Home About us Contact
|
Home About us Contact | ||
|
|
||
Serum Proteome (serum + proteome)
Selected AbstractsA 2-DE MALDI-TOF study to identify disease regulated serum proteins in lung cancer of c-myc transgenic micePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2009Bijon Chatterji Abstract We previously reported targeted overexpression of c-myc to alveolar epithelium to cause lung cancer. We now extended our studies to the serum proteome of tumor bearing mice. Proteins were extracted with a thiourea-containing lysis buffer and separated by 2-DE at pH,4,7 and 3,10 followed by MALDI-TOF/TOF analysis. Forty-six proteins were identified in tumor bearing mice of which n,=,9 were statistically significant. This included disease regulated expression of orosomucoid-8, ,-2-macroglobulin, apolipoprotein-A1, apolipoprotein-C3, glutathione peroxidase-3, plasma retinol-binding protein, and transthyretin, while expression of apolipoprotein-E was decreased at late stages of disease. Moreover, serum amyloid P component was uniquely expressed at late stages of cancer. It is of considerable importance that most disease regulated proteins carried the E-Box sequence (CACGTG) in the promoter of the coding gene, therefore providing evidence for their regulation by c-myc. Notably, expression of ,-2-macroglobulin, transthyretin, ,-1-antitrypsin, and properdin was in common in different lung tumor models, but regulation of orosomucoid-8, apolipoprotein-A1, apolipoprotein-C3, apolipoprotein-E, glutathione peroxidase-3, plasma retinol-binding protein, and serum amyloid P component was unique when the serum proteomes of c-myc and c-raf tumor bearing mice were compared. Therefore, candidate biomarkers to differentiate between atypical adenomatous hyperplasias (AAH) and bronchiolo-alveolar carcinomas (BAC)/papillary adenocarcinomas (PLAC) can be proposed. [source] Analysis of chicken serum proteome and differential protein expression during development in single-comb White Leghorn hensPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 7 2006San-Yuan Huang Abstract Serum is believed to harbor thousands of distinct proteins that are either actively secreted or leak from various blood cells or tissues. Exploring protein composition in serum may accelerate the discovery of novel protein biomarkers for specific economic traits in livestock species. This study analyzed serum protein composition to establish a 2-DE reference map, and monitored protein dynamics of single-comb White Leghorn hens at 8, 19 and 23,weeks after hatching. A total of 119,CBB-stained and 315,silver-stained serum protein spots were analyzed by MALDI-TOF,MS. Of these, 98,CBB-stained and 94,silver-stained protein spots were significantly matched to existing chicken proteins. The identified spots represented 30,distinctive proteins in the serum of laying hens. To compare protein expression during development, expression levels of 47,protein spots were quantified by relative spot volume with Melanie,3 software. Ten protein spots increased and 3,protein spots decreased as hen age increased. Previous research has suggested that some of these proteins play critical roles in egg production. The differentially expressed proteins with unknown identities will be valuable candidates for further explorations of their roles in egg production of laying hens. [source] Analysis of chicken serum proteome and differential protein expression during development in single-comb White Leghorn hensPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 7 2006San-Yuan Huang No abstracts. [source] Reference maps of mouse serum acute-phase proteins: Changes with LPS-induced inflammation and apolipoprotein,A-I and A-II transgenesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 16 2005Robin Wait Abstract We present reference maps of the mouse serum proteome (run under reducing and non-reducing conditions), from control animals, from mice injected with lipopolysaccharide (LPS) to induce systemic inflammation, and from mice transgenic for human apolipoproteins,A-I and A-II. Seventy-seven spots/spot chains from the reducing gels were identified by HPLC MS/MS, representing 28,distinct proteins, including a species-specific protease inhibitor, contrapsin, and high levels of carboxylesterase. The concentrations of acute-phase reactants were monitored for 96,h after LPS challenge. The greatest changes (four-fold 48,h after LPS administration) were observed for haptoglobin and hemopexin. Orosomucoid/,1 -acid glycoprotein and apolipoprotein,A-I increased steadily, to 50,60% above baseline at 96,h from stimulation. In mice transgenic for human apolipoprotein,A-I the levels of expression of orosomucoid/,1 -acid glycoprotein, ,1 -macroglobulin, esterase, kininogen and contrapsin were altered compared to knockout mice lacking apolipoprotein,A-I. In contrast, except for the presence of apolipoprotein,A-II, no statistically significant difference was observed in mice transgenic for human apolipoprotein,A-II. [source] Comparison of alternative analytical techniques for the characterisation of the human serum proteome in HUPO Plasma Proteome ProjectPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 13 2005Xiaohai Li Abstract Based on the same HUPO reference specimen (C1-serum) with the six proteins of highest abundance depleted by immunoaffinity chromatography, we have compared five proteomics approaches, which were (1) intact protein fractionation by anion-exchange chromatography followed by 2-DE-MALDI-TOF-MS/MS for protein identification (2-DE strategy); (2) intact protein fractionation by 2-D HPLC followed by tryptic digestion of each fraction and microcapillary RP-HPLC/microESI-MS/MS identification (protein 2-D HPLC fractionation strategy); (3) protein digestion followed by automated online microcapillary 2-D HPLC (strong cation-exchange chromatography (SCX)-RPC) with IT microESI-MS/MS; (online shotgun strategy); (4) same as (3) with the SCX step performed offline (offline shotgun strategy) and (5) same as (4) with the SCX fractions reanalysed by optimised nanoRP-HPLC-nanoESI-MS/MS (offline shotgun-nanospray strategy). All five approaches yielded complementary sets of protein identifications. The total number of unique proteins identified by each of these five approaches was (1) 78, (2) 179, (3) 131, (4) 224 and (5) 330 respectively. In all, 560 unique proteins were identified. One hundred and sixty-five proteins were identified through two or more peptides, which could be considered a high-confidence identification. Only 37 proteins were identified by all five approaches. The 2-DE approach yielded more information on the pI -altered isoforms of some serum proteins and the relative abundance of identified proteins. The protein prefractionation strategy slightly improved the capacity to detect proteins of lower abundance. Optimising the separation at the peptide level and improving the detection sensitivity of ESI-MS/MS were more effective than fractionation of intact proteins in increasing the total number of proteins identified. Overall, electrophoresis and chromatography, coupled respectively with MALDI-TOF/TOF-MS and ESI-MS/MS, identified complementary sets of serum proteins. [source] The human plasma proteome: Analysis of Chinese serum using shotgun strategyPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 13 2005Ping He Abstract We have investigated the serum proteome of Han-nationality Chinese by using shotgun strategy. A complete proteomics analysis was performed on two reference specimens from a total of 20,healthy donors, in which each sample was made from ten-pooled male or female serum, respectively. The methodology used encompassed (1),removal of six high-abundant proteins; (2),tryptic digestion of low- and high-abundant proteins of serum; (3),separation of peptide mixture by RP-HPLC followed by ESI-MS/MS identification. A total of 944,nonredundant proteins were identified under a stringent filter condition (Xcorr,,,1.9, ,2.2, and ,3.75, ,Cn,,,0.1, and Rsp,,,4.0) in both pooled male and female samples, in which 594 and 622,entire proteins were found, respectively. Compared with the total 3020 protein identifications confirmed by more than one laboratory or more than one specimen in HUPO Plasma Proteome Project (PPP) participating laboratories recently, 206,proteins were identified with at least two distinct peptides per protein and 185,proteins were considered as high-confidence identification. Moreover, some lower abundance serum proteins (ng/mL range) were detected, such as complement,C5 and CA125, routinely used as an ovarian cancer marker in plasma and serum. The resulting nonredundant list of serum proteins would add significant information to the knowledge base of human plasma proteome and facilitate disease markers discovery. [source] An integrated serum proteomic approach capable of monitoring the low molecular weight proteome with sequencing of intermediate to large peptidesRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 17 2009Karen Merrell The low-abundance, low molecular weight serum proteome has high potential for the discovery of new biomarkers using mass spectrometry (MS). Because the serum proteome is large and complex, defining relative quantitative differences for a molecular species between comparison groups requires an approach with robust separation capability, high sensitivity, as well as high mass resolution. Capillary liquid chromatography (cLC)/MS provides both the necessary separation technique and the sensitivity to observe many low-abundance peptides. Subsequent identification of potential serum peptide biomarkers observed in the cLC/MS step can in principle be accomplished by in series cLC/MS/MS without further sample preparation or additional instrumentation. In this report a novel cLC/MS/MS method for peptide sequencing is described that surpasses previously reported size limits for amino acid sequencing accomplished by collisional fragmentation using a tandem time-of-flight MS instrument. As a demonstration of the approach, two low-abundance peptides with masses of ,4000,5000,Da were selected for MS/MS sequencing. The multi-channel analyzer (MCA) was used in a novel way that allowed for summation of 120 fragmentation spectra for each of several customized collision energies, providing