International journal of proteomics最新文献_第5页

Serum biomarkers identification by mass spectrometry in high-mortality tumors. 高死亡率肿瘤血清生物标志物的质谱鉴定。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-01-15 DOI: 10.1155/2013/125858

Alessandra Tessitore, Agata Gaggiano, Germana Cicciarelli, Daniela Verzella, Daria Capece, Mariafausta Fischietti, Francesca Zazzeroni, Edoardo Alesse

{"title":"Serum biomarkers identification by mass spectrometry in high-mortality tumors.","authors":"Alessandra Tessitore, Agata Gaggiano, Germana Cicciarelli, Daniela Verzella, Daria Capece, Mariafausta Fischietti, Francesca Zazzeroni, Edoardo Alesse","doi":"10.1155/2013/125858","DOIUrl":"https://doi.org/10.1155/2013/125858","url":null,"abstract":"Cancer affects millions of people worldwide. Tumor mortality is substantially due to diagnosis at stages that are too late for therapies to be effective. Advances in screening methods have improved the early diagnosis, prognosis, and survival for some cancers. Several validated biomarkers are currently used to diagnose and monitor the progression of cancer, but none of them shows adequate specificity, sensitivity, and predictive value for population screening. So, there is an urgent need to isolate novel sensitive, specific biomarkers to detect the disease early and improve prognosis, especially in high-mortality tumors. Proteomic techniques are powerful tools to help in diagnosis and monitoring of treatment and progression of the disease. During the last decade, mass spectrometry has assumed a key role in most of the proteomic analyses that are focused on identifying cancer biomarkers in human serum, making it possible to identify and characterize at the molecular level many proteins or peptides differentially expressed. In this paper we summarize the results of mass spectrometry serum profiling and biomarker identification in high mortality tumors, such as ovarian, liver, lung, and pancreatic cancer.","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/10.1155/2013/125858","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31323028","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}

引用次数: 46

Issues and applications in label-free quantitative mass spectrometry. 无标记定量质谱的问题与应用。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-01-16 DOI: 10.1155/2013/756039

Xianyin Lai, Lianshui Wang, Frank A Witzmann

{"title":"Issues and applications in label-free quantitative mass spectrometry.","authors":"Xianyin Lai, Lianshui Wang, Frank A Witzmann","doi":"10.1155/2013/756039","DOIUrl":"10.1155/2013/756039","url":null,"abstract":"To address the challenges associated with differential expression proteomics, label-free mass spectrometric protein quantification methods have been developed as alternatives to array-based, gel-based, and stable isotope tag or label-based approaches. In this paper, we focus on the issues associated with label-free methods that rely on quantitation based on peptide ion peak area measurement. These issues include chromatographic alignment, peptide qualification for quantitation, and normalization. In addressing these issues, we present various approaches, assembled in a recently developed label-free quantitative mass spectrometry platform, that overcome these difficulties and enable comprehensive, accurate, and reproducible protein quantitation in highly complex protein mixtures from experiments with many sample groups. As examples of the utility of this approach, we present a variety of cases where the platform was applied successfully to assess differential protein expression or abundance in body fluids, in vitro nanotoxicology models, tissue proteomics in genetic knock-in mice, and cell membrane proteomics.","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/PMC3562690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31323029","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}

引用次数: 0

Quantitative Proteomics via High Resolution MS Quantification: Capabilities and Limitations. 通过高分辨率质谱定量的定量蛋白质组学:能力和局限性。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-04-23 DOI: 10.1155/2013/674282

