Showing papers in "Molecular & Cellular Proteomics in 2019"

TL;DR: A robust and cost-effective protocol for TMT labeling that reduces the quantity of required labeling reagent by a factor of eight and achieves complete labeling is described and evaluated and demonstrated in a deep-scale proteome and phosphoproteome analysis of patient-derived xenograft tumor tissue.

TL;DR: The first version of PTMsigDB is presented, a database of modification site-specific signatures of perturbations, kinase activities and signaling pathways curated from more than 2,500 publications, and outperformed gene-centric analysis in detection of EGF induced phospho signaling events.

TL;DR: A novel mechanism that exploits the inherent instability of denatured proteins for nonspecific immobilization on microparticles by protein aggregation capture is described, enabling generation of clean peptide mixtures from cell lines, tissues, and protein pulldowns for proteomics, phosphoproteomics, and secretomics analysis.

TL;DR: The first large-scale plasma DIA study and one of the largest clinical research proteomic studies to date is presented, demonstrating high robustness and quality of biomarker candidates identified.

TL;DR: It is shown that without normalization strategies to address the batch effects, the high precision of quantitation within a single multiplexed TMT batch is not reproduced when data from multiple TMT batches are integrated, and this pattern is aggravated at the peptide level.

TL;DR: 6 synaptic biomarkers that demonstrate changes in preclinical AD prior to markers of neurodegeneration, which could have clinical value for assessing disease progression are reported, which is a much-needed prognostic biomarker.

TL;DR: It is confirmed that epididymosomes encapsulate an extremely rich and diverse proteomic cargo, which is commensurate with their putative role in coordinating the post-testicular maturation and storage of spermatozoa.

TL;DR: A new strategy enabling the discovery of the LFQs of simultaneously enhanced precision, robustness, and accuracy from thousands of LFQ manipulation chains is described and validated and might provide useful guidance for the research field requiring the mass-spectrometry-based LFQ technique.

TL;DR: Limits of TCGA proteomics array data can be overcome while also providing a user-friendly web interface, a web API, and an R client to query the mass spectrometry data together with genomic, epigenomic, and clinical data.

TL;DR: A global targeting approach in which an arbitrary number of precursors of interest are detected in real-time, followed by standard fragmentation or advanced peptide-specific analyses, which unifies shotgun and targeted proteomics.

TL;DR: An in-depthADP-ribosylome is described using the Af1521-based proteomics methodology for comprehensive profiling of ADP- ribosylation sites, by systematically assessing complementary proteolytic digestions and precursor fragmentation through application of electron-transfer higher-energy collisional dissociation (EThcD) and electron transfer Dissociation (ETD), respectively.

TL;DR: IPSA provides supports for annotating spectra collecting using negative-mode ionization and facilitates the characterization of experimental MS/MS performance through the optional export of fragment ion statistics from one to many peptide spectral matches.

TL;DR: While the combination of methods proved to be the most beneficial for the analysis of total serum protein N-glycosylation, informed method choices can be made for the glycosylated analysis of single proteins or samples of varying complexity.

TL;DR: NNAlign_MA is a computational method designed to address this challenge and fully benefit from large, poly-specific data sets of MS-eluted MHC ligand data, effectively expanding the coverage of alleles for which accurate predictions can be made, resulting in improved identification of both eluted ligands and T-cell epitopes.

TL;DR: It was revealed that this stabilizing effect is mediated by the strong positive charge of alkaline virulence factors and ribosomal proteins in an acidic ECM environment, which is caused by the release of fermentation products like formate, lactate, and acetate because of oxygen limitation in biofilms.

TL;DR: It is shown that low input proteomics is precise, and the data generated accurately reflects many aspects of known immunology, while expanding the list of cell-type specific proteins across the cell types profiled.

TL;DR: It is demonstrated for the first time that N-glycosylation is required for a specific enzyme activity (Nap nitrate reductase) that is associated with reduced abundance of the NapAB glycoproteins and indicates a multifactorial role for N-gresylation in C. jejuni physiology.

TL;DR: The FlashPack cUHPLC columns are inexpensive, robust and deliver performance comparable to commercially available cU HPLC columns.

TL;DR: Nonparametric analysis of response curves (NPARC), a statistical method for TPP based on functional data analysis and nonlinear regression, is presented and observed that it is able to detect subtle changes in any region of the melting curves, reliably detects the known targets, and outperforms a melting point-centric, single-parameter fitting approach in terms of specificity and sensitivity.

TL;DR: Broad applicability is demonstrated by the first N-terminome analysis of sorted human primary immune cells and enriched mitochondrial fractions from pediatric cancer patients, as well as protease substrate identification from individual Arabidopsis thaliana wild type and Vacuolar Processing Enzyme-deficient mutant seedlings.

TL;DR: This article applied label-free quantitative proteomics to Drosophila melanogaster male reproductive tissue and quantified Sfps before and immediately after mating to infer those transferred during copulation.

TL;DR: The results indicate that CAF-derived LOXL2 is an important mediator of intercellular communication within the prostate tumor microenvironment and is a potential therapeutic target.

TL;DR: It is found that bisecting GlcNAc, a branching sugar residue in N-glycan, suppresses the biosynthesis of various types of terminal epitopes inN-glycans, including fucose, sialic acid and human natural killer-1.

TL;DR: It is argued that the determination of site-specific glycosylation of IAV glycoproteins would enable development of vaccines that take advantage of glycosolation-dependent mechanisms whereby virus glycoprotein hemagglutinin cells are processed by antigen presenting cells.

TL;DR: The value of this module is demonstrated by examining the correlations of RPPA proteins with significantly mutated genes, assessing the predictive power of somatic copy-number alterations, DNA methylation, and mRNA onprotein expression, inferring the regulatory effects of miRNAs on protein expression, constructing a co-expression network of proteins and pathways, and identifying clinically relevant protein markers.

TL;DR: The results suggest that three proteins (CFH, FGA, and SERPINA1) have the potential as diagnosis and prognosis biomarkers of oral cancer, and analysis of salivary proteome is a feasible strategy for biomarker discovery.

TL;DR: Omics analysis is set out to probe omics analysis as a novel diagnostic platform for patients with defective differentiation and function of neutrophil granulocytes for which routine clinical diagnostics proved inconclusive.

TL;DR: A new computation method termed multi-omics gene-set analysis (MOGSA), a multivariate single sample gene- set analysis method that integrates multiple experimental and molecular data types measured over the same set of samples is introduced.

TL;DR: It is argued that productive data integration differs from parallel acquisition and interpretation and should move toward quantitative modeling of the relationships between the data.

TL;DR: It is confirmed that a major part of the O- glycoproteome is covered by redundancy, whereas distinct O-glycosite subsets are covered by nonredundant GalNAc-T isoform-specific functions.