We describe a largely unbiased method for rapid and large-scale proteome analysis by multidimensional liquid chromatography, tandem mass spectrometry, and database searching by the SEQUEST algorithm, named multidimensional protein identification technology (MudPIT). MudPIT was applied to the proteome of the Saccharomyces cerevisiae strain BJ5460 grown to mid-log phase and yielded the largest proteome analysis to date. A total of 1,484 proteins were detected and identified. Categorization of these hits demonstrated the ability of this technology to detect and identify proteins rarely seen in proteome analysis, including low-abundance proteins like transcription factors and protein kinases. Furthermore, we identified 131 proteins with three or more predicted transmembrane domains, which allowed us to map the soluble domains of many of the integral membrane proteins. MudPIT is useful for proteome analysis and may be specifically applied to integral membrane proteins to obtain detailed biochemical ...
The Human Proteome Project (HPP) is an international project organized by the Human Proteome Organization (HUPO) that aims to revolutionize our understanding of the human proteome via a coordinated effort by many research laboratories around the world. It is designed to map the entire human proteome in a systematic effort using currently available and emerging techniques. Completion of this project will enhance understanding of human biology at the cellular level and lay a foundation for development of diagnostic, prognostic, therapeutic, and preventive medical applications. ...
Title:Global Cell Proteome Profiling, Phospho-signaling and Quantitative Proteomics for Identification of New Biomarkers in Acute Myeloid Leukemia Patients. VOLUME: 17 ISSUE: 1. Author(s):Elise Aasebø, Rakel B. Forthun, Frode Berven, Frode Selheim and Maria Hernandez-Valladares. Affiliation:Department of Biomedicine, Faculty of Medicine, Building for Basic Biology, University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway.. Keywords:Acute myeloid leukemia, biomarker, mass spectrometry, proteomics, phosphoproteomics, diagnosis, prognosis.. Abstract:The identification of protein biomarkers for acute myeloid leukemia (AML) that could find applications in AML diagnosis and prognosis, treatment and the selection for bone marrow transplant requires substantial comparative analyses of the proteomes from AML patients. In the past years, several studies have suggested some biomarkers for AML diagnosis or AML classification using methods for sample preparation with low proteome coverage and low ...
The word proteome was coined in 1995 to refer to the total protein complement of a genome. The human genome encodes roughly 100,000 genes, corresponding to a similar number of proteins. Not all genes are expressed in all tissues; roughly 10,000 proteins are found in any particular cell. The fraction of the proteome that is expressed by an organism varies between tissues and in response to the environment. Conventional proteome analysis is preformed by two-dimensional gel electrophoresis and requires the protein from roughly a million cells. We have improved the sensitivity of proteome analysis by six orders of magnitude. In preliminary work, we have demonstrated that we can perform a simple analysis of the proteome in a single human cancer cell. Our Preliminary work will be expanded in this R33 proposal. We will automate the manipulations of single cells, we will multiplex the instrument so that 96 cells can be analyzed simultaneously, we will expand our proteome analysis to two-dimensional ...
Plant cells are routinely exposed to various pathogens and environmental stresses that cause cell wall perturbations. Little is known of the mechanisms that plant cells use to sense these disturbances and transduce corresponding signals to regulate cellular responses to maintain cell wall integrity. Previous studies in rice have shown that removal of the cell wall leads to substantial chromatin reorganization and histone modification changes concomitant with cell wall re-synthesis. But the genes and proteins that regulate these cellular responses are still largely unknown. Here we present an examination of the nuclear proteome differential expression in response to removal of the cell wall in rice suspension cells using multiple nuclear proteome extraction methods. A total of 382 nuclear proteins were identified with two or more peptides, including 26 transcription factors. Upon removal of the cell wall, 142 nuclear proteins were up regulated and 112 were down regulated. The differentially ...
Author: Henriksen, Peter et al.; Genre: Journal Article; Published in Print: 2012-11; Open Access; Keywords: SISTER-CHROMATID COHESION; MASS-SPECTROMETRY; HISTONE ACETYLATION;|br/| SIGNALING NETWORKS; ESCHERICHIA-COLI; C-TRAP; YEAST; COMPLEXES;|br/| DEACETYLATION; PHOSPHORYLATION; Title: Proteome-wide Analysis of Lysine Acetylation Suggests its Broad|br/| Regulatory Scope in Saccharomyces cerevisiae
Fibroblasts are mesenchymal stromal cells which occur in all tissue types. While their main function is related to ECM production and physical support, they are also important players in wound healing, and have further been recognized to be able to modulate inflammatory processes and support tumor growth. Fibroblasts can display distinct phenotypes, depending on their tissue origin, as well as on their functional state. In order to contribute to the proteomic characterization of fibroblasts, we have isolated primary human fibroblasts from human skin, lung and bone marrow and generated proteome profiles of these cells by LC-MS/MS. Comparative proteome profiling revealed characteristic differences therein, which seemed to be related to the cells tissue origin. Furthermore, the cells were treated in vitro with the pro-inflammatory cytokine IL-1beta. While all fibroblasts induced the secretion of Interleukins IL-6 and IL-8 and the chemokine GRO-alpha, other inflammation-related proteins were up-regulated
MAPU contains several body fluid proteomes; including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. The liver proteome is represented with 3200 proteins. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:1000. Thus MAPU datasets can serve as reference proteomes in biomarker discovery. MAPU contains the peptides identifying each protein, measured masses, scores and intensities using a clickable interface of cell or body parts. Proteome data can be queried across proteomes by protein name, accession number, sequence similarity, peptide sequence and annotation information. More than 4500 mouse and 2500 human proteins have already been identified in at least one proteome ...
The proteome can be larger than the genome, especially in eukaryotes, as more than one protein can be produced from one gene due to alternative splicing (e.g. human proteome consists 92,179 proteins[citation needed] out of which 71,173 are splicing variants[citation needed]).[3] On the other hand, not all genes are translated to proteins, and many known genes encode only RNA which is the final functional product. Moreover, complete proteome size vary depending the kingdom of life. For instance, eukaryotes, bacteria, archaea and viruses have on average 15,145, 3,200, 2,358 and 42 proteins respectively encoded in their genomes.[4]. The term dark proteome coined by Perdigão and colleagues, defines regions of proteins that have no detectable sequence homology to other proteins of known three-dimensional structure and therefore cannot be modeled by homology. For 546,000 Swiss-Prot proteins, 44-54% of the proteome in eukaryotes and viruses was found to be dark, compared with only ∼14% in ...
The use of dialyzed serum is essential in the application of the conventional stable isotope labeling by amino acids in cell culture (SILAC) approach to achieve complete labeling of proteins for quantitative proteomics. Here, we first evaluated the impact of dialyzed serum on the proteome and phosphoproteome
TY - JOUR. T1 - Mass-spectrometry based proteome comparison of extracellular vesicle isolation methods. T2 - Comparison of ME-kit, size-exclusion chromatography, and high-speed centrifugation. AU - Askeland, Anders. AU - Borup, Anne. AU - Østergaard, Ole. AU - Olsen, Jesper V.. AU - Lund, Sigrid M.. AU - Christiansen, Gunna. AU - Kristensen, Søren R.. AU - Heegaard, Niels H.H.. AU - Pedersen, Shona. PY - 2020. Y1 - 2020. N2 - Extracellular vesicles (EVs) are small membrane-enclosed particles released by cells under various conditions specific to cells biological states. Hence, mass-spectrometry (MS) based proteome analysis of EVs in plasma has gained much attention as a method to discover novel protein biomarkers. MS analysis of EVs in plasma is challenging and EV isolation is usually necessary. Therefore, we compared differences in abundance, subtypes, and contamination for EVs isolated by high-speed centrifugation, size exclusion chromatography (SEC), and peptide-affinity precipitation ...