Richard E Higgs, Jon P Butler, Bomie Han, Michael D Knierman

{"title":"Quantitative Proteomics via High Resolution MS Quantification: Capabilities and Limitations.","authors":"Richard E Higgs, Jon P Butler, Bomie Han, Michael D Knierman","doi":"10.1155/2013/674282","DOIUrl":"https://doi.org/10.1155/2013/674282","url":null,"abstract":"Recent improvements in the mass accuracy and resolution of mass spectrometers have led to renewed interest in label-free quantification using data from the primary mass spectrum (MS1) acquired from data-dependent proteomics experiments. The capacity for higher specificity quantification of peptides from samples enriched for proteins of biological interest offers distinct advantages for hypothesis generating experiments relative to immunoassay detection methods or prespecified peptide ions measured by multiple reaction monitoring (MRM) approaches. Here we describe an evaluation of different methods to post-process peptide level quantification information to support protein level inference. We characterize the methods by examining their ability to recover a known dilution of a standard protein in background matrices of varying complexity. Additionally, the MS1 quantification results are compared to a standard, targeted, MRM approach on the same samples under equivalent instrument conditions. We show the existence of multiple peptides with MS1 quantification sensitivity similar to the best MRM peptides for each of the background matrices studied. Based on these results we provide recommendations on preferred approaches to leveraging quantitative measurements of multiple peptides to improve protein level inference.","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/10.1155/2013/674282","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31460189","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}

引用次数: 23

Proteomic Analysis and Label-Free Quantification of the Large Clostridium difficile Toxins. 大型艰难梭菌毒素的蛋白质组学分析和无标记定量。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-08-27 DOI: 10.1155/2013/293782

Hercules Moura, Rebecca R Terilli, Adrian R Woolfitt, Yulanda M Williamson, Glauber Wagner, Thomas A Blake, Maria I Solano, John R Barr

{"title":"Proteomic Analysis and Label-Free Quantification of the Large Clostridium difficile Toxins.","authors":"Hercules Moura, Rebecca R Terilli, Adrian R Woolfitt, Yulanda M Williamson, Glauber Wagner, Thomas A Blake, Maria I Solano, John R Barr","doi":"10.1155/2013/293782","DOIUrl":"https://doi.org/10.1155/2013/293782","url":null,"abstract":"Clostridium difficile is the leading cause of antibiotic-associated diarrhea in hospitals worldwide, due to hypervirulent epidemic strains with the ability to produce increased quantities of the large toxins TcdA and TcdB. Unfortunately, accurate quantification of TcdA and TcdB from different toxinotypes using small samples has not yet been reported. In the present study, we quantify C. difficile toxins in <0.1 mL of culture filtrate by quantitative label-free mass spectrometry (MS) using data-independent analysis (MS(E)). In addition, analyses of both purified TcdA and TcdB as well as a standard culture filtrate were performed using gel-based and gel-independent proteomic platforms. Gel-based proteomic analysis was then used to generate basic information on toxin integrity and provided sequence confirmation. Gel-independent in-solution digestion of both toxins using five different proteolytic enzymes with MS analysis generated broad amino acid sequence coverage (91% for TcdA and 95% for TcdB). Proteomic analysis of a culture filtrate identified a total of 101 proteins, among them TcdA, TcdB, and S-layer proteins. ","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/10.1155/2013/293782","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31758973","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}

引用次数: 19

The Human Urinary Proteome Fingerprint Database UPdb. 人类尿蛋白质组指纹数据库。

International journal of proteomics Pub Date : 2013-01-01 Epub Date: 2013-10-09 DOI: 10.1155/2013/760208

Holger Husi, Janice B Barr, Richard J E Skipworth, Nathan A Stephens, Carolyn A Greig, Henning Wackerhage, Rona Barron, Kenneth C H Fearon, James A Ross

