EuPA Open Proteomics最新文献

{"title":"Proteomic profiling of hyperplasia/atypia and adenoma-induced by NNK in mouse lung identified multiple proteins as potential biomarkers for early detection","authors":"Arunangshu Das ,&nbsp;James D. Bortner Jr. ,&nbsp;Cesar Aliaga ,&nbsp;Timothy Cooper ,&nbsp;Anne Stanley ,&nbsp;Bruce A. Stanley ,&nbsp;Chandra P. Belani ,&nbsp;Karam El-Bayoumy","doi":"10.1016/j.euprot.2015.07.015","DOIUrl":"10.1016/j.euprot.2015.07.015","url":null,"abstract":"<div><p>We used a proteomics approach (iTRAQ) to identify differentially expressed lung proteins during early stages of the tobacco carcinogen, NNK-induced lung tumorigenesis (hyperplasia/atypia, 4–10 weeks and adenoma, 25 week) prior to the detection of adenocarcinoma in A/J mice. We identified 790 proteins at week 4 and 710 proteins at weeks 10 and 25 with &gt;95% confidence and a Local False Discovery Rate estimation less than 5%. We have demonstrated that NNK altered multiple protein (e.g., Carbonyl Reductase, Annexin A5/6, Selenbp1, Hmgb1 and Hsp90b1) expressions in early lesions which can be used as potential biomarkers for early detection of lung cancer.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Pages 23-33"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.015","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257469","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":"Improving productivity and quality in Biobanking: The need for synergy between industry, academia, and the public sector","authors":"Åsa Wheelock","doi":"10.1016/j.euprot.2015.07.005","DOIUrl":"10.1016/j.euprot.2015.07.005","url":null,"abstract":"","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"9 ","pages":"Page 77"},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257294","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 proteomic landscape of glioma stem-like cells","authors":"Cheryl F. Lichti ,&nbsp;Norelle C. Wildburger ,&nbsp;Alexander S. Shavkunov ,&nbsp;Ekaterina Mostovenko ,&nbsp;Huiling Liu ,&nbsp;Erik P. Sulman ,&nbsp;Carol L. Nilsson","doi":"10.1016/j.euprot.2015.06.008","DOIUrl":"10.1016/j.euprot.2015.06.008","url":null,"abstract":"<div><p>Glioma stem-like cells (GSCs) are hypothesized to provide a repository of cells in tumors that can self-replicate and are radio- and chemo-resistant. GSC lines, representing several glioma subtypes, have been isolated and characterized at the transcript level. We sought to characterize 35 GSC lines at the protein level using label-free quantitative proteomics. Resulting relative fold changes were used to drive unsupervised hierarchical clustering for the purpose of classifying the cell lines based on proteomic profiles. Bioinformatics analysis identified synoviolin, serine/arginine-rich splicing factor 2, symplekin, and IL-5 as molecules of interest in progression and/or treatment of glioma.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 85-93"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.06.008","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257230","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 Breast Cell Atlas: Organelle analysis of the MDA-MB-231 cell line by density-gradient fractionation using isotopic marking and label-free analysis","authors":"Marianne Sandin ,&nbsp;Linn Antberg ,&nbsp;Fredrik Levander,&nbsp;Peter James","doi":"10.1016/j.euprot.2015.06.002","DOIUrl":"10.1016/j.euprot.2015.06.002","url":null,"abstract":"<div><p>Protein translocation between organelles in the cell is an important process that regulates many cellular functions. However, organelles can rarely be isolated to purity so several methods have been developed to analyse the fractions obtained by density gradient centrifugation. We present an analysis of the distribution of proteins amongst organelles in the human breast cell line, MDA-MB-231 using two approaches: an isotopic labelling and a label-free approach.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 68-77"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.06.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257156","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":"Pathway-centric analysis of the DNA damage response to chemotherapeutic agents in two breast cell lines","authors":"Linn Antberg ,&nbsp;Paolo Cifani ,&nbsp;Fredrik Levander ,&nbsp;Peter James","doi":"10.1016/j.euprot.2015.05.002","DOIUrl":"10.1016/j.euprot.2015.05.002","url":null,"abstract":"<div><p>The response to DNA damage by alkylation and DNA topoisomerase inhibition was studied in two breast cancer cells lines. We present data from both a shotgun and a targeted, pathway-centric approach to highlight the different DNA repair pathway modulation in the cell lines and the correlation with viability and DNA damage assays. This type of focussed profiling may be of utility in rapidly defining non-responders undergoing systemic neoadjuvant therapy.