Peptide KE exhibits immunoprotective, geroprotective, and oncostatic activities and stimulates functional activity of fibroblasts. The KE motif is present in amino acid sequences of some cytokines and peptide hormones functionally similar to KE peptide. However, the relationship between the presence of KE motif and protein functions on the scale of known human proteome has not yet received sufficient attention. The incidence of bioregulatory peptide KE in proteins of various functional groups constituting human proteome is studied. The study is carried out with the use of the available data on the human proteome (UniProt portal) comprising 20,417 proteins. The levels of KE motifs were maximum in cytoplasmic and nuclear proteins, while the presence of KE in the membrane and all other proteins was the minimum. KE peptide molecules released from nuclear proteins during limited proteolysis can bind to DNA and regulate gene expression.. ...
Most catalytic, structural and regulatory functions of the cell are carried out by functional modules, typically complexes containing or consisting of proteins. The composition and abundance of these complexes and the quantitative distribution of specific proteins across different modules are therefore of major significance in basic and translational biology. However, detection and quantification of protein complexes on a proteome-wide scale is technically challenging. We have recently extended the targeted proteomics rationale to the level of native protein complex analysis (complex-centric proteome profiling). The complex-centric workflow described herein consists of size exclusion chromatography (SEC) to fractionate native protein complexes, data-independent acquisition mass spectrometry to precisely quantify the proteins in each SEC fraction based on a set of proteotypic peptides and targeted, complex-centric analysis where prior information from generic protein interaction maps is used to detect
Background. Thoracic aortic aneurysm (TAA) is a degenerative disease of the aortic wall and is associated with an increased risk of aortic rupture. TAA is a more prevalent complication in patients with bicuspid aortic valve (BAV) compared to those with tricuspid aortic valve (TAV). Objectives. We aimed to investigate first, changes in intracellular proteins by comparing BAV and TAV patients with aneurysm, and second, regional changes in extracellular matrix (ECM) proteins by comparing the lesser (concavity) and the greater (convexity) aortic curvatures of BAV patients with and without aneurysm. The findings obtained in human patients were followed up by mechanistic studies in mice. Methods. Human and murine aortic specimens were analysed by mass spectrometry (MS) after extraction of intracellular and ECM proteins. Immunoblotting and gene expression analysis were used to validate the proteomics findings. An ECM protease knockout mouse model was used to better characterise proteolytic processing ...
The term proteome was coined by Mark Wilkins first in 1994 in the symposium: 2D Electrophoresis: from protein maps to genomes in Siena, Italy, and was subsequently published in 1995 (1), which was part of his PhD thesis. The term proteome is a blend of proteins and genome and Wilkins used it to describe the entire complement of proteins expressed by a genome, cell, tissue or organism. Subsequently this term has been specified to contain all the expressed proteins at a given time point under defined conditions. The term has been applied to several different types of biological systems. A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation. It can also be useful to consider an organisms complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes. This is very roughly the protein equivalent of the genome. The term ...
The objective of the international Chromosome-Centric Human Proteome Project (C-HPP) is to map and annotate all proteins encoded by the genes on each human chromosome. The C-HPP consortium was established to organize a collaborative network among the research teams responsible for protein mapping of individual chromosomes and to identify compelling biological and genetic mechanisms influencing colocated genes and their protein products. The C-HPP aims to foster the development of proteome analysis and integration of the findings from related molecular -omics technology platforms through collaborations among universities, industries, and private research groups. The C-HPP consortium leadership has elicited broad input for standard guidelines to manage these international efforts more efficiently by mobilizing existing resources and collaborative networks. The C-HPP guidelines set out the collaborative consensus of the C-HPP teams, introduce topics associated with experimental approaches, data ...
article{c8bd2452-0966-4124-b995-eef3ae4c8ede, abstract = {The objective of the international Chromosome-Centric Human Proteome Project (C-HPP) is to map and annotate all proteins encoded by the genes on each human chromosome. The C-FIPP consortium was established to organize a collaborative network among the research teams responsible for protein mapping of individual chromosomes and to identify compelling biological and genetic mechanisms influencing colocated genes and their protein products. The C-HPP aims to foster the development of proteome analysis and integration of the findings from related molecular -omics technology platforms through collaborations among universities, industries, and private research groups. The C-HPP consortium leadership has elicited broad input for standard guidelines to manage these international efforts more efficiently by mobilizing existing resources and collaborative networks. The C-HPP guidelines set out the collaborative consensus of the C-HPP teams, ...
We used 2H2O metabolic labeling to assess large scale plasma proteome dynamics in vivo. Administration of 2H2O in a bolus injection followed by 5% supplementation in the drinking water enabled accurate measurement of the FSR of multiple plasma proteins in less than 8 h. This approach considers 2H2O as the labeling precursor and is based on the assumption that 2H from 2H2O rapidly equilibrates with the carbon-bound hydrogen atoms of proteogenic amino acids before they are incorporated into newly synthesized proteins (12, 17). This key assumption was validated based on the analysis of temporal changes in 2H labeling of body water and hepatic proteogenic amino acids. The steady state labeling of nonexchangeable hydrogen atoms in free amino acids within 1 h of 2H2O administration demonstrates that the rate-limiting step of 2H incorporation into long-lived proteins (t½ , ∼3 h) is protein synthesis from amino acids. Protein synthesis is assessed from the rate of 2H incorporation into a proteolytic ...
Interferons (IFNs) are pleotropic cytokines secreted upon encounter of pathogens and tumors. Applying their antipathogenic, antiproliferative, and immune stimulatory capacities, recombinant IFNs are frequently prescribed as drugs to treat different diseases. IFNs act by changing the gene expression profile of cells. Due to characteristics such as rapid gene induction and signaling, IFNs also represent prototypical model systems for various aspects of biomedical research (e.g., signal transduction). In regard to the signaling and activated promoters, IFNs can be subdivided into two groups. Here, alterations of the cellular proteome of human cells treated with IFNα and IFNγ were elucidated in a time-resolved manner by quantitative proteome analysis. The majority of protein regulations were strongly IFN type and time dependent. In addition to the expected upregulation of IFN-responsive proteins, an astonishing number of proteins became profoundly repressed especially by IFNγ. Thus, our comprehensive
Jennifer E Van Eyk, Fernando Jose Corrales, Ruedi Aebersold, Ferdinando Cerciello, Eric W Deutsch, Paola Roncada, Jean-Charles Sanchez, Tadashi Yamamoto, Pengyuan Yang, Hui Zhang, Gilbert S Omenn Highlights of the Biology and Disease-driven Human Proteome Project, 2015-2016. Journal or Proteome Research, DOI: 10.1021/acs.jproteome.6b00444 Publication Date (Web): August 30, 2016. 2. NIH Bio-specimens National Cancer Institute (NCI) Specimen resource locator https://specimens.cancer.gov/. 3. CPTAC publications. Zhang, H, Liu T, Zhang Z, Payne S. et al (2016) Integrated proteogenomic characterization of human high grade serous ovarian cancer. Cell. http://www.cell.com/cell/home. Mertins P, et al (2016) Proteogenomic Analysis of Human Breast Cancer Connects Genetic Alterations to Phosphorylation NetworksNature . http://www.nature.com/nature.. Zhang B, Wang J, Wang X, Zhu J, et al. (2014) Proteogenomic characterization of human colon and rectal cancer Nature 513 (7518): 382-7. ...
