Abundance Proteins (abundance + protein)

Distribution by Scientific Domains

Kinds of Abundance Proteins

  • low abundance protein

  • Selected Abstracts

    Beyond chloride transport: CFTR in the 21st century,introductory remarks to a new state of the art series

    Anil Mehta MB, FRCP (Edin), FRCPCH
    This new series of articles on cystic fibrosis provides an overview of the confusing plethora of problems that arise from the loss of function in a low abundance protein, the cystic fibrosis membrane conductance regulator CFTR. The references are designed to take the clinical reader into areas and journals that they might not normally read. In particular we have concentrated on recent advances that suggest CFTR has functions that do not relate to chloride transport alone. In forthcoming issues of the journal the topics covered range from prospects and difficulties in the translation of new therapies into clinical practice, the regulation of the defective gene (promoters, enhancers, silencers, etc.), regulation and interaction of the CFTR protein product with other proteins in the cell, to functional approaches using developmental and secretory paradigms. These themes have been chosen to bring controversies at the cutting edge of cystic fibrosis research to the practicing pulmonologist in order to stimulate lateral thinking, which we hope will ultimately benefit our patients. Pediatr Pulmonol. 2005; 39:289,291. © 2004 Wiley-Liss, Inc. [source]

    Cover Picture: Electrophoresis 16'2010

    ELECTROPHORESIS, Issue 16 2010
    Article first published online: 19 AUG 2010
    Issue no. 16 is a regular issue with an Emphasis on "Proteins and Proteomics" comprising 20 manuscripts distributed over 4 separate parts. Part I has 7 research articles on various aspects of proteins and proteomics including combinatorial peptide ligand library for accessing low abundance proteins, analysis of membrane proteins, proteomic profiling of human colon cancer cells, quantitative determinations of biomarkers in clinical diagnostics, recombinant factor VIII, analysis of E. coli soluble proteins, and a weakly basic amino-reactive fluorescent label for IEF of proteins and chip electrophoresis. Part II has 2 research articles dealing with the CE analysis of magnetic nanoparticles and a microfluidic magnetic bead impact for cell stimulation. Part III consists of 2 research articles dealing with on-line preconcentration in CE. Instrumentation, devices and various methodologies are described in 9 research articles, which make the content of Part IV. Featured articles include: Combinatorial peptide ligand library plasma treatment: Advantages for accessing low-abundance proteins ((doi: 10.1002/elps.201000188)) Precautions to improve the accuracy of quantitative determinations of biomarkers in clinical diagnostics ((doi: 10.1002/elps.201000243)) Rapid identification of Candida albicans in blood by combined capillary electrophoresis and fluorescence in situ hybridization ((doi: 10.1002/elps.201000138)) [source]

    Cover Picture: Electrophoresis 3'2010

    ELECTROPHORESIS, Issue 3 2010
    Article first published online: 29 JAN 2010
    Issue no. 3 is a regular issue with Emphasis on "Proteins and Proteomics". The first part has 8 articles on proteins and proteomics covering various topics, e.g. preparative divergent flow IEF, multichannel gel electrophoresis, capillary gel electrophoresis, nanoparticle-based CE of proteins, 2-DE in a radial gel format, depletion of high abundance proteins, and proteomic investigation of fetal brain and lentil seed. The remaining 10 articles are concerned with nucleic acids, gene expression, methodologies and application. Featured articles include: Preparative divergent flow IEF without carrier ampholytes for separation of complex biological samples ((10.1002/elps.200900484)) SDS-PAGE and two-dimensional maps in a radial gel format ((10.1002/elps.200900526)) Analysis of Effect of Electrolyte Types on Electrokinetic Energy Conversion in Nanoscale Capillaries ((10.1002/elps.200900409)) A simple method to determine the surface charge in microfluidic channels ((10.1002/elps.200900603)) [source]

    Cover Picture: Electrophoresis 21'2008

    ELECTROPHORESIS, Issue 21 2008
    Article first published online: 14 NOV 200
    This issue has an emphasis on "Proteomics and Related Topics". It comprises 11 research articles including the "Fast Track" article on the topic of proteomics, glycoproteomics, proteins and peptides. The "Fast Track" article describes a CE-LIF detection-based assay for the simultaneous measurements of the electrophoretic mobility, catalytic activity and the variation of activity over time of the individual enzymes molecules of Escherichia coli beta-galactosidase. The remaining 10 research articles of the Emphasis deal with the development of sensitive fluorescent staining for proteomic analysis, depletion of high abundance proteins form human serum, lectin affinity chromatography in the identification of rat urinary glycoproteome, lab-on-chip screening strategy of mouse serum samples prior to proteomics analysis, identification of proteins from membrane preparations, capillary coating for CE of proteins, characterization of rabbit liver apothioneins by CE-ESI-MS, quantitative analysis of recombinant protein charge heterogeneity by imaging CIEF, dye staining and immunodetection of proteins on a PVDF membrane, and separation of multiphosphorylated peptide isomers by CZE. [source]