{"title":"The Human Urinary Proteome Fingerprint Database UPdb.","authors":"Holger Husi, Janice B Barr, Richard J E Skipworth, Nathan A Stephens, Carolyn A Greig, Henning Wackerhage, Rona Barron, Kenneth C H Fearon, James A Ross","doi":"10.1155/2013/760208","DOIUrl":"https://doi.org/10.1155/2013/760208","url":null,"abstract":"The use of human urine as a diagnostic tool has many advantages, such as ease of sample acquisition and noninvasiveness. However, the discovery of novel biomarkers, as well as biomarker patterns, in urine is hindered mainly by a lack of comparable datasets. To fill this gap, we assembled a new urinary fingerprint database. Here, we report the establishment of a human urinary proteomic fingerprint database using urine from 200 individuals analysed by SELDI-TOF (surface enhanced laser desorption ionisation-time of flight) mass spectrometry (MS) on several chip surfaces (SEND, HP50, NP20, Q10, CM10, and IMAC30). The database currently lists 2490 unique peaks/ion species from 1172 nonredundant SELDI analyses in the mass range of 1500 to 150000. All unprocessed mass spectrometric scans are available as \".xml\" data files. Additionally, 1384 peaks were included from external studies using CE (capillary electrophoresis)-MS, MALDI (matrix assisted laser desorption/ionisation), and CE-MALDI hybrids. We propose to use this platform as a global resource to share and exchange primary data derived from MS analyses in urinary research. ","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/10.1155/2013/760208","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31858067","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}

引用次数: 15

Clinical Proteomics 临床蛋白质组学

International journal of proteomics Pub Date : 2012-08-15 DOI: 10.1007/978-1-4939-1872-0

Á. Végvári, T. Kondo, John G. Marshall

引用次数: 63

Reconstruction of Sugar Metabolic Pathways of Giardia lamblia. 贾第鞭毛虫糖代谢途径的重建。

International journal of proteomics Pub Date : 2012-01-01 Epub Date: 2012-10-18 DOI: 10.1155/2012/980829

Jian Han, Lesley J Collins

引用次数: 17

Optimization of an Efficient Protein Extraction Protocol Compatible with Two-Dimensional Electrophoresis and Mass Spectrometry from Recalcitrant Phenolic Rich Roots of Chickpea (Cicer arietinum L.). 鹰嘴豆(Cicer arietinum L.)富酚根蛋白质双向电泳和质谱法提取方案的优化

International journal of proteomics Pub Date : 2012-01-01 Epub Date: 2012-10-31 DOI: 10.1155/2012/536963

Moniya Chatterjee, Sumanti Gupta, Anirban Bhar, Sampa Das

{"title":"Optimization of an Efficient Protein Extraction Protocol Compatible with Two-Dimensional Electrophoresis and Mass Spectrometry from Recalcitrant Phenolic Rich Roots of Chickpea (Cicer arietinum L.).","authors":"Moniya Chatterjee, Sumanti Gupta, Anirban Bhar, Sampa Das","doi":"10.1155/2012/536963","DOIUrl":"https://doi.org/10.1155/2012/536963","url":null,"abstract":"Two-dimensional electrophoresis and mass spectrometry are undoubtedly two essential tools popularly used in proteomic analyses. Utilization of these techniques however largely depends on efficient and optimized sample preparation, regarded as one of the most crucial steps for recovering maximum amount of reliable information. The present study highlights the optimization of an effective and efficient protocol, capable of extraction of root proteins from recalcitrant phenolic rich tissues of chickpea. The widely applicable TCA-acetone and phenol-based methods have been comparatively evaluated, amongst which the latter appeared to be better suited for the sample. The phenol extraction-based method further complemented with sodium dodecyl sulphate (SDS) and pulsatory treatments proved to be the most suitable method represented by greatest spot number, good resolution, and spot intensities. All the randomly selected spots showed successful identification when subjected to further downstream MALDI-TOF and MS/MS analyses. Hence, the information obtained collectively proposes the present protein extraction protocol to be an effective one that could be applicable for recalcitrant leguminous root samples.","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/10.1155/2012/536963","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31082768","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}

引用次数: 36

Proteolytic Potential of the MSC Exosome Proteome: Implications for an Exosome-Mediated Delivery of Therapeutic Proteasome. MSC外泌体蛋白质组的蛋白水解潜力:外泌体介导的治疗性蛋白酶体递送的意义。

International journal of proteomics Pub Date : 2012-01-01 Epub Date: 2012-07-18 DOI: 10.1155/2012/971907

Ruenn Chai Lai, Soon Sim Tan, Bao Ju Teh, Siu Kwan Sze, Fatih Arslan, Dominique P de Kleijn, Andre Choo, Sai Kiang Lim

