International journal of proteomics最新文献

{"title":"The application of a three-step serum proteome analysis for the discovery and identification of novel biomarkers of hepatocellular carcinoma.","authors":"Asako Kimura,&nbsp;Kazuyuki Sogawa,&nbsp;Mamoru Satoh,&nbsp;Yoshio Kodera,&nbsp;Osamu Yokosuka,&nbsp;Takeshi Tomonaga,&nbsp;Fumio Nomura","doi":"10.1155/2012/623190","DOIUrl":"https://doi.org/10.1155/2012/623190","url":null,"abstract":"<p><p>The representative tumor markers for HCC, AFP, and PIVKA-II are not satisfactory in terms of sensitivity and specificity in the early diagnosis of HCC. In search for novel markers for HCC, three-step proteome analyses were carried out in serum samples obtained from 12 patients with HCC and 10 with LC. As a first step, serum samples were subjected to antibody-based immunoaffinity column system that simultaneously removes twelve of abundant serum proteins. The concentrated flow-through was then fractionated using reversed-phase HPLC. Proteins obtained in each fraction were separated by SDS-PAGE. Serum samples obtained from patient with HCC and with LC were analyzed in parallel and their protein expression patterns were compared. A total of 83 protein bands were found to be upregulated in HCC serum. All the protein bands, the intensity of which was different between HCC and LC groups, were identified. Among them, clusterin was most significantly overexpressed (P = 0.023). The overexpression of serum clusterin was confirmed by ELISA using another validation set of HCC samples. Furthermore, serum clusterin was elevated in 40% of HCC cases in which both AFP and PIVKA-II were within their cut-off values. These results suggested that clusterin is a potential novel serum marker for HCC.</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/10.1155/2012/623190","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30888609","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":"Functional Proteomic Profiling of Phosphodiesterases Using SeraFILE Separations Platform.","authors":"Amita R Oka,&nbsp;Matthew P Kuruc,&nbsp;Ketan M Gujarathi,&nbsp;Swapan Roy","doi":"10.1155/2012/515372","DOIUrl":"https://doi.org/10.1155/2012/515372","url":null,"abstract":"<p><p>Functional proteomic profiling can help identify targets for disease diagnosis and therapy. Available methods are limited by the inability to profile many functional properties measured by enzymes kinetics. The functional proteomic profiling approach proposed here seeks to overcome such limitations. It begins with surface-based proteome separations of tissue/cell-line extracts, using SeraFILE, a proprietary protein separations platform. Enzyme kinetic properties of resulting subproteomes are then characterized, and the data integrated into proteomic profiles. As a model, SeraFILE-derived subproteomes of cyclic nucleotide-hydrolyzing phosphodiesterases (PDEs) from bovine brain homogenate (BBH) and rat brain homogenate (RBH) were characterized for cAMP hydrolysis activity in the presence (challenge condition) and absence of cGMP. Functional profiles of RBH and BBH were compiled from the enzyme activity response to the challenge condition in each of the respective subproteomes. Intersample analysis showed that comparable profiles differed in only a few data points, and that distinctive subproteomes can be generated from comparable tissue samples from different animals. These results demonstrate that the proposed methods provide a means to simplify intersample differences, and to localize proteins attributable to sample-specific responses. It can be potentially applied for disease and nondisease sample comparison in biomarker discovery and drug discovery profiling.</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/10.1155/2012/515372","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31113154","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":"High mass accuracy phosphopeptide identification using tandem mass spectra.","authors":"Rovshan G Sadygov","doi":"10.1155/2012/104681","DOIUrl":"https://doi.org/10.1155/2012/104681","url":null,"abstract":"<p><p>Phosphoproteomics is a powerful analytical platform for identification and quantification of phosphorylated peptides and assignment of phosphorylation sites. Bioinformatics tools to identify phosphorylated peptides from their tandem mass spectra and protein sequence databases are important part of phosphoproteomics. In this work, we discuss general informatics aspects of mass-spectrometry-based phosphoproteomics. Some of the specifics of phosphopeptide identifications stem from the labile nature of phosphor groups and expanded peptide search space. Allowing for modifications of Ser, Thr, and Tyr residues exponentially increases effective database size. High mass resolution and accuracy measurements of precursor mass-to-charge ratios help to restrict the search space of candidate peptide sequences. The higher-order fragmentations of neutral loss ions enhance the fragment ion mass spectra of phosphorylated peptides. We show an example of a phosphopeptide identification where accounting for fragmentation from neutral loss species improves the identification scores in a database search algorithm by 50%.