    Utilizing a library of synthetic affinity ligands for the enrichment, depletion and one-step purification of leech proteins

    Dexian Dong
    Abstract Although the concept of affinity purification using synthetic ligands had been utilized for many years, there are few articles related to this research area, and they focus only on the affinity purification of specific protein by a defined library of synthetic ligands. This study presents the design and construction of a 700-member library of synthetic ligands in detail. We selected 297 ligand columns from a 700-member library of synthetic ligands to screen leech protein extract. Of the 297, 154 columns had an enrichment effect, 83 columns had a depletion effect, 36 columns had a one-step purification effect, and 58 columns had a one-step purification via flowthrough effect. The experimental results achieved by this large library of affinity ligands provide solid convincing data for the theory that affinity chromatography could be used for the enrichment of proteins that are present in low abundance, the depletion of high abundance proteins, and one-step purification of special proteins. Copyright © 2008 John Wiley & Sons, Ltd. [source]

    Extensive fractionation and identification of proteins within nasal lavage fluids from allergic rhinitis and asthmatic chronic rhinosinusitis patients

    Linda M. Benson
    Abstract Allergic rhinitis (AR), chronic rhinosinusitis (CRS), and asthma are prevalent airway diseases that can have a substantial impact on a patient's quality of life. MS analyses of biological fluids can effectively screen for proteins associated with disease processes, however, initial detection of diagnostic proteins is difficult due to protein complexity and dynamic range. To enhance the detection of lower abundance proteins, intact nasal lavage fluid (NLF) proteins from nonpolypoid AR and from asthmatic CRS patients were extensively fractionated prior to LC/MS/MS analysis. Pooled NLF samples were processed to remove low molecular weight molecules and high abundance plasma proteins. Anion exchange (AX) chromatography followed by RP-LC further separated the remaining intact NLF proteins. The resulting fractions were digested with trypsin and the peptides analyzed by LC/MS/MS. Spectra were searched with MASCOT, SEQUEST, and X!Tandem to obtain peptide identifications and subsequently analyzed by Scaffold software to identify parent proteins with at least 99% confidence. The 197 identified proteins are compared to those previously cited in the literature and the workflow evaluated to determine the usefulness for the detection of lower abundance proteins. This is the first extensive list of NLF proteins generated from CRS patients with coexisting asthma. [source]

    Analysis of nuclear proteome in C57 mouse liver tissue by a nano-flow 2-D-LC,ESI-MS/MS approach

    Jie Zhang
    Abstract The analysis of whole cell or tissue extracts is too complex for current protein identification technology and not suitable for the study of proteins with low copy levels. To concentrate and enrich low abundance proteins, organelle proteomics is a promising strategy. This approach can not only reduce the protein sample complexity but also provide information about protein location in cells, organs, or tissues under analysis. Nano-flow two-dimensional strong-cation exchange chromatography (SCX),RPLC,ESI-MS/MS is an ideal platform for analyzing organelle extracts because of its advantages of sample non-bias, low amounts of sample required, powerful separation capability, and high detection sensitivity. In this study, we apply nano-scale multidimensional protein identification technology to the analysis of C57 mouse liver nuclear proteins. Organelle isolation has been optimized to obtain highly pure nuclei. Evaluation of nucleus integrity and purity has been performed to demonstrate the effectiveness of the optimized isolation procedure. The extracted nuclear proteins were identified by five independent nano-flow on-line SCX,RPLC,ESI-MS/MS analyses to improve the proteome coverage. Finally, a total of 462 proteins were identified. Corresponding analyses of protein molecular mass and pI distribution and biological function categorization have been undertaken to further validate our identification strategy. [source]

    Combining subproteome enrichment and Rubisco depletion enables identification of low abundance proteins differentially regulated during plant defense