more thorough fragmentation coverage of each peptide with improved signal to noise. The peak list from this composite analysis was submitted to Mascot for identification. The two index peptides, 4279,Da and 5061,Da, were successfully identified. The peptides were a 39 amino acid immunoglobulin G heavy chain variable region fragment and a 47 amino acid fibrin alpha isoform C-terminal fragment. The method described here provides the ability both to survey thousands of serum molecules and to couple that with markedly enhanced cLC/MS/MS peptide sequencing capabilities, providing a promising technique for serum biomarker discovery. Copyright © 2009 John Wiley & Sons, Ltd. [source] Proteomics: Recent Applications and New TechnologiesBASIC AND CLINICAL PHARMACOLOGY & TOXICOLOGY, Issue 5 2006Mollisa M. Elrick Proteomic analyses have recently been conducted on tissues, biofluids, subcellular components and enzymatic pathways as well as various disease and toxicological states, in both animal models and man. In addition, several recent studies have attempted to integrate proteomics data with genomics and/or metabonomics data in a systems biology approach. The translation of proteomic technology and bioinformatics tools to clinical samples, such as in the areas of disease and toxicity biomarkers, represents one of the major opportunities and challenges facing this field. An ongoing challenge in proteomics continues to be the analysis of the serum proteome due to the vast number and complexity of proteins estimated to be present in this biofluid. Aside from the removal of the most abundant proteins, a number of interesting approaches have recently been suggested that may help reduce the overall complexity of serum analysis. In keeping with the increasing interest in applications of proteomics, the tools available for proteomic analyses continue to improve and expand. For example, enhanced tools (such as software and labeling procedures) continue to be developed for the analysis of 2D gels and protein quantification. In addition, activity-based probes are now being used to tag, enrich and isolate distinct sets of proteins based on enzymatic activity. One of the most active areas of development involves microarrays. Antibody-based microarrays have recently been released as commercial products while numerous additional capture agents (e.g. aptamers) and many additional types of microarrays are being explored. [source] A 2-DE MALDI-TOF study to identify disease regulated serum proteins in lung cancer of c-myc transgenic micePROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2009Bijon Chatterji Abstract We previously reported targeted overexpression of c-myc to alveolar epithelium to cause lung cancer. We now extended our studies to the serum proteome of tumor bearing mice. Proteins were extracted with a thiourea-containing lysis buffer and separated by 2-DE at pH,4,7 and 3,10 followed by MALDI-TOF/TOF analysis. Forty-six proteins were identified in tumor bearing mice of which n,=,9 were statistically significant. This included disease regulated expression of orosomucoid-8, ,-2-macroglobulin, apolipoprotein-A1, apolipoprotein-C3, glutathione peroxidase-3, plasma retinol-binding protein, and transthyretin, while expression of apolipoprotein-E was decreased at late stages of disease. Moreover, serum amyloid P component was uniquely expressed at late stages of cancer. It is of considerable importance that most disease regulated proteins carried the E-Box sequence (CACGTG) in the promoter of the coding gene, therefore providing evidence for their regulation by c-myc. Notably, expression of ,-2-macroglobulin, transthyretin, ,-1-antitrypsin, and properdin was in common in different lung tumor models, but regulation of orosomucoid-8, apolipoprotein-A1, apolipoprotein-C3, apolipoprotein-E, glutathione peroxidase-3, plasma retinol-binding protein, and serum amyloid P component was unique when the serum proteomes of c-myc and c-raf tumor bearing mice were compared. Therefore, candidate biomarkers to differentiate between atypical adenomatous hyperplasias (AAH) and bronchiolo-alveolar carcinomas (BAC)/papillary adenocarcinomas (PLAC) can be proposed. [source] Discovery of diagnostic serum biomarkers of gastric cancer using proteomicsPROTEOMICS - CLINICAL APPLICATIONS, Issue 2 2008Katie Wing-kei Lam Abstract Gastric cancer has significant morbidity and mortality worldwide and locally. Good prognosis relies on an early diagnosis. However, this remains a challenge due to the lack of specific and sensitive serum biomarkers for early detection. Hence, there is a constant search for these biomarkers for screening purposes. Proteomic profiling enables a new approach to the discovery of biomarkers in disease. This review presents recent attempts in search of gastric cancer serum biomarker using proteomics. Different methodologies and different types of samples were employed by different groups of researchers. Major difficulties were encountered in the discovery processes, including interference from abundant proteins and continuous changing serum proteomes from different individuals. [source] | ||||||||||