Showing papers in "Molecular & Cellular Proteomics in 2002"

TL;DR: SILAC is a simple, inexpensive, and accurate procedure that can be used as a quantitative proteomic approach in any cell culture system and is applied to the relative quantitation of changes in protein expression during the process of muscle cell differentiation.

TL;DR: The relationship between gene expression measured at the mRNA level and the corresponding protein level is not well characterized in human cancer, and it is shown that only a subset of the proteins exhibited a significant correlation with mRNA abundance.

TL;DR: This study has performed the most extensive analysis of serum proteins to date and laid the foundation for future refinements in the identification of novel protein biomarkers of disease.

TL;DR: EPR and PVM were applied to the Database of Interacting Proteins, a large and diverse collection of protein-protein interactions that contains over 8000 Saccharomyces cerevisiae pairwise protein interactions and estimate that ∼50% of them are reliable, and with the aid of PVM the authors identify confidently 3003 of them.

TL;DR: Insights into the perturbative effects on genes involved in respiration, energy generation, and protein synthesis were obtained that would not have been apparent from measurements made at either the messenger RNA or protein level alone, illustrating the power of integrating different types of data obtained from the same sample for the comprehensive characterization of biological systems and processes.

TL;DR: In this article, a comprehensive proteomic analysis of isolated ciliary axonemes was performed, which resulted in the identification of a subset of the proteins present in the axoneme.

TL;DR: This paper describes a mass spectrometry-based method for the identification of sites modified by O-GlcNAc that relies on mild β-elimination followed by Michael addition with dithiothreitol (BEMAD), and provides a strategy that uses modification-specific antibodies and enzymes to discriminate between the two post-translational modifications.

TL;DR: Stable isotope-labeled amino acids can be used to define the rate of breakdown of individual proteins by inspection of mass shifts in tryptic fragments and this approach has been applied to an analysis of abundant proteins in glucose-limited yeast cells grown in aerobic chemostat culture at steady state.

TL;DR: Several antibodies are described that recognize phosphoserine/phosphothreonine-containing proteins by Western blotting and can be used to enrich for proteins phosphorylated on serine/threonine residues by immunoprecipitation, as well.

TL;DR: Global quantification of protein expression between laser capture microdissection-microdissected patient-matched cancer cells and normal cells using 2D DIGE in combination with mass spectrometry is a powerful tool for the molecular characterization of cancer progression and identification of cancer-specific protein markers.

TL;DR: A functional proteomic methodology that makes use of chemically reactive fluorescent probes to profile and identify enzymes in complex mixtures by virtue of their catalytic activity, which allows the rapid identification of potential drug targets and small molecule lead compounds targeted to them.

TL;DR: SyproRuby staining was shown to be a highly sensitive and 2D difference gel electrophoresis-compatible method for post-electrophoretic visualization of proteins, which could then be picked and identified by matrix-assisted laser-desorption ionization mass spectroscopy.

TL;DR: This is the first study to identify several novel secreted proteins by adipocytes by a proteomic approach using mass spectrometry.

TL;DR: It is suggested that the CWP-chitin linkage is an important retention mechanism of CWPs in C. albicans mycelial forms and this approach is therefore a powerful tool for obtaining a comprehensive and integrated view of the cell wall proteome.

TL;DR: A novel gel-free proteomic technology was used to identify more than 800 proteins from 50 million Escherichia coli K12 cells in a single analysis, demonstrating the high dynamic range and the flexibility in the peptide sorting chemistry.

TL;DR: Two novel sequence similarity search algorithms, FASTS and FASTF, that use multiple short peptide sequences to identify homologous sequences in protein or DNA databases are described, allowing proteomic identification from organisms whose genomes have not been sequenced.

TL;DR: The results showed that there is a gene dosage effect that in some cases superimposes on other regulatory mechanisms and a good correlation between transcript alterations and protein levels is found.

TL;DR: This study describes how columns packed with immobilized pepsin can be used to reduce the digestion time and to provide an effective means for separating the pepin from the isotopically labeled fragments.

TL;DR: The plasma membranes of Synechocystis 6803, which can be completely purified by density centrifugation and polymer two-phase partitioning, have been found to be more complex than previously anticipated, i.e. they appear to be essential for assembly of the two photosystems.

TL;DR: The acetylation isoforms of histone H4 from butyrate-treated HeLa cells were separated by C4 reverse-phase high pressure liquid chromatography and by polyacrylamide gel electrophoresis and revealed that lysine 20 is di-methylated in all modified isoforms, as well as the non-acetylated isoform of H4.

TL;DR: Fluorescence resonance energy transfer is used to test the hypothesis that the cell surface interferon γ receptor chains are preassembled rather than associated by ligand and to assess the molecular changes on ligand binding.

TL;DR: A promising new class of proteomic strategies that utilizes synthetic chemistry to create tools and assays for the characterization of protein samples of high complexity are reviewed.

TL;DR: It is concluded that a distinct repertoire of autoantibodies is associated with HCC that may have utility in early diagnosis of HCC among high risk subjects with chronic hepatitis.

TL;DR: Highly active cytochrome b6f complexes from spinach and the cyanobacterium Mastigocladus laminosus have been analyzed by liquid chromatography with electrospray ionization mass spectrometry (LCMS+).

TL;DR: Intact mass proteomics of organellar subfractions and more highly purified protein complexes provides increasingly detailed insights into functional genomics of photosynthetic membranes.

TL;DR: An integrated and modular microsystem providing rapid analyses of trace-level tryptic digests for proteomics applications and affinity selection of target peptides prior to electrophoretic separation and mass spectrometry analyses on a quadrupole/time-of-flight instrument is described.

TL;DR: Results in this investigation proved the effectiveness of proteomic approaches for discovering new proteins of WSSV.

TL;DR: The yeast two-hybrid system can be used for the mapping of the interaction domains and the isolation of interaction-defective mutants, it would serve as a technical basis for the latter purpose, thereby playing another important role in the next phase of protein interactome research.

TL;DR: This simple method accurately quantifies changes in protein abundance even in cases in which multiple proteins migrate to the same gel coordinates, and is therefore expected to find wide application in proteomics research.

TL;DR: The identification of nitrotyrosine-containing proteins from rats maintained in the dark, under non-pathological conditions, provides the first evidence of a possible role for protein nitration in normal retinal physiology.