    Ivy Widjaja
    Abstract Transgenic Arabidopsis conditionally expressing the bacterial avrRpm1 type III effector under the control of a dexamethasone-responsive promoter were used for proteomics studies. This model system permits study of an individual effector without interference from additional bacterial components. Coupling of different prefractionation approaches to high resolution 2-DE facilitated the discovery of low abundance proteins , enabling the identification of proteins that have escaped detection in similar experiments. A total of 34 differentially regulated protein spots were identified. Four of these (a remorin, a protein phosphatase 2C (PP2C), an RNA-binding protein, and a C2-domain-containing protein) are potentially early signaling components in the interaction between AvrRpm1 and the cognate disease resistance gene product, resistance to Pseudomonas syringae pv. maculicola 1 (RPM1). For the remorin and RNA-binding protein, involvement of PTM and post-transcriptional regulation are implicated, respectively. [source]

    Quantification of change in phosphorylation of BCR-ABL kinase and its substrates in response to Imatinib treatment in human chronic myelogenous leukemia cells

    Xiquan Liang Dr.
    Abstract Phosphorylation by the constitutively activated BCR-ABL tyrosine kinase is associated with the pathogenesis of the human chronic myelogenous leukemia,(CML). It is difficult to characterize kinase response to stimuli or drug treatment because regulatory phosphorylation events are largely transient changes affecting low abundance proteins. Stable isotope labeling with amino acids in cell culture,(SILAC) has emerged as a pivotal technology for quantitative proteomics. By metabolically labeling proteins with light or heavy tyrosine, we are able to quantify the change in phosphorylation of BCR-ABL kinase and its substrates in response to drug treatment in human CML cells. In this study, we observed that BCR-ABL kinase is phosphorylated at tyrosines,393 and 644, and that SH2-domain containing inositol phosphatase (SHIP)-2 and downstream of kinase (Dok)-2 are phosphorylated at tyrosine,1135 and 299, respectively. Based on the relative intensity of isotopic peptide pairs, we demonstrate that the level of phosphorylation of BCR-ABL kinase as well as SHIP-2 and Dok-2 is reduced approximately 90% upon treatment with Imatinib, a specific inhibitor of BCR-ABL kinase. Furthermore, proteins, such as SHIP-1, SH2-containing protein (SHC) and Casitas B-lineage lymphoma proto-oncogene (CBL), are also regulated by Imatinib. These results demonstrate the simplicity and utility of SILAC as a method to quantify dynamic changes in phosphorylation at specific sites in response to stimuli or drug treatment in cell culture. [source]

    Albumin depletion of human plasma also removes low abundance proteins including the cytokines

    Jill Granger
    Abstract The use of proteomics for efficient, accurate, and complete analysis of clinical samples poses a variety of technical challenges. The presence of higher abundance proteins in the plasma, such as albumin, may mask the detection of lower abundance proteins such as the cytokines. Methods have been proposed to deplete the sample of these higher abundance proteins to facilitate detection of those with lower abundance. In this study, a commercially available albumin depletion kit was used to determine if removal of albumin would measurably reduce detection of lower abundance cytokine proteins in human plasma. The Montage® Albumin Deplete Kit (Millipore) was used to deplete albumin from LPS-stimulated whole blood from 15 normal human donors. Albumin depletion was measured using the BCG reagent and SDS-PAGE, and cytokine recovery was determined by a microassay immunoassay that measures both pro- and anti-inflammatory cytokines. Average albumin depletion from the samples was 72%. However, several cytokines were also significantly reduced when the albumin was removed from the plasma. Additionally, there was a variable reduction in cytokine recovery from a known mixture of cytokines in a minimal amount of plasma that were loaded onto the columns. These data demonstrate that there may be a non-specific loss of cytokines following albumin depletion, which may confound subsequent proteomic analysis. [source]

    Improved proteome coverage by using high efficiency cysteinyl peptide enrichment: The human mammary epithelial cell proteome

    Tao Liu
    Abstract Automated multidimensional capillary liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been increasingly applied in various large scale proteome profiling efforts. However, comprehensive global proteome analysis remains technically challenging due to issues associated with sample complexity and dynamic range of protein abundances, which is particularly apparent in mammalian biological systems. We report here the application of a high efficiency cysteinyl peptide enrichment (CPE) approach to the global proteome analysis of human mammary epithelial cells (HMECs) which significantly improved both sequence coverage of protein identifications and the overall proteome coverage. The cysteinyl peptides were specifically enriched by using a thiol-specific covalent resin, fractionated by strong cation exchange chromatography, and subsequently analyzed by reversed-phase capillary LC-MS/MS. An HMEC tryptic digest without CPE was also fractionated and analyzed under the same conditions for comparison. The combined analyses of HMEC tryptic digests with and without CPE resulted in a total of 14,416 confidently identified peptides covering 4294 different proteins with an estimated 10%,gene coverage of the human genome. By using the high efficiency CPE, an additional 1096 relatively low abundance proteins were identified, resulting in 34.3% increase in proteome coverage; 1390,proteins were observed with increased sequence coverage. Comparative protein distribution analyses revealed that the CPE method is not biased with regard to protein Mr,, pI, cellular location, or biological functions. These results demonstrate that the use of the CPE approach provides improved efficiency in comprehensive proteome-wide analyses of highly complex mammalian biological systems. [source]