Agilent Technologies Inc. (NYSE: A) and Proteome Systems a leading in...Proteome Systems developed GlycomIQ to address the emerging field of g... Analysis of protein glycosylation is a demanding task that has often ...The co-marketed product is expected to be available this summer. Agile... Agilent is proud of this collaboration with Proteome Systems said T...,Integration,of,Agilents,MS,technology,,Proteome,Systems,software,to,help,scientists,in,proteomics,research,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
The role of mass spectrometry in proteome studies.: Mass spectrometry (MS) is an important tool in modern protein chemistry. In proteome analyses the expression
Human proteome analysis Since the human proteome was first revealed, scientists have been increasing their efforts to repeat the process more quickly in order to lay the groundwork for routine systems biology experiments, accelerate disease biomarker discovery and guide us towards the realm of personalised medicine. Many improvements have been...
The Human Eye Proteome Project Perspectives on an emerging proteome Proteomics , 2013, 13 , 2500-2511 Richard D. Semba, Jan J. Enghild, Vidya Venkatraman, Thomas F. Dyrlund, Jennifer E. Van Eyk Abstract There are an estimated 285 million people with visual impairment worldwide, of whom 39 million are blind. The pathogenesis of many eye diseases...
TY - JOUR. T1 - Global secretome analysis identifies novel mediators of bone metastasis. AU - Blanco, Mario Andres. AU - Leroy, Gary. AU - Khan, Zia. AU - Alečković, Maša. AU - Zee, Barry M.. AU - Garcia, Benjamin A.. AU - Kang, Yibin. PY - 2012/9. Y1 - 2012/9. N2 - Bone is the one of the most common sites of distant metastasis of solid tumors. Secreted proteins are known to influence pathological interactions between metastatic cancer cells and the bone stroma. To comprehensively profile secreted proteins associated with bone metastasis, we used quantitative and non-quantitative mass spectrometry to globally analyze the secretomes of nine cell lines of varying bone metastatic ability from multiple species and cancer types. By comparing the secretomes of parental cells and their bone metastatic derivatives, we identified the secreted proteins that were uniquely associated with bone metastasis in these cell lines. We then incorporated bioinformatic analyses of large clinical metastasis ...
Comprehensive, systematic characterization of the plasma proteome in healthy and diseased states greatly facilitates the development of biosignatures for early disease detection, clinical diagnosis, and therapy. Blood plasma is the most complex human-derived proteome containing other tissue proteome subsets as well as a wide dynamic range of protein concentrations. Therefore, the characterization of biosignatures in the human plasma proteome is a very complicated task. Advances in methods and technology for profiling plasma proteins now enable construction of a comprehensive pipeline from candidate discovery, qualification, verification, research assay optimization, validation to eventual commercialization.. Analysis of the proteome from samples obtained from this population is of prime importance. The plasma and serum is isolated from the blood sample collected and flash frozen on site prior to be being shipped to our central cryostorage facility. The sample is then analyzed using a 2D-gel ...
Antibodies are crucial for the study of human proteins and have been defined as one of the three pillars in the human chromosome-centric Human Proteome Project (CHPP). In this article the chromosome-centric structure has been used to analyze the availability of antibodies as judged by the presence within the portal Antibodypedia, a database designed to allow comparisons and scoring of publicly available antibodies toward human protein targets. This public database displays antibody data from more than one million antibodies toward human protein targets. A summary of the content in this knowledge resource reveals that there exist more than 10 antibodies to over 70% of all the putative human genes, evenly distributed over the 24 human chromosomes. The analysis also shows that at present, less than 10% of the putative human protein-coding genes (n = 1882) predicted from the genome sequence lack antibodies, suggesting that focused efforts from the antibody-based and mass spectrometry-based proteomic ...
Egea, J., Fabregat, I., Frapart, Y. M., Ghezzi, P., Görlach, A., Kietzmann, T., Kubaichuk, K., Knaus, U. G., Lopez, M. G., Olaso-Gonzalez, G., Petry, A., Schulz, R., Vina, J., Winyard, P., Abbas, K., Ademowo, O. S., Afonso, C. B., Andreadou, I., Antelmann, H., Antunes, F., Aslan, M., Bachschmid, M. M., Barbosa, R. M., Belousov, V., Berndt, C., Bernlohr, D., Bertrán, E., Bindoli, A., Bottari, S. P., Brito, P. M., Carrara, G., Casas, A. I., Chatzi, A., Chondrogianni, N., Conrad, M., Cooke, M. S., Costa, J. G., Cuadrado, A., My-Chan Dang, P., De Smet, B., Debelec-Butuner, B., Dias, I. H. K., Dunn, J. D., Edson, A. J., El Assar, M., El-Benna, J., Ferdinandy, P., Fernandes, A. S., Fladmark, K. E., Förstermann, U., Giniatullin, R., Giricz, Z., Görbe, A., Griffiths, H., Hampl, V., Hanf, A., Herget, J., Hernansanz-Agustín, P., Hillion, M., Huang, J., Ilikay, S., Jansen-Dürr, P., Jaquet, V., Joles, J. A., Kalyanaraman, B., Kaminskyy, D., Karbaschi, M., Kleanthous, M., Klotz, L. O., Korac, B., ...
Cold adapted or psychrophilic organisms grow at low temperatures, where most of other organisms cannot grow. This adaptation requires a vast array of sequence, structural and physiological adjustments. To understand the molecular basis of cold adaptation of proteins, we analyzed proteomes of psychrophilic and mesophilic bacterial species and compared the differences in amino acid composition and substitution patterns to investigate their likely association with growth temperatures. In psychrophilic bacteria, serine, aspartic acid, threonine and alanine are overrepresented in the coil regions of secondary structures, whilst glutamic acid and leucine are underrepresented in the helical regions. Compared to mesophiles, psychrophiles comprise a significantly higher proportion of amino acids that contribute to higher protein flexibility in the coil regions of proteins, such as those with tiny/small or neutral side chains. Amino acids with aliphatic, basic, aromatic and hydrophilic side chains are
Current conventions limit the size and complexity of the detectable proteome and prevent mass-spectrometry-based proteomics from providing a comprehensive characterization of biological systems. OpenProt enables improved mapping of the proteome because, in addition to currently annotated CDSs and proteins, OpenProt displays the sequence, functional annotation and expression evidence of previously hidden altORFs and their corresponding altProts. The OpenProt platform is freely available to users.. ...
TY - JOUR. T1 - Novel surgical approaches for sampling the ovarian surface epithelium and proximal fluid proteome. AU - Rungruang, Bunja. AU - Hood, Brian L.. AU - Sun, Mai. AU - Hoskins, Ebony. AU - Conrads, Thomas P.. AU - Zorn, Kristin K.. PY - 2010/11/5. Y1 - 2010/11/5. N2 - The pathogenesis of ovarian, fallopian tube, and peritoneal cancers has been difficult to elucidate despite intense effort. Recently, though, the care of women felt to be at high risk due to a strong family history of breast and/or ovarian cancer or a known germline BRCA1 or BRCA2 mutation has provided potential insight into the development of these malignancies. Risk-reducing surgical removal of the fallopian tubes and ovaries, called risk-reducing bilateral salpingo-oopherectomy (RRBSO), is commonly performed as a laparoscopic procedure to minimize recovery time. We describe here an optimized surgical sampling workflow for analyzing the proteomes of peritoneal, fallopian tube, and ovarian surface epithelial (OSE) ...
