Showing papers in "Molecular & Cellular Proteomics in 2011"

TL;DR: This work combines single-step immunoenrichment of ubiquitylated peptides with peptide fractionation and high-resolution mass spectrometry to investigate endogenous ubiquitylation sites, and for the first time demonstrates proteome-wide, site-specific quantification of endogenous putative ubiquitylations sites.

TL;DR: High performance in a robust benchtop format together with the ability to perform complex multiplexed scan modes make the Q Exactive an exciting new instrument for the proteomics and general analytical communities.

TL;DR: The resulting standard data format, mzML, is a well tested open-source format formass spectrometer output files that can be readily utilized by the community and easily adapted for incremental advances in mass spectrometry technology.

TL;DR: The results reveal a new type of PTM pathway and identify the first enzyme that can regulate lysine malonylation and lysines succinylation status, and suggest the possibility of nondeacetylation activity of other class IIIlysine deacetylases, especially those without obvious acetylation protein substrates.

TL;DR: The use of iProphet in the Trans-Proteomics Pipeline increases the number of correctly identified peptides at a constant false discovery rate as compared with both PeptideProphet and another state-of-the-art tool Percolator.

TL;DR: This work has identified 20,433 distinct peptides, from which it inferred a highly nonredundant set of 1929 protein sequences at a false discovery rate of 1%, and compiled a high-confidence human plasma proteome reference set with well over twice the identified proteins of previous high- confidence sets.

TL;DR: The majority of the structural features of the IgG glycome were consistent with previous studies, but sialylation was somewhat higher than reported previously, indicating that the final glycan structures are not a simple result of competing enzymatic activities, but a carefully regulated outcome designed to meet the prevailing physiological needs.

TL;DR: The Human Proteome Organization urges each national research funding agency and the scientific community at large to identify their preferred pathways to participate in aspects of this highly promising project in a HPP consortium of funders and investigators.

TL;DR: The results imply an unexpectedly large dynamic range of the MS signal and sensitivity for liquid chromatography-tandem MS alone, which has the potential to radically simplify many proteomic studies while maintaining a systems-wide view of the proteome.

TL;DR: This work developed a novel cross-linking strategy using a newly designed MS-cleavable cross-linker, disuccinimidyl sulfoxide (DSSO), which can find a broad range of applications in elucidating the structural topology of proteins and protein complexes.

TL;DR: The identification of 753 unique lysine ubiquitylation sites on 471 proteins using higher-energy collisional dissociation on the LTQ Orbitrap Velos is reported, providing novel insights into the site-specific selection and regulatory function of lysin ubiquitylations.

TL;DR: This work shows that metabolomic profiling approach is a promising screening tool for the diagnosis and stratification of HCC patients with alpha fetoprotein values lower than 20 ng/ml with an accuracy of 100% using a panel of metabolite markers.

TL;DR: The data demonstrate that peptide-centric approaches coupled to novel mass spectrometric fragmentation techniques may be suitable for application to eukaryotic glycoproteins for simultaneous elucidation of glycan structures and peptide sequence.

TL;DR: Better understanding of molecular mechanisms underlying proteasome function in response to oxidative stress will provide a basis for developing new strategies aimed at improving cell viability and recovery as well as attenuating oxidation-induced cytotoxicity associated with aging and disease.

TL;DR: The Mascot Delta Score is validated as a simple method that achieves similar sensitivity and specificity for phosphosite localization as the published Ascore and it is shown that the ability to call sites correctly increases with increasing distance of two candidate sites within a peptide sequence.

TL;DR: This review article focuses mainly on the exploration of the underlying ionization mechanism and some ionization characteristics are discussed that are related to this mechanism.

TL;DR: A key observation was the elevation of a high-mannose type glycan containing nine mannoses, Man9, m/z 1905.630 in both mouse and human sera in the presence of breast cancer, suggesting an incompletion of the glycosylation process that normally trims back Man9 to produce complex and hybrid type oligosaccharides.

TL;DR: An overview of the recent advances in mass spectrometry based glycoproteomic methods and technology, in the context of biomarker discovery and clinical application is provided.

TL;DR: Emerging evidence suggests that small molecule USP14 inhibitors can enhance proteasome function in cells, which is consistent with this model, and the responsiveness of substrates to inhibition of proteasomal deubiquitinating enzymes may vary substantially.

TL;DR: Primary sequences, predicted secondary structures, and solved crystal structures of known methyltransferases were analyzed by hidden Markov models, Fisher-based statistical matrices, and fold recognition prediction-based threading algorithms to create a model, or profile, of each methyltransferase superfamily.

TL;DR: The proteomics methodology allowed the first detailed analysis of the ECM in AAA and identified markers of pathological ECM remodeling related to MMP-12 activity.

TL;DR: This study identified 358 unique Plk1-dependent phosphorylation sites on spindle proteins, including novel substrates, illustrating the complexity of the Plk2-dependent signaling network and the functional interaction between PlK1 and Aurora A on the early mitotic spindle.

TL;DR: P pulsed SILAC and microarray analyses identified miR-34a-induced changes in protein and mRNA expression that presumably participates in multiple tumor suppressive pathways by directly and indirectly suppressing the expression of numerous, critical proteins.

TL;DR: The key performance characteristics of Fourier transform-based mass spectrometry, mass accuracy and resolution, are presented in the view of how they impact the interpretation of measurements in proteomic applications.

TL;DR: Combinedprotein expression and phosphorylation surveys uncovered both independent and concerted changes in protein expression andosphorylation, while highlighting the partially redundant role of a second MAPK (Kss1) in the mating pathway.

TL;DR: For large-scale phosphoproteomics, CID fragmentation with rapid detection in the ion trap still produced substantially richer data sets, but the back-to-back experiments demonstrated the promise of HCD and orbitrap detection for the future.

TL;DR: Investigation of the cellular response of strain GG toward bile under defined bioreactor conditions revealed significant reduction in the abundance of a protein catalyzing the synthesis of exopolysaccharides, whereas a protein dedicated for active removal of bile compounds from the cells was up-regulated, suggesting a role for these proteins in facilitating the well founded interaction of strainGG with the host mucus in the presence of sublethal doses of biles.

TL;DR: A new data acquisition paradigm is presented in which selected reaction monitoring is performed in two ways to simultaneously quantify and confirm the identity of the targeted peptides, enabling large scale proteomic studies.

TL;DR: The results demonstrate the feasibility of performing phosphoproteome analysis of organelles isolated from human tissue and provide novel targets for functional studies of reversible phosphorylation in mitochondria.

TL;DR: Dengue virus (DENV), an emerging mosquito-transmitted pathogen capable of causing severe disease in humans, interacts with host cell factors to create a more favorable environment for replication and provides additional support for the hypothesis that viruses preferentially target cellular proteins that occupy central position in the human protein interaction network.