{"title":"Proteolytic Potential of the MSC Exosome Proteome: Implications for an Exosome-Mediated Delivery of Therapeutic Proteasome.","authors":"Ruenn Chai Lai, Soon Sim Tan, Bao Ju Teh, Siu Kwan Sze, Fatih Arslan, Dominique P de Kleijn, Andre Choo, Sai Kiang Lim","doi":"10.1155/2012/971907","DOIUrl":"https://doi.org/10.1155/2012/971907","url":null,"abstract":"Mesenchymal stem cells (MSCs) are used in many of the current stem cell-based clinical trials and their therapeutic efficacy has increasingly been attributed to secretion of paracrine factors. We have previously demonstrated that a therapeutic constituent of this secretion is exosome, a secreted bilipid membrane vesicle of ~50-100 nm with a complex cargo that is readily internalized by H9C2 cardiomyocytes. It reduces infarct size in a mouse model of myocardial ischemia/reperfusion (MI/R) injury. We postulate that this therapeutic efficacy is derived from the synergy of a select permutation of individual exosome components. To identify protein candidates in this permutation, the proteome was profiled and here we identified 20S proteasome as a protein candidate. Mass spectrometry analysis detected all seven α and seven β chains of the 20S proteasome, and also the three beta subunits of \"immunoproteasome\" with a very high confidence level. We demonstrated that a functional proteasome copurified with MSC exosomes with a density of 1.10-1.18 g/mL, and its presence correlated with a modest but significant reduction in oligomerized protein in a mouse model of myocardial infarction. Circulating proteasomes in human blood also copurified with exosomes. Therefore, 20S proteasome is a candidate exosome protein that could synergize with other constituents to ameliorate tissue damage.","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/10.1155/2012/971907","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30804770","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}

引用次数: 393

Plasma fractionation enriches post-myocardial infarction samples prior to proteomics analysis. 血浆分离在蛋白质组学分析之前丰富心肌梗死后样品。

International journal of proteomics Pub Date : 2012-01-01 Epub Date: 2012-06-18 DOI: 10.1155/2012/397103

Lisandra E de Castro Brás, Kristine Y Deleon, Yonggang Ma, Qiuxia Dai, Kevin Hakala, Susan T Weintraub, Merry L Lindsey

{"title":"Plasma fractionation enriches post-myocardial infarction samples prior to proteomics analysis.","authors":"Lisandra E de Castro Brás, Kristine Y Deleon, Yonggang Ma, Qiuxia Dai, Kevin Hakala, Susan T Weintraub, Merry L Lindsey","doi":"10.1155/2012/397103","DOIUrl":"https://doi.org/10.1155/2012/397103","url":null,"abstract":"Following myocardial infarction (MI), matrix metalloproteinase-9 (MMP-9) levels increase, and MMP-9 deletion improves post-MI remodeling of the left ventricle (LV). We provide here a technical report on plasma-analysis from wild type (WT) and MMP-9 null mice using fractionation and mass-spectrometry-based proteomics. MI was induced by coronary artery ligation in male WT and MMP-9 null mice (4-8 months old; n = 3/genotype). Plasma was collected on days 0 (pre-) and 1 post-MI. Plasma proteins were fractionated and proteins in the lowest (fraction 1) and highest (fraction 12) molecular weight fractions were separated by 1-D SDS-PAGE, digested in-gel with trypsin and analyzed by HPLC-ESI-MS/MS on an Orbitrap Velos. We tried five different fractionation protocols, before reaching an optimized protocol that allowed us to identify over 100 proteins. Serum amyloid A substantially increased post-MI in both genotypes, while alpha-2 macroglobulin increased only in the null samples. In fraction 12, extracellular matrix proteins were observed only post-MI. Interestingly, fibronectin-1, a substrate of MMP-9, was identified at both day 0 and day 1 post-MI in the MMP-9 null mice but was only identified post-MI in the WT mice. In conclusion, plasma fractionation offers an improved depletion-free method to evaluate plasma changes following MI.","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/10.1155/2012/397103","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30750240","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}

引用次数: 6