Whole-proteome distributions of protein isoelectric point (pI) values in different organisms are bi- or trimodal with some variations. It was suggested that the observed multimodality of the proteome-wide pI distributions is associated with subcellular localization-specific differences in the local pI distributions. However, the factors responsible for variation of the intracellular localization-specific pI profiles have not been investigated in detail. In this work, we explored proteome-wide pI distributions of 32,138 human proteins predicted to reside in 10 subcellular compartments, as well as the pI distributions of experimentally observed lysosomal and Golgi proteins. The distributions were found to differ significantly, although all of them adhered to the major recurrent bimodal pattern. Grossly, acid-biased and alkaline-biased patterns with various minor statistical features were observed at different subcellular locations. Bioinformatics analysis revealed the existence of strong statistically
The high-throughput identification and accurate quantification of proteins are essential strategies for exploring cellularfunctions and processes in quantitative proteomics. Stable isotope tagging is a key technique in quantitative proteomicresearch, accompanied by automated tandem mass spectrometry. For the differential proteome analysis of mouse neuronal celllines, we used a multiplexed isobaric tagging method, in which a four-plex set of amine-reactive isobaric tags are available forpeptide derivatization. Using the four-plex set of isobaric tag for relative and absolute quantitation (iTRAQ) reagents, we analyzedthe differential proteome in several stroke time pathways (0, 4, and 8 h) after the mouse neuronal cells have been stressed usinga glutamate oxidant. In order to obtain a list of the differentially expressed proteins, we selected those proteins which had apparentlychanged significantly during the stress test. With 95% of the peptides showing only a small variation in quantity before ...
textit{Proteome research : mass spectrometry}. Edited by Peter James. Berlin: Springer-Verlag, 2001. xxi, 274 s. ISBN~3-540-67255-9 ...
Soon after the introduction of high resolution two-dimensional electrophoresis (2-DE) in 1975 by Klose (16), OFarrell (17), and others, the technique was applied to the plasma proteins by the present authors (18) with the result that the number of resolved species increased to 300 or more. The 2-DE map of human plasma that resulted is recognizably the same as those produced later by many investigators: in contrast to cellular protein patterns, the plasma 2-DE pattern appears basically the same in everyones hands perhaps due to the very high solubility of the proteins involved and the ease with which the distinctive glycosylation trains of specific proteins can be recognized. A more comprehensive database was reported in 1991 in which 727 spots were resolved, of which 376 were identified as 49 different proteins (19). A plasma map using an immobilized pH gradient first dimension separation was presented the following year with 40 protein identifications carried out by microsequencing (20), and ...
Source: Journal of Proteome Research - October 28, 2019 Category: Biochemistry Authors: Alexander I. Archakov* †, Alexander L. Aseev‡, Victor A. Bykov§, Anatoly I. Grigoriev?, Vadim M. Govorun?, Ekaterina V. Ilgisonis†, Yuri D. Ivanov†, Vadim T. Ivanov#, Olga I. Kiseleva†, Arthur T. Kopylov†, Andrey V. Lisitsa†, Sergey N. Mazu Source Type: research. [ASAP] Brain Region-Specific nAChR and Associated Protein Abundance Alterations Following Chronic Nicotine and/or Menthol Exposure ...
Prior, M. J., Larance, M., Lawrence, R. T., Soul, J., Humphrey, S., Burchfield, J., Kistler, C., Davey, J. R., La-Borde, P. J., Buckley, M., Kanazawa, H., Parton, R. G., Guilhaus, M. & James, D. E. 4 Nov 2011 In : Journal of Proteome Research. 10, 11, p. 4970-4982 13 p.. Research output: Contribution to journal › Article ...
Changes in nuclear proteome inrinmutant reveal the potential downstream targets ofRIN. (a) Nuclear proteins were isolated from wild-type (WT)and rin mutant frui
The quantitative proteome analysis is a key technology for most of the projects within the CRC 1218. The aim of the Z02 project is to support the projects with mass spectrometric expertise. Besides the assessment of global protein expression profiles, the major focus of the facility is the identification of protein-protein interaction in order to decipher molecular networks within mitochondria. In addition, we will investigate activated signalling pathways by the enrichment of post translational modifications, including phosphorylated and ubiquitinated peptides. Moreover, the Z02 project will also support the CRC with statistical and bioinformatics data analysis.. Latest publication ...
The Korea-led Global Human ChromosomeCentric Human Proteome Project (C-HPP) (Chair: Paik Young-Ki, Underwood Distinguished Prof.) made its official launch on September 10, 2012. As the largest project since the human genome, the C-HPP is planned to be implemented over the next ten years (September 2012-September 2022). The project consortium consists of 25 international teams, which focus on each human chromosome (1-22, X, Y and mitochondria). The headquarters office is located at Yonsei Proteome Research Center, directed by Prof. Paik at Yonsei University. The launching ceremony of the C-HPP was held during the annual congress of the Human Proteome Organization (HUPO) in Boston in 2012, which was attended by officials from the U.S. National Institute of Health, the Canadian Institute of Health Research, and key figures in the fields of biomedical research and bio industries who delivered congratulatory speeches on the vision and significance of the project. Historically, the initial C-HPP team ...
Characterizing the molecular components of the basic unit of life; the cell, is crucial for a complete understanding of human biology. The cell is divided into compartments to create a suitable environment for the resident proteins to fulfill their functions. Therefore, spatial mapping of the human proteome is essential to understand protein function in health and disease.. Spatial proteomics is most commonly investigated using mass spectrometry or imaging, combined with machine learning for the data analysis. Until now, studies have been limited to high abundant proteins and relied on the purification of organelle fractions from a bulk of cells. Within the scope of this thesis, we were able to systematically localize proteins in their native cellular environment using antibody-based imaging techniques, and to investigate protein subcellular localization and dynamics on a single cell level, introducing a major advance within the field of spatial proteomics.. Paper I of this thesis presents a ...
TY - JOUR. T1 - Data detailing the platelet acetyl-lysine proteome. AU - Aslan, Joseph E.. AU - David, Larry L.. AU - McCarty, Owen J.T.. N1 - Funding Information: We thank P. Wilmarth (OHSU) for assistance with proteomics analyses. Proteomics studies were supported by a Research Core award from the OHSU School of Medicine , and NIH Grants P30EY010572, P30CA069533, and S10OD012246 . This work was supported by Grants from the National Institutes of Health ( R01HL101972 to O.J.T.M.), the American Heart Association ( 13POST13730003 to J.E.A. and 13EIA12630000 to O.J.T.M). The authors have no conflicts of interest to declare. PY - 2015/12/1. Y1 - 2015/12/1. N2 - Here we detail proteomics data that describe the acetyl-lysine proteome of blood platelets (Aslan et al., 2015 [1]). An affinity purification - mass spectrometry (AP-MS) approach was used to identify proteins modified by Nε-lysine acetylation in quiescent, washed human platelets. The data provide insights into potential regulatory ...
agilent_technologies_inc_nyse_a_and_proteome_systems_a_leading_international_proteomics_company_today_announced_they_have_signed_a_marketing_agreement_to_collaborate_on_an_integrated_solution_for_the_analysis_of_glycoproteins_molecules_that_are_important_in_the_study_of_many_diseases_including_cancer_influenza_and_arthritis_under_the_agreement_proteome_systems_will_make_its_glycomiq_
JPT Peptide Technologies is a DIN ISO 9001:2015 certified and GCLP compliant integrated provider of innovative peptide based catalog products and custom services.