    Mining biomarkers in human sera using proteomic tools

    Rulin Zhang
    Abstract One of the major difficulties in mining low abundance biomarkers from serum or plasma is due to the fact that a small number of proteins such as albumin, ,2-macroglobulin, transferrin, and immunoglobulins, may represent as much as 80% of the total serum protein. The large quantity of these proteins makes it difficult to identify low abundance proteins in serum using traditional 2-dimensional electrophoresis. We recently used a combination of multidimensional liquid chromatography and gel electrophoresis coupled to matrix-assisted laser desorption/ionization-quadrupole-time of flight and Ion Trap liquid chromatography-tandem mass spectrometry to identify protein markers in sera of Alzheimer's disease (AD), insulin resistance/type-2 diabetes (IR/D2), and congestive heart failure (CHF) patients. We identified 8 proteins that exhibit higher levels in control sera and 36 proteins that exhibit higher levels in disease sera. For example, haptoglobin and hemoglobin are elevated in sera of AD, IR/D2, and CHF patients. The levels of several other proteins including fibrinogen and its fragments, alpha 2-macroglobulin, transthyretin, pro-platelet basic protein, protease inhibitors clade A and C, as well as proteins involved in the classical complement pathway such as complement C3, C4, and C1 inhibitor, were found to differ between IR/D2 and control sera. The sera levels of proteins, such as the 10 kDa subunit of vitronectin, alpha 1-acid glycoprotein, apolipoprotein B100, fragment of factor H, and histidine-rich glycoprotein were observed to be different between AD and controls. The differences observed in these biomarker candidates were confirmed by Western blot and the enzyme-linked immunosorbent assay. The biological meaning of the proteomic changes in the disease states and the potential use of these changes as diagnostic tools or for therapeutic intervention will be discussed. [source]

    Proteomics and the lung: Analysis of bronchoalveolar lavage fluid

    Praveen Govender
    Abstract Our knowledge of the complex bronchoalveolar lavage fluid (BALF) proteome has increased significantly over the last decade; but still, there remain many aspects of the BALF proteome that need characterization. Current proteomic methodologies resolve proteins within limited dynamic ranges: thereby, being limited in their ability to examine important areas of the BALF proteome, such as low molecular weight, low abundance proteins. To ensure proper coverage of these proteins in the BALF proteome, a refined 2-DE standard operation protocol is presented, highlighting important issues in sample collection, sample preparation, and 2-D DIGE analysis. It is hoped that this will help advance the field of BALF proteomics, BALFomics, which has lagged behind similar biofluids such as plasma and serum. [source]

    Cysteine-reactive covalent capture tags for enrichment of cysteine-containing peptides

    Priscille Giron
    Considering the tremendous complexity and the wide dynamic range of protein samples from biological origin and their proteolytic peptide mixtures, proteomics largely requires simplification strategies. One common approach to reduce sample complexity is to target a particular amino acid in proteins or peptides, such as cysteine (Cys), with chemical tags in order to reduce the analysis to a subset of the whole proteome. The present work describes the synthesis and the use of two new cysteinyl tags, so-called cysteine-reactive covalent capture tags (C3T), for the isolation of Cys-containing peptides. These bifunctional molecules were specifically designed to react with cysteines through iodoacetyl and acryloyl moieties and permit efficient selection of the tagged peptides. To do so, a thioproline was chosen as the isolating group to form, after a deprotection/activation step, a thiazolidine with an aldehyde resin by the covalent capture (CC) method. The applicability of the enrichment strategy was demonstrated on small synthetic peptides as well as on peptides derived from digested proteins. Mass spectrometric (MS) analysis and tandem mass spectrometric (MS/MS) sequencing confirmed the efficient and straightforward selection of the cysteine-containing peptides. The combination of C3T and CC methods provides an effective alternative to reduce sample complexity and access low abundance proteins. Copyright © 2009 John Wiley & Sons, Ltd. [source]