</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/10.1155/2012/104681","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30798063","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":"SELDI-TOF-MS Serum Profiling Reveals Predictors of Cardiac MRI Changes in Marathon Runners.","authors":"George D Wilson,&nbsp;Timothy J Geddes,&nbsp;Barbara L Pruetz,&nbsp;Bryan J Thibodeau,&nbsp;Amy Murawka,&nbsp;James M Colar,&nbsp;Peter A McCullough,&nbsp;Justin E Trivax","doi":"10.1155/2012/679301","DOIUrl":"https://doi.org/10.1155/2012/679301","url":null,"abstract":"<p><p>Purpose. To utilize proteomics to discover proteins associated with significant cardiac magnetic resonance imaging (MRI) changes in marathon runners. Methods. Serum from 25 runners was analyzed by surface enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Proteomic profiles were compared in serum samples obtained prior to the race, at the finish line and within 7 hours after race to identify dynamic proteins correlated with cardiac MRI changes. Results. 693 protein/peptide clusters were identified using two ProteinChip surface chemistries and, of these, 116 were significantly different between the three time points. We identified 7 different patterns of protein expression change within the runners and 5 prerace protein peaks, 16 finish-line protein levels, and 15 postrace proteins which were correlated with significant postrace cardiac MRI changes. Conclusions. This study has identified baseline levels of proteins which may be predictive of risk of significant cardiac damage following a marathon race. Preliminary identification of the significant proteins suggested the involvement of cytokines and other proteins involved in stress and inflammatory response.</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/10.1155/2012/679301","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30914931","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":"Identification of human serum peptides in fourier transform ion cyclotron resonance precision profiles.","authors":"Simone Nicolardi,&nbsp;Hans Dalebout,&nbsp;Marco R Bladergroen,&nbsp;Wilma E Mesker,&nbsp;Rob A E M Tollenaar,&nbsp;André M Deelder,&nbsp;Yuri E M van der Burgt","doi":"10.1155/2012/804036","DOIUrl":"https://doi.org/10.1155/2012/804036","url":null,"abstract":"<p><p>The continuous efforts to find new prognostic or diagnostic biomarkers have stimulated the use of mass spectrometry (MS) profiles in a clinical setting. In the early days (about one decade ago), a single low-resolution mass spectrum derived from an individual's body fluid was used for comparative studies. However, a peptide profile of a complex mixture is most informative when recorded on an ultrahigh resolution instrument such as a Fourier transform ion cyclotron resonance (FTICR) mass spectrometer. In this study we show the benefits of the ultrahigh resolving power and the high mass accuracy and precision provided by an FTICR mass spectrometer equipped with a 15-tesla magnet. The ultrahigh-resolution data not only allow assignment of fragment ions with high charge states (4+, 5+) but also enhance confidence of human serum peptide identifications from tandem MS experiments. This is exemplified with collision-induced dissociation (CID) and electron transfer dissociation (ETD) data of middle-down-sized endogenous or protein-breakdown peptides that are of interest in biomarker discovery studies.</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/10.1155/2012/804036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30681229","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":"MALDI-MS-Based Profiling of Serum Proteome: Detection of Changes Related to Progression of Cancer and Response to Anticancer Treatment.","authors":"Monika Pietrowska,&nbsp;Piotr Widłak","doi":"10.1155/2012/926427","DOIUrl":"https://doi.org/10.1155/2012/926427","url":null,"abstract":"<p><p>Mass spectrometry-based analyses of the low-molecular-weight fraction of serum proteome allow identifying proteome profiles (signatures) that are potentially useful in detection and classification of cancer. Several published studies have shown that multipeptide signatures selected in numerical tests have potential values for diagnostics of different types of cancer. However due to apparent problems with standardization of methodological details, both experimental and computational, none of the proposed peptide signatures analyzed directly by MALDI/SELDI-ToF spectrometry has been approved for routine diagnostics. Noteworthy, several components of proposed cancer signatures, especially those characteristic for advanced cancer, were identified as fragments of blood proteins involved in the acute phase and inflammatory response. This indicated that among cancer biomarker candidates to be possibly identified by serum proteome profiling were rather those reflecting overall influence of a disease (and the therapy) upon the human organism, than products of cancer-specific genes. Current paper focuses on changes in serum proteome that are related to response of patient's organism to progressing malignancy and toxicity of anticancer treatment. In addition, several methodological issues that affect robustness and interlaboratory reproducibility of MS-based serum proteome profiling are discussed.