The massive characterization of host-associated and environmental microbial communities has represented a real breakthrough in the life sciences in the last years. In this context, metaproteomics specifically enables the transition from assessing the genomic potential to actually measuring the functional expression of a microbiome. However, significant research efforts are still required to develop analysis pipelines optimized for metaproteome characterization. This work presents an efficient analytical pipeline for shotgun metaproteomic analysis, combining bead-beating/freeze-thawing for protein extraction, filter-aided sample preparation for cleanup and digestion, and single-run liquid chromatography-tandem mass spectrometry for peptide separation and identification. The overall procedure is more time-effective and less labor-intensive when compared to state-of-the-art metaproteomic techniques. The pipeline was first evaluated using mock microbial mixtures containing different types of bacteria and
After all the press surrounding the first human proteome drafts last year, it might be easy to forget about the chromosome centric human proteome project (C-HPP). This HUGE, multinational project represents years of work into getting a full picture of the human proteome ...
Two independent research collaborations have released highly detailed maps of the human proteome in the same publication, identifying a high proportion of the proteins encoded by the human genome. They will help efforts worldwide in the search for new biomarkers of disease. Both methods relied on mass spectrometry to deliver the results, which...
Tobacco BY-2 proteome display, protein profiling and annotation using two-dimensional electrophoresis and mass spectrometry-based cross-species identification ...
Scope and method of study: To study the plant cell wall degradation process and changes in overall physiology during the growth of A. nidulans on sorghum stover at proteomic and genomic level, A. nidulans was grown on sorghum stover under solid-state culture conditions for 1, 2, 3, 5, 7 and 14 days. Semi-quantitative extracellular proteome analysis (1-D PAGE LC-MS/MS), whole genome microarray analysis, scanning and transmission electron microscopy, along with qualitative and quantitative analysis of extracellular hydrolytic enzyme activities, and analysis of the breakdown products by enzymes was used to study sorghum cell wall degradation by A. nidulans.Findings and conclusions: Based on analysis of chitin content, A. nidulans grew to be 4-5% of the total biomass in the culture. A hyphal mat developed on the surface of the sorghum by day one and as seen by scanning electron microscopy the hyphae enmeshed the sorghum particles by day 5. A total of 294 extracellular proteins were identified with ...
TY - JOUR. T1 - Copper exposure effects on yeast mitochondrial proteome. AU - Banci, Lucia. AU - Bertini, Ivano. AU - Ciofi-Baffoni, Simone. AU - DAlessandro, Annamaria. AU - Jaiswal, Deepa. AU - Marzano, Valeria. AU - Neri, Sara. AU - Ronci, Maurizio. AU - Urbani, Andrea. PY - 2011/10/1. Y1 - 2011/10/1. N2 - Mitochondria play an important role on the entire cellular copper homeostatic mechanisms. Alteration of cellular copper levels may thus influence mitochondrial proteome and its investigation represents an important contribution to the general understanding of copper-related cellular effects. In these study we have performed an organelle targeted proteomic investigation focusing our attention on the effect of non-lethal 1 mM copper concentration on Saccharomyces cerevisiae mitochondrial proteome. Functional copper effects on yeast mitochondrial proteome were evaluated by using both 2D electrophoresis (2-DE) and liquid chromatography coupled with tandem mass spectrometry. Proteomic data have ...
The last 30 years Enterococcus faecium has become an important nosocomial pathogen in hospitals worldwide. The aim of this study was to obtain insight in the cell surface proteome of E. faecium when grown in laboratory and clinically relevant conditions. Enterococcus faecium E1162, a clinical blood stream isolate, was grown ... read more until mid-log phase in brain heart infusion medium (BHI) with, or without 0.02% bile salts, Tryptic Soy Broth with 1% glucose (TSBg) and urine, and its cell surface was shaved using immobilized trypsin. Peptides were identified using MS/MS. Mapping against the translated E1162 whole genome sequence identified 67 proteins that were differentially detected in different conditions. In urine, 14 proteins were significantly more and nine proteins less abundant relative to the other conditions. Growth in BHI-bile and TSBg, revealed four and six proteins, respectively, which were uniquely present in these conditions while two proteins were uniquely present in both ...
The purpose of this study was to characterize the cell surface proteome of native compared to cultured equine retinal pigment epithelium (RPE) cells. The RPE plays an essential role in visual function and represents the outer blood-retinal barrier. We are investigating immunopathomechanisms of equine recurrent uveitis, an autoimmune inflammatory disease in horses leading to breakdown of the outer blood-retinal barrier and influx of autoreactive T-cells into affected horses vitrei. Cell surface proteins of native and cultured RPE cells from eye-healthy horses were captured by biotinylation, analyzed by high resolution mass spectrometry coupled to liquid chromatography (LC MS/MS), and the most interesting candidates were validated by PCR, immunoblotting and immunocytochemistry. A total of 112 proteins were identified, of which 84% were cell surface membrane proteins. Twenty-three of these proteins were concurrently expressed by both cell states, 28 proteins exclusively by native RPE cells. Among the
Time-Course Proteome Analysis Reveals the Dynamic Response of Cryptococcus gattii Cells to Fluconazole. . Biblioteca virtual para leer y descargar libros, documentos, trabajos y tesis universitarias en PDF. Material universiario, documentación y tareas realizadas por universitarios en nuestra biblioteca. Para descargar gratis y para leer online.
Human Plasma Proteome Analysis Following Endotoxin Challenge Identifies New Proteins that Contribute to Molecular Phenotype of Innate Immunity
phdthesis{be258743-7e2f-4e1a-b45d-bbfdaaa3d645, abstract = {Proteomics is expected to generate new insights into biological processes as well as identify novel biomarkers and therapeutic targets since most biological functions are transmitted through proteins. However, due to the complexity displayed by a proteome and inherent limitations associated with current methodologies, proteomic analyses often result in incomplete coverage and inconsistent measurements. Clearly, the development of novel high-performing proteomic platforms will be essential in order to successfully decipher the human proteome(s).,br/,,br, ,br/,,br, This thesis, based on four original papers denoted I to IV, describes the development and applicability of a novel proteomic technology platform entitled Global Proteome Survey (GPS) capable of transforming affinity proteomics into a global discovery engine. The GPS methodology combines the best features of affinity proteomics and mass spectrometry, and is based on using ...
Bifidobacterium animalis subsp. lactis BB-12 is a widely used probiotic strain associated with a variety of health-promoting traits. There is, however, only limited knowledge available regarding the membrane proteome and the proteins involved in oligosaccharide transport in BB-12. We applied two enrichment strategies to improve the identification of membrane proteins from BB-12 cultures grown on glucose and on xylo-oligosaccharides, the latter being an emerging prebiotic substrate recently reported to be fermented by BB-12. Our approach encompassed consecutive steps of detergent- and carbonate-treatment in order to generate inside-out membrane vesicles and to interfere with binding of membrane-associated proteins to the membrane, respectively. Proteins in the enriched membrane fraction and membrane-associated fraction were digested by lysyl endopeptidase and trypsin followed by peptide sequencing by LC-ESI-Q-TOF MS/MS. Ninety of a total of 248 identified unique proteins were predicted to possess ...
Fingerprint Dive into the research topics of The genome and structural proteome of an ocean siphovirus: A new window into the cyanobacterial mobilome. Together they form a unique fingerprint. ...
TY - JOUR. T1 - Testing the significance of microorganism identification by mass spectrometry and proteome database search. AU - Pineda, Fernando J.. AU - Lin, Jeffrey S.. AU - Fenselau, Catherine. AU - Demirev, Plamen A.. PY - 2000/8/15. Y1 - 2000/8/15. N2 - We derive and validate a simple statistical model that predicts the distribution of false matches between peaks in matrix-assisted laser desorption/ionization mass spectrometry data and proteins in proteome databases. The model allows us to calculate the significance of previously reported microorganism identification results. In particular, for Δm = ±1.5 Da, we find that the computed significance levels are sufficient to demonstrate the ability to identify microorganisms, provided the number of candidate microorganisms is limited to roughly three Escherichia coli-like or roughly 10 Bacillus subtilis-like microorganisms (in the sense of having roughly the same number of proteins per unit-mass interval). We conclude that, given the ...
