Project description:Advancing Negative Ion Mode Proteomics. The main objective of the project is the exploration of the unconvetional negative ion mode for proteomics studies. In this work, we thoroughly studied the best chromatographic conditions for negative ion mode proteomics before testing different enzymatic digestion. The final goal is to establish the best working conditions in the negative polarity for negative ion mode. The method also refrains from any fragmentation events, which are unpredictable in negative ion mode.
Project description:Xylem sap proteome studies on susceptible or resistant tomato (Solanum lycopersicum) inoculated with endophytic and/or pathogenic strains of Fusarium oxysporum f.sp. lycopersici were conducted to get insights into the molecular differences between endophyte- and R-gene-mediated resistance (EMR and RMR). The EMR and RMR proteomes were compared to each other and to the mock control. Interestingly, specific PR-5 isoforms were found to exclusively accumulate during endophyte or genetic resistance, providing excellent markers to distinguish both resistance types at the molecular level.
Project description:In this work, we present an extended characterization of the proteome of the tomato pericarp in its ripe red stage. An extensive fractionation of peptides through high pH reverse phase was performed associated to LC-MS/MS analysis on a Thermofisher scientific Q-Exactive
Project description:Proteomics and transcriptomics data of tomato fruits (Solanum lycopersicum L. var. Moneymaker) at 9 developmental stages were used to calculate with a mathematical model the rate constants of synthesis and degradation for over 1,000 proteins. Proteome and transcriptome were extracted from the pericarp tissue and analyzed using label-free LC-MS/MS (Orbitrap Q-Exactive) and RNA Sequencing (Illumina), respectively. Absolute quantification of transcriptome has been obtained by spiking-in internal standard before total-RNA extraction. Absolute quantification of the proteome has been approximated using the "Total Protein" approach. An OD equation defining the changes of protein content has been used to determine the synthesis and degradation rate constants (day -1). Almost 2,400 transcript-protein pairs were identified and the translation and degradation rate constants were determined for more than a thousand proteins. The model predicted median values of about 2 min for the translation and a lifetime of approximately 11 days. Proteins involved in protein synthesis had higher ks and kd values, indicating that the protein machinery is particularly flexible. None sequenced-based features were found that could be used to predict these rate constants.
Project description:Samples from mice infected and then treated with vehicle, carnitine or benznidazole in the chronic stage of infection. Tissue samples extracted with 50% methanol followed by 3:1 dichloromethane:methanol. C8 chromatography with negative mode data acquisition