Showing papers in "Molecular & Cellular Proteomics in 2010"

TL;DR: An immunoaffinity capture method using the colon epithelial cell-specific A33 antibody to purify colorectal cancer cell (LIM1215)-derived exosomes is described and the presence of the enzyme phospholipid scramblase implicated in transbilayer lipid distribution membrane remodeling is reported.

TL;DR: In this article, the authors observed that tumor cells produce a secretion that modifies their microenvironment to facilitate tumor angiogenesis and metastasis under hypoxia, and the secreted proteins were predominantly cytoplasmic and membrane proteins.

TL;DR: This study proposed using an additive-multiplicative error model for peak intensities in MS/MS quantitation and demonstrated that a variance-stabilizing normalization is able to address the error structure and stabilize the variance across the entire intensity range.

TL;DR: The establishment of a reproducible, high resolution method for peptidome analysis of naturally occurring human urinary peptides and proteins, ranging from 800 to 17,000 Da, using samples from 3,600 individuals analyzed by capillary electrophoresis coupled to MS is reported.

TL;DR: In this article, the authors discuss the critical steps of chemical cross-linking and its implications for (structural) biology: reagent design and cross-link protocols, separation and mass spectrometric analysis of cross-linked samples, dedicated software for data analysis, and the use of crosslink data for computational modeling.

TL;DR: A unique knowledge base containing extensive information on the proteins identified in envelope fractions was obtained, allowing new insights into this membrane system to be revealed, and the data obtained provide unexpected information about plastidial or subplastidials localization of some proteins that were not suspected to be associated to this membranes system.

TL;DR: It was found that FcγRIIIa binding was strongly influenced by both the glycan structure/composition and conformational changes that were induced by some of the modifications, and fucosylation appears to have little or no impact to the conformation.

TL;DR: The first proteomics analysis of bladder cancer cell exosomes is presented, revealing a strong association of this proteome with carcinoma of bladder and other sites and how homology among human leukocyte antigen haplotypes may confound MASCOT designation of major histocompatability complex Class I nomenclature.

TL;DR: A method for an automated magnetic bead-based platform capable of high throughput processing is developed and it is demonstrated that enrichment of peptides from larger volumes of plasma can extend the limits of detection to the low pg/ml range of protein concentration.

TL;DR: It is found that FG domains are structurally and chemically heterogeneous, and adopt distinct categories of intrinsically disordered structures in non-random distributions.

TL;DR: A novel proteomics approach, designated palmitoyl protein identification and site characterization (PalmPISC), for proteome scale enrichment and characterization of S-acylated proteins extracted from lipid raft-enriched and non-raft membranes and bioinformatics analysis suggested that S-ACYlated proteins are highly enriched within core complexes of caveolae and tetraspanin-en enriched microdomains.

TL;DR: Analysis of the intracellular levels of members of the semaphorin family and their corresponding secretion dynamics demonstrated that the release ofsecreted proteins is tightly regulated by the secretory pathway, the stability of the protein, and/or the processing of secreted proteins.

TL;DR: It is shown that MS-GFDB outperforms Mascot for ETD spectra or peptides digested with Lys-N, and proposes a statistical framework for analyzing multiple spectra from the same precursor and assigning p values to peptide-spectrum-Spectrum matches.

TL;DR: N-terminomics analyses using iTRAQ-TAILS links gelatinases with new mechanisms of action in angiogenesis and reveals unpredicted restrictions in substrate repertoires for these two very similar proteases.

TL;DR: In this article, the authors describe a methodology for the extraction of extracellular proteins from human aortas and their identification by proteomics, which is based on effective decellularization to enrich for scarce ECM proteins, successful solubilization and deglycosylation of ECM protein and relative estimation of protein abundance using spectral counting.

TL;DR: In this method, O-GlcNAc-modified peptides are tagged with a novel biotinylation reagent, enriched by affinity chromatography, released from the solid support by photochemical cleavage, and analyzed by electron transfer dissociation mass spectrometry to characterize sites of GlcNAcylation.

TL;DR: The data extend the number of known phosphorylation sites regulated by DNA damage, provides so far unprecedented temporal dissection of DNA damage-modifiedosphorylation events, and elucidate the cross-talk between different types of post-translational modifications in the dynamic regulation of a multifaceted DNA damage response.

TL;DR: This work indicates that protein export profoundly marks early sexual differentiation in P. falciparum, probably contributing to host cell remodeling in this phase of the life cycle, and that gametocyte-enriched molecules are recruited to modulate this process in gametocytogenesis.

TL;DR: This instrument can efficiently characterize protein mixtures by alternating MS and “all-ion fragmentation” (AIF) MS/MS scans in a manner similar to that previously described for quadrupole time-of-flight instruments.

TL;DR: A novel software tool, Musite, specifically designed for large scale predictions of both general and kinase-specific phosphorylation sites, aimed at being an open platform for community-based development of machine learning-based phosphorylated site prediction applications.

TL;DR: In this article, the authors used membrane-enriched fractions derived from retinas of the only available spontaneous animal model for the disease equine recurrent uveitis, and compared expression levels by a label-free LC-MSMS-based strategy to healthy control samples.

TL;DR: This combined experimental and bioinformatics analyses resolved chloroplast ribosomes in different assembly and functional states, which enabled the identification of plastid homologues of prokaryotic ribosome assembly factors as well as proteins involved in co-translational modifications, targeting, and folding.

TL;DR: The quantitative data confirmed proteins previously characterized as induced at the transcript level as well as identified several new proteins of unknown function induced under anaerobic conditions that could bring insights for the engineering of hydrogen-producing alga strains.

TL;DR: The proteins identified from the secretomes of 23 cancer cell lines and the Human Protein Atlas represent a focused reservoir of potential cancer biomarkers.

TL;DR: Mass spectrometry-based proteomics is used to provide an unbiased, quantitative, and high throughput approach for measuring the subcellular distribution of the proteome, termed “spatial proteomics” and facilitates a proteome-wide comparison of changes in protein localization in response to a wide range of physiological and experimental perturbations.

TL;DR: The data show that the SILAC fly can be used to accurately quantify protein abundance in vivo, making SILAC flies an attractive model system for the emerging field of in vivo quantitative proteomics.

TL;DR: 46 system performance metrics for monitoring chromatographic performance, electrospray source stability, MS1 and MS2 signals, dynamic sampling of ions for MS/MS, and peptide identification are described.

TL;DR: The combination of immunoaffinity purification of tyrosine phosphorylated peptides with large scale stable isotope dimethyl labeling provides a cost-effective approach that can alleviate variation in sample preparation and analysis as samples can be combined early on.

TL;DR: These data provide the most comprehensive set of caspase-1-cleaved products reported to date and indicate that caspases-4 and -5 have far fewer substrates than previously reported, and suggest that inducers of inflammation may subtly alter caspasing-1 substrate profiles.

TL;DR: The superior sensitivity of PolyMAC allowed us to identify novel components in a variety of major signaling networks, including cell migration and apoptosis, and offers a powerful and widely applicable tool for phosphoproteomics and molecular signaling.