DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics.

UNLABELLED: DAPAR and ProStaR are software tools to perform the statistical analysis of label-free XIC-based quantitative discovery proteomics experiments. DAPAR contains procedures to filter, normalize, impute missing value, aggregate peptide intensities, perform null hypothesis significance tests and select the most likely differentially abundant proteins with a corresponding false discovery rate. ProStaR is a graphical user interface that allows friendly access to the DAPAR functionalities through a web browser. AVAILABILITY AND IMPLEMENTATION: DAPAR and ProStaR are implemented in the R language and are available on the website of the Bioconductor project (http://www.bioconductor.org/). A complete tutorial and a toy dataset are accompanying the packages. CONTACT: [email protected], [email protected], [email protected] (ChloroTypes), ANR-10-INBS-08 (ProFI project, ‘Infrastructures Nationales en Biologie et Sante´’, ‘Investissements d’Avenir’), European Union FP7 program (Prime-XS Project, Contract no. 262067), Prospectom project (Mastodons 2012 CNRS Challenge), Biotechnology and Biological Sciences Research Council (Strategic Longer and Larger Grant ID: BB/L002817/1)This is the final version of the article. It first appeared from Oxford University Press via https://doi.org/10.1093/bioinformatics/btw58

Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism

Variants in ribosomal protein (RP) genes drive Diamond-Blackfan anemia (DBA), a bone marrow failure syndrome that can also predispose individuals to cancer. Inherited and sporadic RP gene variants are also linked to a variety of phenotypes, including malignancy, in individuals with no anemia. Here we report an individual diagnosed with DBA carrying a variant in the 5'UTR of RPL9 (uL6). Additionally, we report two individuals from a family with multiple cancer incidences carrying a RPL9 missense variant. Analysis of cells from these individuals reveals that despite the variants both driving pre-rRNA processing defects and 80S monosome reduction, the downstream effects are remarkably different. Cells carrying the 5'UTR variant stabilize TP53 and impair the growth and differentiation of erythroid cells. In contrast, ribosomes incorporating the missense variant erroneously read through UAG and UGA stop codons of mRNAs. Metabolic profiles of cells carrying the 5'UTR variant reveal an increased metabolism of amino acids and a switch from glycolysis to gluconeogenesis while those of cells carrying the missense variant reveal a depletion of nucleotide pools. These findings indicate that variants in the same RP gene can drive similar ribosome biogenesis defects yet still have markedly different downstream consequences and clinical impacts

ETUDE DU PEPTIDOME DU STRATUM CORNEUM HUMAIN PAR UNE APPROCHE PROTEOMIQUE

Cette thèse se place dans le contexte de l'analyse protéomique et peptidomique. D'un point de vue analytique, l'objectif de ma thèse a été d'implémenter au laboratoire des techniques capables de fournir rapidement des identifications fiables de protéines et de peptides en mélange complexe, quelles que soient leurs propriétés physico-chimiques. D'un point de vue biologique, nous souhaitions appréhender le phénomène de desquamation du stratum corneum chez l'Homme, en collaboration avec la société L'Oréal. Ce phénomène implique la dégradation par des enzymes spécifiques des protéines des cornéodesmosomes, jonctions cellulaires qui assurent la cohésion des cellules entre elles. Contrairement aux approches biochimiques classiques utilisées généralement dans ce type d'application (ciblage de protéases spécifiques), nous avons choisi d'adopter une méthodologie sans a priori, qui fait le lien entre la peptidomique et la dégradomique. Pour ce faire, nous avons centré notre étude sur les peptides endogènes issus de la dégradation des protéines du stratum corneum afin d'identifier des peptides spécifiques de la desquamation.Non disponibl

Etude du peptidome du stratum corneum humain par une approche protéomique

PARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Quantitative phosphoproteomic analysis reveals shared and specific targets of Arabidopsis mitogen-activated protein kinases (MAPKs) MPK3, MPK4, and MPK6

In Arabidopsis, mitogen-activated protein kinases MPK3, MPK4, and MPK6 constitute essential relays for a variety of functions including cell division, development and innate immunity. Although some substrates of MPK3, MPK4 and MPK6 have been identified, the picture is still far from complete. To identify substrates of these MAPKs likely involved in cell division, growth and development we compared the phosphoproteomes of wild-type and mpk3, mpk4, and mpk6. To study the function of these MAPKs in innate immunity, we analyzed their phosphoproteomes following microbe-associated molecular pattern (MAMP) treatment. Partially overlapping substrates were retrieved for all three MAPKs, showing target specificity to one, two or all three MAPKs in different biological processes. More precisely, our results illustrate the fact that the entity to be defined as a specific or a shared substrate for MAPKs is not a phosphoprotein but a particular (S/T) P phosphorylation site in a given protein. One hundred fifty-two peptides were identified to be differentially phosphorylated in response to MAMP treatment and/or when compared between genotypes and 70 of them could be classified as putative MAPK targets. Biochemical analysis of a number of putative MAPK substrates by phosphorylation and interaction assays confirmed the global phosphoproteome approach. Our study also expands the set of MAPK substrates to involve other protein kinases, including calcium-dependent (CDPK) and sugar nonfermenting (SnRK) protein kinases

CHICKN: extraction of peptide chromatographic elution profiles from large scale mass spectrometry data by means of Wasserstein compressive hierarchical cluster analysis

International audienc

Well Plate Maker: A user-friendly randomized block design application to limit batch effects in largescale biomedical studies

International audienc

Statistical analysis of quantitative peptidomics and peptide-level proteomics data with Prostar

Prostar is a software tool dedicated to the processing of quantitative data resulting from mass spectrometrybased label-free proteomics. Practically, once biological samples have been analyzed by bottom-up proteomics, the raw mass spectrometer outputs are processed by bioinformatics tools, so as to identify peptides and quantify them, notably by means of precursor ion chromatogram integration. From that point, the classical workflows aggregate these pieces of peptide-level information to infer protein level identities and amounts. Finally, protein abundances can be statistically analyzed to find out proteins that are significantly differentially abundant between compared conditions. Prostar original workflow has been developed based on this strategy. However, recent works have demonstrated that processing peptide-level information is often more accurate when searching for differentially abundant proteins, as the aggregation step tends to hide some of the data variabilities and biases. As a result, Prostar has been extended by workflows that manage peptide-level data, and this protocol details their use. The first one, deemed "peptidomics", implies that the differential analysis is conducted at peptide level, independently of the peptide-to-protein relationship. The second workflow proposes to aggregate the peptide abundances after their preprocessing (i.e., after filtering, normalization and imputation), so as to minimize the amount of protein-level preprocessing prior to differential analysis