TY - JOUR. T1 - Comparative proteome and peptidome analysis of the cephalic fluid secreted by Arapaima gigas (Teleostei Osteoglossidae) during and outside parental care. AU - Torati, Lucas S.. AU - Migaud, Hervé. AU - Doherty, Mary K.. AU - Siwy, Justyna. AU - Mullen, Willian. AU - Mesquita, Pedro E.C.. AU - Albalat, Amaya. N1 - ©2017 The Authors. PY - 2017/10/24. Y1 - 2017/10/24. N2 - Parental investment in Arapaima gigas includes nest building and guarding, followed by a care provision when a cephalic fluid is released from the parents head to the offspring. This fluid has presumably important functions for the offspring but so far its composition has not been characterised. In this study the proteome and peptidome of the cephalic secretion was studied in parental and non-parental fish using capillary electrophoresis coupled to mass spectrometry (CE-MS) and GeLC-MS/MS analyses. Multiple comparisons revealed 28 peptides were significantly different between males and parental males ...
Title: Amino Acid Sequence Database Suitable for the Protein and Proteome Analysis. VOLUME: 5 ISSUE: 4. Author(s):Takao Kawakami, Junko Ozaki, Kazuhiro Kondo, Shinji Sato and Harunobu Yunokawa. Affiliation:Clinical Proteome Center, Tokyo Medical University, Shinjuku Sumitomo Building 17th Floor, 2-6-1 Nishi Shinjuku, Shinjuku, Tokyo 163-0217, Japan.. Keywords:Alternative splicing, database search program, peptide identification, posttranslational processing, sequence annotation, sequence database, tandem mass spectrometry. Abstract: Amino acid sequence database is one of the essential components in the current proteomics with mass spectrometry. Protein identification routine as well as posttranslational modification analysis is based on correlation between the mass spectrometry data of peptides obtained from proteome and the entry sequences in the database. While different sequence databases are available from public resources for the correlation search, these primary sequence data can be ...
Like other DNA viruses, herpes simplex virus type 1 (HSV-1) replicates and proliferates in host cells continuously modulating the host molecular environment. Following a sophisticated temporal expression pattern, HSV-1 encodes at least 89 multifunctional proteins that interplay with and modify the host cell proteome. During the last decade, advances in mass spectrometry applications coupled to the development of proteomic separation methods have allowed to partially monitor the impact of HSV-1 infection in human cells. In this review, we discuss the current use of different proteome fractionation strategies to define HSV-1 targets in two major application areas: (i) viral-protein interactomics to decipher viral-protein interactions in host cells and (ii) differential quantitative proteomics to analyze the virally induced changes in the cellular proteome. Moreover, we will also discuss the potential application of high-throughput proteomic approaches to study global proteome dynamics and also post
2017 The Author(s). Rhizoctonia solani is a fungal pathogen causing substantial damage to many of the worlds largest food crops including wheat, rice, maize and soybean. Despite impacting global food security, little is known about the pathogenicity mechanisms employed by R. solani. To enable prediction of effectors possessing either broad efficacy or host specificity, a combined secretome was constructed from a monocot specific isolate, a dicot specific isolate and broad host range isolate infecting both monocot and dicot hosts. Secretome analysis suggested R. solani employs largely different virulence mechanisms to well-studied pathogens, despite in many instances infecting the same host plants. Furthermore, the secretome of the broad host range AG8 isolate may be shaped by maintaining functions for saprophytic life stages while minimising opportunities for host plant recognition. Analysis of possible co-evolution with host plants and in-planta up-regulation in particular, aided ...
TY - JOUR. T1 - Rapid identification of monospecific monoclonal antibodies using a human proteome microarray.. AU - Jeong, Jun Seop. AU - Jiang, Lizhi. AU - Albino, Edisa. AU - Marrero, Josean. AU - Rho, Hee Sool. AU - Hu, Jianfei. AU - Hu, Shaohui. AU - Vera, Carlos. AU - Bayron-Poueymiroy, Diane. AU - Rivera-Pacheco, Zully Ann. AU - Ramos, Leonardo. AU - Torres-Castro, Cecil. AU - Qian, Jiang. AU - Bonaventura, Joseph. AU - Boeke, Jef D.. AU - Yap, Wendy Y.. AU - Pino, Ignacio. AU - Eichinger, Daniel J.. AU - Zhu, Heng. AU - Blackshaw, Seth. PY - 2012/6. Y1 - 2012/6. N2 - To broaden the range of tools available for proteomic research, we generated a library of 16,368 unique full-length human ORFs that are expressible as N-terminal GST-His(6) fusion proteins. Following expression in yeast, these proteins were then individually purified and used to construct a human proteome microarray. To demonstrate the usefulness of this reagent, we developed a streamlined strategy for the production of ...
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
The Human Cell chapters provide a knowledge-based analysis of the human cellular proteomes and an entry into the Human Protein Atlas from different perspectives. The Cell Atlas can be explored on the basis of the transcriptomes of a large panel of human cell lines. This includes the classification of genes with variable and stable expression across the panel. Furthermore, various spatiotemporal aspects of the human proteome can be explored, such as the organelle proteomes, the multilocalizing proteome and the proteome showing single-cell variation. The human proteome can further be explored based on the expression in different organelles and cellular structures. This enables the definition of organelle proteomes that indicates the distinct organelle structures and functions. Each separate chapter includes a description of a particular proteome and explorations of protein expression patterns, a complete list of proteins that build a proteome, as well as examples of detailed images ...
Carboxylate efflux from roots is a crucial and differential response of soybean genotypes to low phosphorus (P) stress. Exudation of carboxylic acids including oxalate, citrate, succinate and fumarate was induced under low P stress, particularly in P-efficient soybean genotypes. Enhancement of root length, surface area and volume further improved P acquisition under low P stress. To understand the molecular basis of carboxylate efflux under low P stress, the root proteome of contrasting genotypes (P-efficient: EC-232019 and P-inefficient: EC-113396) was compared. Among a total of 325 spots, 105 (32%) were differentially abundant proteins (DAPs) between sufficient (250 µM) and low P (4 µM) levels. Abundance of 44 (14%) proteins decreased by more than two-fold under low P stress, while 61 (19%) proteins increased by more than two-fold. Protein identification and annotation revealed that the DAPs were involved in a myriad of functions including carboxylic acid synthesis, carbohydrate, protein and lipid
In line with the aims of the Chromosome-centric Human Proteome Project (C-HPP) to completely annotate proteins of each chromosome and biology/disease driven HPP (B/D-HPP) to decipher their relation to diseases, we have generated a nonredundant catalogue of protein-coding genes for Chromosome 12 (Chr …
Our study showed for the first time the effect of the long term consumption of four dietary models, providing different quantity and quality of dietary lipids, on the whole proteome of peripheral blood mononuclear cells (PBMC) from patients with MetS. In this study, we analyzed separately the changes induced in the nuclear and cytoplasmic proteome after the long-term consumption of a high saturated fatty acid diet (HSFA), a high monounsaturated fatty acids-rich diet (HMUFA), a low-fat high carbohydrates diet (LFHCC) and a low-fat high carbohydrates diet supplemented with n-3 fatty acids (LFHCC n-3).. The proteins responding to the quantity and quality of dietary lipids identified in our study showed that dietary lipids regulate different biomechanisms directly involved in the etiology of MetS. This idea is supported by the relationship found between MetS parameters, mainly in changes in the TAG and glucose levels and several changes in the proteome. Long-term consumption of an HSFA diet leads to ...
