Showing papers in "Molecular & Cellular Proteomics in 2007"

TL;DR: The Paragon™ Algorithm, a novel database search engine for the identification of peptides from tandem mass spectrometry data, is presented and a comparison with Mascot is presented for a series of analogous searches to explore the relative impact of increasing search space.

TL;DR: A novel probabilistic metric is created that takes advantage of the high density of data, including both the presence and absence of individual associations, to provide a measure of the relative confidence of each potential protein-protein interaction and organized proteins into coherent multisubunit complexes using hierarchical clustering.

TL;DR: The development of quantitative, multiplexed assays for six proteins in plasma that achieve limits of quantitation in the 1–10 ng/ml range with percent coefficients of variation from 3 to 15% without immunoaffinity enrichment of either proteins or peptides is described.

TL;DR: This study presents the largest quantitative Arabidopsis phosphoproteomics data set to date and provides a new resource that can be used to gain novel insight into plant defense signal transduction and early defense response.

TL;DR: It is confirmed, by in vitro labeling and peptide mapping by mass spectrometry, that two previously known acetyltransferases, p300 and CREB-binding protein, could catalyze lysine propionylation and lysines butyrylation in histones.

TL;DR: A substituted Coomassie dye was substituted in the cathode buffer of blue native electrophoresis by non-colored mixtures of anionic and neutral detergents that imposed a charge shift on the membrane proteins to enhance their anodic migration and improved membrane protein solubility during electrophoreis.

TL;DR: The power of the Protein Standard Absolute Quantification methodology for accurate absolute quantification of biomarkers was demonstrated both on water and urine samples contaminated with Staphylococcus aureus superantigenic toxins as typical biomarkers of public health interest.

TL;DR: This is the first successful application of a single MOC-based approach to phosphopeptide enrichment from complex biological samples such as cell lysates, and the combined results provided 1646 uniqueosphopeptides.

TL;DR: A significantly enlarged number of bacterial proteins known to be phosphorylated on Ser/Thr/Tyr residues strongly supports the emerging view that protein phosphorylation is a general and fundamental regulatory process, not restricted only to eukaryotes, and opens the way for its detailed functional analysis in bacteria.

TL;DR: In this largest scale study of ETD to date, ETD continues to show great promise to propel the field of proteomics and, for small- to medium-sized peptides, is highly complementary to ion trap CAD.

TL;DR: The unprecedented sensitivity of the mass spectrometric analysis of minimally fractionated plasma samples is the result of the significantly reduced sample complexity of the isolated N-glycosites compared with whole plasma proteome digests and the selectivity of the MRM process.

TL;DR: M mammalian cilia is revealed to be several times more complex than the cilia of unicellular organisms and open novel avenues for studies of how cilia are built and maintained and how these processes are disrupted in human disease.

TL;DR: Induction of the acetate-phosphotransacetylase pathway for ATP production and a down-regulated tricarboxylic acid cycle indicated the activation of the Arc two-component system, which mediates adaptive responses to changing respiratory states.

TL;DR: A proteomics approach was developed to identify the protein components present in both the membrane and soluble fractions of the Arabidopsis cell vacuoles, and about 20% of the proteins identified were known previously to be associated with vacuolar activities.

TL;DR: This study demonstrates that this two step strategy, the development of high quality aptamer probes and then the identification of their target proteins, can be used to discover new disease related potential markers and thus enhance tumor diagnosis and therapy.

TL;DR: A large number of MSC secretory products that have the potential to act as paracrine modulators of tissue repair and replacement in diseases of the cardiovascular, hematopoietic, and skeletal tissues are identified.

TL;DR: A simple and highly selective strategy for purification of sialic acid-containing glycopeptides (the sialiome) from complex peptide mixtures is presented and the potential of this method in biomarker discovery is illustrated.

TL;DR: First results of externally induced phosphorylation changes of plasma membrane proteins in Arabidopsis are provided, providing a means for identification of fast responses to external stimuli in plants as a basis for further functional characterization.

TL;DR: A generalized in situ proximity ligation assay is established to investigate phosphorylation of platelet-derived growth factor receptor β (PDGFRβ) in cells stimulated with Platelet- derived growth factor BB and detected tyrosine phosphorylated PDGFR β in tissue sections from fresh frozen human scar tissue undergoing wound healing.

TL;DR: A novel IMAC adsorbent through Zr4+ chelation to the phosphonate-modified poly(glycidyl methacrylate-co-ethylene dimethacrylated) polymer beads provides a powerful approach for large scale phosphoproteome analysis.

TL;DR: A combined approach of cross-linking, mass spectrometry, and bioinformatics to two human complexes containing large coiled-coil segments, the NDEL1 homodimer and the NDC80 heterotetramer, reports the results of a combined approach to address complexes that are difficult in addressing by standard structural methods.

TL;DR: A profiled proteome alterations in HCC tissues, and these results may provide useful insights for understanding the mechanism involved in the process of HCC carcinogenesis.

TL;DR: “Peptide mapping,” the location of multiple peptides identified within a particular protein by iTRAQ in combination with their relative abundance ratios, enabled the domain shed and general location of the cleavage site to be identified in the native cellular substrate.

TL;DR: This study significantly extends the known spectrum of linker histone variability by identifying a range of phosphorylation, acetylation, and methylation sites and mapped sites of ubiquitination.

TL;DR: Results indicate that obesity is accompanied by an increase in the carbonylation of a number of adipose-regulatory proteins that may serve as a mechanistic link between increased oxidative stress and the development of insulin resistance.

TL;DR: The development and application of a high throughput tandem affinity purification/mass spectrometry platform for cell suspension cultures to analyze cell cycle-related protein complexes in Arabidopsis thaliana is described and 28 new molecular associations are identified and confirmed.

TL;DR: This work identified a novel Ring1B-Fbxl10 complex that also includes Bcl6 corepressor (BcoR), CK2α, Skp1, and Nspc1/Pcgf1 and potentially provides additional mechanisms for chromatin modification/recruitment to chromatin and more evidence for Ring1b/Rnf2 activities beyond those typically associated with PcG function.

TL;DR: A remarkable compartmentalization of enzymes involved in methionine biosynthesis between the seed tissues was revealed that may regulate the availability of sulfur-containing amino acids for embryo protein synthesis during seed filling, which is relevant to strategies for modifying the nutritional value of legume seeds.

TL;DR: Data from this study illustrate that mass spectrometry-based methods can be used to determine activity-dependent changes in phosphorylation stoichiometry on candidate phosphopeptides following large scale phosphoproteome analysis of brain tissue.

TL;DR: The hypothesis that examining the CM of cell lines, as opposed to the cell lysates, leads to a significant enrichment in secreted proteins is confirmed, and the approach to mining for low abundance molecules could identify proteins in various stages of breast cancer development.