</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/10.1155/2012/926427","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30840845","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":"Cathepsin D Expression in Colorectal Cancer: From Proteomic Discovery through Validation Using Western Blotting, Immunohistochemistry, and Tissue Microarrays.","authors":"Chandra Kirana,&nbsp;Hongjun Shi,&nbsp;Emma Laing,&nbsp;Kylie Hood,&nbsp;Rose Miller,&nbsp;Peter Bethwaite,&nbsp;John Keating,&nbsp;T William Jordan,&nbsp;Mark Hayes,&nbsp;Richard Stubbs","doi":"10.1155/2012/245819","DOIUrl":"https://doi.org/10.1155/2012/245819","url":null,"abstract":"<p><p>Despite recent advances in surgical techniques and therapeutic treatments, survival from colorectal cancer (CRC) remains disappointing with some 40-50% of newly diagnosed patients ultimately dying of metastatic disease. Current staging by light microscopy alone is not sufficiently predictive of prognosis and would benefit from additional support from biomarkers in order to stratify patients appropriately for adjuvant therapy. We have identified that cathepsin D expression was significantly greater in cells from invasive front (IF) area and liver metastasis (LM) than those from main tumour body (MTB). Cathepsin D expression was subsequently examined by immunohistochemistry in tissue microarrays from 119 patients with CRC. Strong expression in tumour cells at the IF did not correlate significantly with any clinico-pathological parameters examined or patient survival. However, cathepsin D expression in cells from the MTB was highly elevated in late stage CRC and showed significant correlation with subsequent distant metastasis and shorter cancer-specific survival. We also found that macrophages surrounding tumour cells stained strongly for cathepsin D but there was no significant correlation found between cathepsin D in macrophages at IF and MTB of CRC patient with the clinic-pathological parameters examined.</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/10.1155/2012/245819","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30854825","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":"Proteomics sample preparation, preservation, and fractionation.","authors":"Gary B Smejkal","doi":"10.1155/2012/701230","DOIUrl":"https://doi.org/10.1155/2012/701230","url":null,"abstract":"In eukaryotic cells, protein synthesis occurs at the rate of 6–9 amino acid residues per second. With a median length of 360 amino acids, the synthesis of an “average” protein takes about a minute to complete [1]. At this rate, the synthesis of a single molecule of the muscle protein titin, being over 34,000 residues in length, requires over two hours to complete [2]. While this seems slow as biological processes go, the cellular requirement for protein synthesis is satisfied by the huge numbers of ribosomes, which can comprise 30% of a cell's total mass [3]. Human HeLa cells, for example, can contain over nine million ribosomes [4]. Extrapolated from the finding that as many as 80% of the ribosomes can be actively synthesizing protein in metabolically active cells [5], a single cell could theoretically generate 120,000 protein molecules per second. \u0000 \u0000In its November 2012 release statistics, UniProt/trEMBL reported 28,395,832 sequence entries in its protein database [6]. At the rate of six amino acids per second, a single eukaryotic ribosome working non-stop would require over 48 years to translate the entire database. However, there is protein evidence for only 0.05% and RNA transcript evidence for only 2.21% of the total entries [6]. With fewer than 112,000 sequence entries, Homo sapiens comprises only 0.04% of the total sequence entries. It would seem that human proteomics is not in its infancy, it is embryonic. \u0000 \u0000The number of human proteins is expected to reach into the millions. Immunoglobulins alone are encoded from 70 genes for which there are 320 possible light chain combinations and 10,530 possible heavy chain combinations resulting in 3,369,600 possible quaternary structures [7]. In even the simplest of organisms, the broad concentration of protein expression frequently spanning over nine orders of magnitude compounds the complexity of the proteomic amalgam. An undeterminable number of possible post-translational modifications that produce multiple isoforms of many proteins add another layer of complexity. For instance, there are 3778 distinct genes encoding plasma proteins of which