The proteomic analysis of human blood and blood-derived products (e.g., plasma) offers an attractive avenue to translate research progress from the laboratory into the clinic. However, due to its unique protein composition, performing proteomics assays with plasma is challenging. Plasma proteomics has regained interest due to recent technological advances, but challenges imposed by both complications inherent to studying human biology (e.g., interindividual variability) and analysis of biospecimens (e.g., sample variability), as well as technological limitations remain. As part of the Human Proteome Project (HPP), the Human Plasma Proteome Project (HPPP) brings together key aspects of the plasma proteomics pipeline. Here, we provide considerations and recommendations concerning study design, plasma collection, quality metrics, plasma processing workflows, mass spectrometry (MS) data acquisition, data processing, and bioinformatic analysis. With exciting opportunities in studying human health and disease
Compartmentalization is a unique feature of eukaryotes that helps in maintaining cellular homeostasis not only in intra- and inter-organellar context, but also between the cells and the external environment. Plant cells are highly compartmentalized with a complex metabolic network governing various cellular events. The membranes are the most important constituents in such compartmentalization, and membrane-associated proteins play diverse roles in many cellular processes besides being part of integral component of many signaling cascades. To obtain valuable insight into the dynamic repertoire of membrane proteins, we have developed a proteome reference map of a grain legume, chickpea, using two-dimensional gel electrophoresis. MALDI-TOF/TOF and LC-ESI-MS/MS analysis led to the identification of 91 proteins involved in a variety of cellular functions viz., bioenergy, stress-responsive and signal transduction, metabolism, protein synthesis and degradation, among others. Significantly, 70% of the
A bottom-up label-free mass spectrometric proteomic strategy was used to analyse the protein profiles of the human embryonic secretome. Culture media samples used for embryonic culture of patients undergoing intracytoplasmic sperm injection cycles were selected as a test case for this exploratory proof-of-principle study. The media were stored after embryo transfer and then pooled into positive (n = 8) and negative (n = 8) implantation groups. The absolute quantitative bottom-up technique employed a multidimensional protein identification technology based on separation by nano-ultra-high pressure chromatography and identification via tandem nano-electrospray ionization mass spectrometry with data-independent scanning in a hydrid QqTOF mass spectrometer. By applying quantitative bottom-up proteomics, unique proteins were found exclusively in both the positive- and negative-implantation groups, which suggest that competent embryos express and secrete unique biomarker proteins into the surrounding ...
Enhanced qualitative and quantitative proteomic analysis using pSMART combines data dependent and data independent acquisition for improved results.
The small intestine is an important human organ that plays a central role in many physiological functions including digestion, absorption, secretion and defense. Duodenal pathologies include, for instance, the ulcer associated to Helicobacter Pylori infection, adenoma and, in genetically predisposed individuals, celiac disease. Alterations in the bowel reduce its capability to absorb nutrients, minerals and fat-soluble vitamins. Anemia and osteopenia or osteoporosis may develop as a consequence of vitamins malabsorption. Adenoma is a benign tumor that has the potential to become cancerous. Adult celiac disease patients present an overall risk of cancer that is almost twice than that found in the general population. These disease processes are not completely known. To date, a two dimensional (2D) reference map of proteins expressed in human duodenal tissue is not yet available: the aim of our study was to characterize the 2D protein map, and to identify proteins of duodenal mucosa of adult individuals
The nucleolus is the cellular organelle that manufactures ribosomes and plays a part in many vital process including cell-cycle regulation and senescence. Using the latest proteomics technologies, Andersen et al. have generated a comprehensive list of nucleolar proteins. Over 690 proteins were found in the in the nucleolar preparation, including Werners syndrome helicase and various regulatory proteins. The technology also allows analysis of changes in relative levels of proteins as a result of perturbing growth conditions with drugs. This paints a picture of a dynamic proteome: in effect there may be no definitive proteome for the nucleolus or any other organelle, rather there is a series of overlapping proteomes corresponding to different cell states. The nucleolus is a key organelle that coordinates the synthesis and assembly of ribosomal subunits and forms in the nucleus around the repeated ribosomal gene clusters. Because the production of ribosomes is a major metabolic activity, the function of
Mass spectrometry (MS) - based proteomics allows the sensitive and accurate quantification of almost complete proteomes of complex biological fluids and tissues. At the moment, however, the routinely usage of MS-based proteomics is prevented and complicated by the very complex work flow comprising sample preparation, chromatography, MS measurement followed by data processing and evaluation. The new technologies, products and assays developed by Precision Proteomics could help enabling and establishing mass spectrometry (MS) - based proteomics in academic and pharmaceutical proteomics research as well as in clinical diagnostics.. ...
Fernandes, I., et al. Secretome Analysis Identifies Potential Virulence Factors of Diplodia corticola, a Fungal Pathogen Involved in Cork Oak (Quercus suber) Decline. Fungal Biotechnology. (118) 5-6, 516-523. 18/05/2014.. ...
TY - JOUR. T1 - Serological immunoreactivity against colon cancer proteome varies upon disease progression. AU - De Monte, Lucia. AU - Sanvito, Francesca. AU - Olivieri, Stefano. AU - Viganò, Fiammetta. AU - Doglioni, Claudio. AU - Frasson, Matteo. AU - Braga, Marco. AU - Bachi, Angela. AU - Dellabona, Paolo. AU - Protti, Maria Pia. AU - Alessio, Massimo. PY - 2008/2. Y1 - 2008/2. N2 - Sera from colon carcinoma patients were used to identify tumor-associated antigens (TAAs) by screening tumor proteome resolved by 2D electrophoresis. A panel of six TAAs eliciting a serological immune response in colorectal cancer was identified, showing a modification in antigen recognition by B cells in patients as a function of colon cancer progression. The expression of these proteins was either confined or increased in tumor as compared to normal mucosa.. AB - Sera from colon carcinoma patients were used to identify tumor-associated antigens (TAAs) by screening tumor proteome resolved by 2D electrophoresis. ...
Citation. Pieper, R., Gatlin, C. L., Makusky, A. J., Russo, P. S., Schatz, C. R., Miller, S. S., Su, Q., McGrath, A. M., Estock, M. A., Parmar, P. P., Zhao, M., Huang, S. T., Zhou, J., Wang, F., Esquer-Blasco, R., Anderson, N. L., Taylor, J., Steiner, S.. The Human Serum Proteome: Display of Nearly 3700 Chromatographically Separated Protein Spots on Two-dimensional Electrophoresis Gels and Identification of 325 Distinct Proteins. Proteomics. 2003 Jul 01; 3(7): 1345-64.. PubMed Citation. Abstract. Plasma, the soluble component of the human blood, is believed to harbor thousands of distinct proteins, which originate from a variety of cells and tissues through either active secretion or leakage from blood cells or tissues. The dynamic range of plasma protein concentrations comprises at least nine orders of magnitude. Proteins involved in coagulation, immune defense, small molecule transport, and protease inhibition, many of them present in high abundance in this body fluid, have been functionally ...
Adaptation, Physiological; Animals; Cattle; Electrophoresis, Gel, Two-Dimensional; Energy Metabolism; Female; Gene Expression; Genotype; Mastitis, Bovine; Plant Proteins; Protein Interaction Maps; Proteome; Proteomics; Prototheca; Signal Transduction ...
