent to which ProDM can be used to monitor and standardize protein digestion to achieve better proteomics outcomes. </p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/125482","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32216062","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":"Combined phosphoproteomics and bioinformatics strategy in deciphering drug resistant related pathways in triple negative breast cancer.","authors":"Xinyu Deng,&nbsp;Morris Kohanfars,&nbsp;Huan Ming Hsu,&nbsp;Puneet Souda,&nbsp;Joe Capri,&nbsp;Julian P Whitelegge,&nbsp;Helena R Chang","doi":"10.1155/2014/390781","DOIUrl":"https://doi.org/10.1155/2014/390781","url":null,"abstract":"<p><p>Because of the absence of a clear therapeutic target for triple negative breast cancer (TNBC), conventional chemotherapy is the only available systemic treatment option for these patients. Despite chemotherapy treatment, TNBC patients still have worse prognosis when compared with other breast cancer patients. The study is to investigate unique phosphorylated proteins expressed in chemoresistant TNBC cell lines. In the current study, twelve TNBC cell lines were subjected to drug sensitivity assays against chemotherapy drugs docetaxel, doxorubicin, gemcitabine, and cisplatin. Based on their half maximal inhibitory concentrations, four resistant and two sensitive cell lines were selected for further analysis. The phosphopeptides from these cells were enriched with TiO2 beads and fractionated using strong cation exchange. 1,645 phosphoprotein groups and 9,585 unique phosphopeptides were identified by a high throughput LC-MS/MS system LTQ-Orbitrap. The phosphopeptides were further filtered with Ascore system and 1,340 phosphoprotein groups, 2,760 unique phosphopeptides, and 4,549 unique phosphosites were identified. Our study suggested that differentially phosphorylated Cdk5, PML, AP-1, and HSF-1 might work together to promote vimentin induced epithelial to mesenchymal transition (EMT) in the drug resistant cells. EGFR and HGF were also shown to be involved in this process. </p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2014/390781","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32882129","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 Internal Standard-Assisted Synthesis and Degradation Proteomic Approach Reveals the Potential Linkage between VPS4B Depletion and Activation of Fatty Acid β-Oxidation in Breast Cancer Cells.","authors":"Zhongping Liao, Stefani N Thomas, Yunhu Wan, H Helen Lin, David K Ann, Austin J Yang","doi":"10.1155/2013/291415","DOIUrl":"10.1155/2013/291415","url":null,"abstract":"<p><p>The endosomal/lysosomal system, in particular the endosomal sorting complexes required for transport (ESCRTs), plays an essential role in regulating the trafficking and destination of endocytosed receptors and their associated signaling molecules. Recently, we have shown that dysfunction and down-regulation of vacuolar protein sorting 4B (VPS4B), an ESCRT-III associated protein, under hypoxic conditions can lead to the abnormal accumulation of epidermal growth factor receptor (EGFR) and aberrant EGFR signaling in breast cancer. However, the pathophysiological consequences of VPS4B dysfunction remain largely elusive. In this study, we used an internal standard-assisted synthesis and degradation mass spectrometry (iSDMS) method, which permits the direct measurement of protein synthesis, degradation and protein dynamic expression, to address the effects of VPS4B dysfunction in altering EGF-mediated protein expression. Our initial results indicate that VPS4B down-regulation decreases the expression of many proteins involved in glycolytic pathways, while increased the expression of proteins with roles in mitochondrial fatty acid β-oxidation were up-regulated in VPS4B-depleted cells. This observation is also consistent with our previous finding that hypoxia can induce VPS4B down-regulated, suggesting that the adoption of fatty acid β-oxidation could potentially serve as an alternative energy source and survival mechanism for breast cancer cells in response to hypoxia-mediated VPS4B dysfunction.</p>","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3575666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31256812","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":"Advances in quantitative mass spectrometry.","authors":"Mu Wang,&nbsp;Bomie Han,&nbsp;Valerie Wasinger","doi":"10.1155/2013/621029","DOIUrl":"https://doi.org/10.1155/2013/621029","url":null,"abstract":"Mass spectrometry (MS) has played an ever-increasing role in the basic sciences since the invention of ESI, trap, and MALDI techniques. MS has been applied extensively in genomics, proteomics, transcriptomics, and metabolomics for biomolecular identification, quantification, and characterization, making it a powerful tool for the analysis of biological processes and biomarker development. In particular, the application of quantitative mass spectrometry offers new opportunity and great potential to develop innovative diagnostic and prognostic tests, to identify novel therapeutic targets, to allow the design of individualized patient treatment, and eventually to extend healthy life and reduce the burdens of illness and disability. \u0000 \u0000In recent years, our capabilities in the “omics” field have been profoundly enhanced due to the advances in both hardware and software. The performance capabilities, easy operation, and robustness of MS over other techniques have made it an ideal platform for quantitative proteomics. This platform offers an analytical tool for faster, higher throughput, and wider dynamic range protein analysis and can be applied in both stable-isotope labeled or label-free manner for relative and absolute quantitation of proteins and peptides in vastly complex samples. \u0000 \u0000The advancement in quantitative mass spectrometry is reflected by the wide range of topics covered in this special issue. \u0000 \u0000H. V. Trinh et al. compare quantitative results using labeled (iTRAQ) and label-free (ion count) approaches to study the proteomes of noninfected and human adenovirus infected cells. In this study, multiple informatics quantitation tools were evaluated. \u0000 \u0000V. Wasinger et al. provide comprehensive and critical overview of quantitative techniques used in biomarker research from the low-cost discovery-driven to hypothesis-driven quantitation using synthetic standards with complimentary analysis of trends by alternative techniques. A comparative overview with associated informatics links provides an excellent snapshot of proteomic quantitative techniques. \u0000 \u0000Z. Liao et al. present novel use of SILAC method to generate internal standard peptides for the kinetic study of protein synthesis and degradation to reveal potential linkage between vacuolar protein sorting 4B (VPS4B) and fatty acid β-oxidation pathway in breast cancer cells. \u0000 \u0000O. Anania et al. illustrate a novel peptide-based SILAC method that, in combination with quantitative mass spectrometry, can be utilized to characterize and quantify protein posttranslational modifications, even those with novel modifications that may not be detected using conventional proteomic workflows or informatics algorithms. \u0000 \u0000X. Lai et al. present common issues associated with the label-free protein quantification approach including qualification of the peptides, chromatographic peak alignment, peak normalization, and an overview of the method and examples of their use to overcome some of the technical challeng","PeriodicalId":73474,"journal":{"name":"International journal of proteomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1155/2013/621029","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31482360","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}