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 128-136"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.05.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257562","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":"Optimization of calmodulin-affinity chromatography for brain and organelles","authors":"Katarzyna Kulej ,&nbsp;Simone Sidoli ,&nbsp;Giuseppe Palmisano ,&nbsp;Alistair V.G. Edwards ,&nbsp;Phillip J. Robinson ,&nbsp;Martin R. Larsen","doi":"10.1016/j.euprot.2015.05.004","DOIUrl":"10.1016/j.euprot.2015.05.004","url":null,"abstract":"<div><p>Calmodulin (CaM) is a Ca²⁺-binding signaling protein that binds to and activates many target proteins, known as calmodulin-binding proteins (CaM-BPs). They are involved in multiple cellular processes. Despite the diversity and importance of CaM-BPs, many remain to be identified and characterized. We performed extensive optimization of a CaM-affinity capture method, using commercial CaM-chromatographic material. We identify both the Ca²⁺-dependent and -independent CaM binding proteomes in both mouse brain and in rat brain neuronal organelles, synaptosomes, and compared cytosolic with membrane associated targets. Fractionation of peptides, derived from on-resin tryptic digestion, using hydrophilic interaction liquid chromatography (HILIC) was combined with reversed-phase liquid chromatography tandem mass spectrometry (LC-MS/MS) to improve identification of low abundance CaM-BPs in a reproducible and sensitive manner. Various detergents were tested for the most efficient membrane protein solubilization for pull-down of membrane-associated CaM-BPs. We identified 3529 putative mouse brain CaM-BPs, of which 1629 were integral membrane or membrane-associated. Among them, 170 proteins were known CaM-BPs or previously reported as potential CaM-BPs while 696 contained predicted CaM binding motifs. In synaptosomes we identified 2698 CaM-BPs and 2783 unique phosphopeptides derived from 984 of the potential synaptosomal CaM-BPs. Overall, our improved workflow provides unmatched sensitivity for the identification of the CaM binding proteome and its associated phosphoproteome and this now enables sensitive analysis of organelle-specific CaM-BPs.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 55-67"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.05.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257589","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":"Reducing protein oxidation in low-flow electrospray enables deeper investigation of proteoforms by top down proteomics","authors":"Kyunggon Kim ,&nbsp;Philip D. Compton ,&nbsp;Timothy K. Toby ,&nbsp;Paul M. Thomas ,&nbsp;John T. Wilkins ,&nbsp;R.Kannan Mutharasan ,&nbsp;Neil L. Kelleher","doi":"10.1016/j.euprot.2015.05.005","DOIUrl":"10.1016/j.euprot.2015.05.005","url":null,"abstract":"<div><p>Enabling the implementation of top down proteomic techniques within clinical workflows requires a dramatic increase in sensitivity. It has been previously demonstrated that electrospray ionization (ESI) becomes more efficient with decreasing volumetric flow rates at the emitter. Therefore, narrow inner diameter (I.D.) columns used in front-end chromatographic separations yield increased sensitivity. However, the smaller cross-sectional area of a narrow I.D. column places a larger fraction of the eluent in fluid communication with the electrode within the high voltage union that facilitates electrospray ionization (ESI), leading to increased oxidation of solution-phase proteins. Oxidation of proteins alters their chemical state of the protein, complicates data analysis, and reduces the depth of proteome coverage attained in a typical top-down proteomics experiment. Excessive protein oxidation results in poor deconvolution and exact mass calculations from MS1 spectra, interferes with peak isolation for MS/MS fragmentation, and effectively reduces sensitivity by splitting ion current. All of these factors deteriorate top down mass spectral data quality, an effect that becomes more pronounced as column diameter decreases. Artificial protein oxidation can also mislead investigations of <em>in vivo</em> protein oxidation. All of these effects are accentuated in comparison to bottom up proteomics due to the increased probability of having oxidizable residues within a particular species with increasing mass. Herein, we describe a configuration (which we term “Low Protein Oxidation (LPOx)”) for proteomics experiments created by re-arranging liquid chromatography (LC) plumbing and present its application to artificial protein oxidation and show a marked improvement in detection sensitivity. Using a standard mixture of five intact proteins, we demonstrate that the LPOx configuration reduces protein oxidation up to 90% using 50<!