Hypothesis:. Differences in the proteome concerning cell death pathways of glaucoma patients correspond to the differences in the mRNA expression of these patients.. Specific aims:. Characterization of the cellular proteome from human leukocytes of glaucoma patients compared to healthy controls and patients with Parkinsons disease.. Background:. Glaucoma is a worldwide leading cause of blindness. The key feature of this ocular neuropathy is characterized by an excavating optic nerve head. Loss of retinal ganglion cells is the final end point in blinding diseases of the optic nerve such as glaucoma. It is known that neuronal cell death in glaucoma occurs by an apoptotic mechanism. In earlier studies we could demonstrate that this cell death is reflected in circulating leukocytes by different parameters, like differential mRNA expression, and an increased fragmentation of the DNA. The differences in mRNA expression indicate a close relationship to cellular stress conditions and apoptotic events: ...
The focus of this article is to review the recent advances in proteome analysis of human body fluids, including plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, and amniotic fluid, as well as its applications to human …
Plasma biomarkers that reflect molecular states of the cardiovascular system are central for clinical decision making. Routinely used plasma biomarkers include troponins, natriuretic peptides, and lipoprotein particles, yet interrogate only a modest subset of pathways relevant to cardiovascular disease. Systematic profiling of a larger portion of circulating plasma proteins (the plasma proteome) will provide opportunities for unbiased discovery of novel markers to improve diagnostic or predictive accuracy. In addition, proteomic profiling may inform pathophysiological understanding and point to novel therapeutic targets. Obstacles for comprehensive proteomic profiling include the immense size and structural heterogeneity of the proteome, and the broad range of abundance levels, as well. Proteome-wide, untargeted profiling can be performed in tissues and cells with tandem mass spectrometry. However, applications to plasma are limited by the need for complex preanalytical sample preparation stages ...
Daphnia pulex (Water flea) is the first fully sequenced crustacean genome. The crustaceans and insects have diverged from a common ancestor. It is a model organism for studying the molecular makeup for coping with the environmental challenges. In the complete proteome, there are 30,550 putative proteins. However, about 10,000 of them have no known homologues. Currently, the UniProtoKB reports on 95% of the Daphnias proteins as putative and uncharacterized proteins. We have applied ProtoNet, an unsupervised hierarchical protein clustering method that covers about 10 million sequences, for automatic annotation of the Daphnias proteome. 98.7% (26,625) of the Daphnia full-length proteins were successfully mapped to 13,880 ProtoNet stable clusters, and only 1.3% remained unmapped. We compared the properties of the Daphnias protein families with those of the mouse and the fruitfly proteomes. Functional annotations were successfully assigned for 86% of the proteins. Most proteins (61%) were mapped to only
78069 avhandlingar från svenska högskolor och universitet. Avhandling: Advancing bioinformatics methods for in-depth proteome analysis based on high-resolution mass spectrometry.
Scientists at the Center for Proteome Analysis (CPA) in Odense, Denmark, have identified a natural protein that seems to protect the bodys insulin-producing beta cells from attack. Their approach is to analyze the thousands of gene products in cells and tissues, with special interest in galectin, a small protein that is vital in insulin dependent diabetes mellitus (IDDM). Every cell, no matter what tissue its in, carries the same full set of genetic information, the species genome. Now that genomic information is pouring in at a breathtaking pace, scientists are rushing to understand which proteins a particular type of cell synthesizes, how much the cell synthesizes, how cells modify proteins after synthesis and how all those proteins interact. This is the new science of proteomics. Among the first to realize the potential of proteomics, biologists Peter Mose Larsen and Stephen Fey founded CPA in 1997. And even today, when proteome centers are sprouting up everywhere, this research compound, ...
A wide range of state-of-the-art proteomics experiments are possible. These include, but are not limited, to intact mass determination, post-translational modification analysis, protein identification, and targeted (e.g. co-immunoprecipitation) or comprehensive (e.g. protein expression profiling) proteome analysis. Proteome analysis may employ a number of different isotope-labeling strategies enabling quantitative measurements on our high resolution discovery platforms (Orbitrap-Elite and Q-Exactive HF mass spectrometers) for deep proteome coverage or multiplexed targeted quantification on our triple quadrupole mass spectrometer (Xevo-TQS). Unique among regional cores is our ability to quantitatively analyze proteomes, phosphoproteomes, ubiquitylomes, and lysine acetylomes at a deep level through a process of serial enrichment. Under development are refinements of statistical and bioinformatic analyses of proteomic results. It is also possible to tailor sensitive and specific methods for ...
Lung cancer is the most common cause of cancer-related death worldwide, less than 7% of patients survive 10 years following diagnosis across all stages of lung cancer. Late stage of diagnosis and lack of effective and personalized medicine reflect the need for a better understanding of the mechanisms that underlie lung cancer progression. Quantitative proteomics provides the relative different protein abundance in normal and cancer patients which offers the information for molecular interactions, signaling pathways, and biomarker identification. Here we introduce both theoretical and practical applications in the use of quantitative proteomics approaches, with principles of current technologies and methodologies including gel-based, label free, stable isotope labeling as well as targeted proteomics. Predictive markers of drug resistance, candidate biomarkers for diagnosis, and prognostic markers in lung cancer have also been discovered and analyzed by quantitative proteomic analysis. Moreover,
Aspergillus fumigatus is a ubiquitously distributed filamentous fungus that has emerged as one of the most serious life-threatening pathogens in immunocompromised patients. The mechanisms for its pathogenicity are poorly understood. Here, we analyzed the proteome of dormant A. fumigatus conidia as the fungal entity having the initial contact with the host. Applying two-dimensional polyacrylamide gel electrophoresis (2-D PAGE), we established a 2-D reference map of conidial proteins. By MALDI-TOF mass spectrometry, we identified a total number of 449 different proteins. We show that 57 proteins of our map are over-represented in resting conidia compared to mycelium. Enzymes involved in reactive oxygen intermediates (ROI) detoxification, pigment biosynthesis, and conidial rodlet layer formation were highly abundant in A. fumigatus spores and most probably account for their enormous stress resistance. Interestingly, pyruvate decarboxylase and alcohol dehydrogenase were detectable in dormant ...
Source: Journal of Proteome Research - August 20, 2018 Category: Biochemistry Authors: Heeyoun Hwang, Ji Eun Jeong, Hyun Kyoung Lee, Ki Na Yun, Hyun Joo An, Bonghee Lee, Young-Ki Paik, Tae Seok Jeong, Gi Taek Yee, Jin Young Kim, Jong Shin Yoo Source Type: research. [ASAP] Transcriptional and Proteomic Analysis Revealed a Synergistic Effect of Aflatoxin M1 and Ochratoxin A Mycotoxins on the Intestinal Epithelial Integrity of Differentiated Human Caco-2 Cells ...
Background: Selection of patients to receive a primary prevention ICD is solely based on LV EF. Plasma biomarkers may compliment this but most have not been evaluated in predicting arrhythmic death. We determined whether plasma proteomic profiling could afford an unbiased, discovery based approach to identify novel biomarkers to predict cause specific event rates from SCA (arrhythmic death or defibrillation for VT/VF).. Methods: Plasma samples were obtained at entry in 203 patients in the PAREPET study. Proteomic profiling was performed in a subset of 10 patients with SCA vs. 10 survivors matched for EF (26%), age (66 years) and creatinine (1.4). We used a tandem affinity depletion method (IgY14-SuperMix) to reduce high- and medium- abundance plasma proteins, followed by extensive ion current based biomarker discovery. Plasma proteins were expressed as SCA/survivors.. Results: SCA developed 1016±735 days after sampling. Stringent cutoff criteria (0.3% peptide identification FDR ; ≥2 unique ...
NEW YORK (GenomeWeb) - A group from the Spanish National Cancer Research Centre has published a critique raising questions about two recent studies in which researchers generated the first relatively comprehensive maps of the human proteome.
PubMed comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.