at least 51% of these genes encode more than one protein isoform [8]. Hence, neither genomics nor transcriptomics can reliably predict the protein constituents of cells, tissues, or biological fluids. \u0000 \u0000The search for biologically important proteins of low abundance is impeded by the enormous range of protein concentrations, as exemplified in human plasma where the mass of albumin is nearly ten billion times greater than that of important signaling proteins such as the interleukins [9, 10]. The diversity of proteins, ranging from very soluble proteins in biological fluids to extremely hydrophobic ones that exist either embedded in lipid membranes or as insoluble aggregates, suggests that the total protein constituency of cells may not be isolated without bias towards or against some protein subpopulations. On the other hand, the complexity of proteomes m","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/10.1155/2012/701230","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31180595","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":"Ethanol exposure alters protein expression in a mouse model of fetal alcohol spectrum disorders.","authors":"Stephen Mason,&nbsp;Bruce Anthony,&nbsp;Xianyin Lai,&nbsp;Heather N Ringham,&nbsp;Mu Wang,&nbsp;Frank A Witzmann,&nbsp;Jin-Sam You,&nbsp;Feng C Zhou","doi":"10.1155/2012/867141","DOIUrl":"https://doi.org/10.1155/2012/867141","url":null,"abstract":"<p><p>Alcohol exposure during development can result in variable growth retardation and facial dysmorphology known as fetal alcohol spectrum disorders. Although the mechanisms underlying the disorder are not fully understood, recent progress has been made that alcohol induces aberrant changes in gene expression and in the epigenome of embryos. To inform the gene and epigenetic changes in alcohol-induced teratology, we used whole-embryo culture to identify the alcohol-signature protein profile of neurulating C6 mice. Alcohol-treated and control cultures were homogenized, isoelectrically focused, and loaded for 2D gel electrophoresis. Stained gels were cross matched with analytical software. We identified 40 differentially expressed protein spots (P < 0.01), and 9 spots were selected for LC/MS-MS identification. Misregulated proteins include serotransferrin, triosephosphate isomerase and ubiquitin-conjugating enzyme E2 N. Misregulation of serotransferrin and triosephosphate isomerase was confirmed with immunologic analysis. Alteration of proteins with roles in cellular function, cell cycle, and the ubiquitin-proteasome pathway was induced by alcohol. Several misregulated proteins interact with effectors of the NF-κB and Myc transcription factor cascades. Using a whole-embryo culture, we have identified misregulated proteins known to be involved in nervous system development and function.</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/10.1155/2012/867141","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30728061","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":"Method for recovery and immunoaffinity enrichment of membrane proteins illustrated with metastatic ovarian cancer tissues.","authors":"Luke V Schneider,&nbsp;Varsha Likhte,&nbsp;William H Wright,&nbsp;Frances Chu,&nbsp;Emma Cambron,&nbsp;Anne Baldwin-Burnett,&nbsp;Jessica Krakow,&nbsp;Gary B Smejkal","doi":"10.1155/2012/838630","DOIUrl":"https://doi.org/10.1155/2012/838630","url":null,"abstract":"<p><p>Integral membrane proteins play key biological roles in cell signaling, transport, and pathogen invasion. However, quantitative clinical assays for this critical class of proteins remain elusive and are generally limited to serum-soluble extracellular fragments. Furthermore, classic proteomic approaches to membrane protein analysis typically involve proteolytic digestion of the soluble pieces, resulting in separation of intra- and extracellular segments and significant informational loss. In this paper, we describe the development of a new method for the quantitative extraction of intact integral membrane proteins (including GPCRs) from solid metastatic ovarian tumors using pressure cycling technology in combination with a new (ProteoSolve-TD) buffer system. This new extraction buffer is compatible with immunoaffinity methods (e.g., ELISA and immunoaffinity chromatography), as well as conventional proteomic techniques (e.g., 2D gels, western blots). We demonstrate near quantitative recovery of membrane proteins EDG2, EDG4, FASLG, KDR, and LAMP-3 by western blots. We have also adapted commercial ELISAs for serum-soluble membrane protein fragments (e.g., sVEGFR2) to measure the tissue titers of their transmembrane progenitors. Finally, we demonstrate the compatibility of the new buffers with immunoaffinity enrichment/mass spectrometric characterization of tissue proteins.</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/10.1155/2012/838630","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30856279","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}