--> <!-->μm I.D. columns when compared to a conventional LC plumbing configuration with 50<!--> <!-->μm I.D. column. As a proof-of-concept study, at least 11 distinct proteoforms of serum Apolipoprotein A1 were detected with the LPOx configuration. This innovative LC configuration can be applied to the top down identification and characterization of proteoforms obscured by abundant artificial protein oxidation at low flowrates, all while using reduced amounts of valuable protein samples.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 40-47"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.05.005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257607","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":"pI-Control in comparative fluorescence gel electrophoresis (CoFGE) using amphoteric azo dyes","authors":"Marina Hanneken ,&nbsp;Karel Šlais ,&nbsp;Simone König","doi":"10.1016/j.euprot.2015.03.003","DOIUrl":"10.1016/j.euprot.2015.03.003","url":null,"abstract":"<div><p>Gel-to-gel variation is a major problem in two-dimensional (2D) gel electrophoresis. Vertical and horizontal comparative fluorescence gel electrophoresis (v/hCoFGE) were recently introduced to improve the reproducibility of protein spot assignment. There, in a combination of 1D- and 2D-PAGE, protein analytes were overlaid with a reference grid which allowed correcting for variation in the <em>y</em>-direction. However, control of the first dimension, p<em>I</em> (<em>x</em>-direction), was missing so far. Here, we applied amphoteric azo dyes for this purpose completing the CoFGE toolkit.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 36-39"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.03.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54256845","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":"Workflow for large-scale analysis of melanoma tissue samples","authors":"Maria E. Yakovleva ,&nbsp;Charlotte Welinder ,&nbsp;Yutaka Sugihara ,&nbsp;Krzysztof Pawłowski ,&nbsp;Melinda Rezeli ,&nbsp;Elisabet Wieslander ,&nbsp;Johan Malm ,&nbsp;György Marko-Varga","doi":"10.1016/j.euprot.2015.07.011","DOIUrl":"10.1016/j.euprot.2015.07.011","url":null,"abstract":"<div><p>The aim of the present study was to create an optimal workflow for analysing a large cohort of malignant melanoma tissue samples. Samples were lysed with urea and enzymatically digested with trypsin or trypsin/Lys C. Buffer exchange or dilution was used to reduce urea concentration prior to digestion. The tissue digests were analysed directly or following strong cation exchange (SCX) fractionation by nano LC–MS/MS. The approach which resulted in the largest number of protein IDs involved a buffer exchange step before enzymatic digestion with trypsin and chromatographic separation in 120<!--> <!-->min gradient followed by SCX–RP separation of peptides.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 78-84"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257429","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 quality control of proteomic experiments based on multiple isotopologous internal standards","authors":"Adele Bourmaud ,&nbsp;Sebastien Gallien ,&nbsp;Bruno Domon","doi":"10.1016/j.euprot.2015.07.010","DOIUrl":"10.1016/j.euprot.2015.07.010","url":null,"abstract":"<div><p>The harmonization of proteomics experiments facilitates the exchange and comparison of results. The definition of standards and metrics ensures reliable and consistent data quality. An internal quality control procedure was developed to assess the different steps of a proteomic analysis workflow and perform a system suitability test. The method relies on a straightforward protocol using a simple mixture of exogenous proteins, and the sequential addition of two sets of isotopically labeled peptides added to reference samples. This internal quality control procedure was applied to plasma samples to demonstrate its easy implementation, which makes it generic for most proteomics applications.</p></div>","PeriodicalId":38260,"journal":{"name":"EuPA Open Proteomics","volume":"8 ","pages":"Pages 16-21"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.euprot.2015.07.010","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"54257421","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}