Project description:In this study, the levels of expression of nine proteins in the presence of ampicillin (LBP_cg0109, Small heat shock protein; LBP_cg0397, L-serine dehydratase, beta subunit; LBP_cg0719, hypothetical protein; LBP_cg0720, hypothetical protein; LBP_cg0721, Alkaline shock protein; LBP_cg0722, Alkaline shock protein; LBP_cg2704, Formate acetyltransferase activating enzyme; LBP_cg0885, Malate dehydrogenase) were validated by parallel reaction monitoring.
Project description:In this study, targeted parallel reaction monitoring assays for phosphopeptides were configured by mining data from large-scale experiments. The capabilities of the method were assessed by performing several benchmarking experiments. The accuracy of retention time prediction using a large-scale database was assessed by using BSA peptides or human phosphopeptides to predict the retention time of distinct peptides in a subsequent run. Data-driven phosphopeptide sequence and charge state was compared to heuristics-based selection using unscheduled PRM assays. Phosphoproteome analysis was performed in technical quadruplicate using parallel reaction monitoring, data-independent acquisition, and data-dependent acquisition. A label-free quantitative parallel reaction monitoring experiment was performed on phosphopeptides enriched from cells stimulated -/+ IGF-1 (n=6).
Project description:<p>Characterization of botanical extracts by mass spectrometry-based metabolomics analysis helps in determining the phytochemical composition that underlies their bioactivity and potential health benefits, while also supporting reproducibility of effects in clinical trials. The quantification of seven withanolides in Withania somnifera using three mass-spectrometry methods was evaluated using Deming regression. Two high-resolution time-of-flight mass spectrometry methods were used, one operating in data-dependent acquisition mode and the other in parallel-reaction-monitoring mode with an inclusion list. The two high-resolution time-of-flight mass spectrometry methods were compared to a multiple-reaction-monitoring method. We evaluated in-source fragmentation of steroidal glycosides and optimized the methods accordingly. A novel software approach to integrating parallel-reaction-monitoring data acquired with an inclusion list was developed. Combining and comparing quantitative results allowed for quantitative specificity, good precision, and adjustment of instrument source conditions for optimal quantification by multiple-reaction-monitoring mass spectrometry, an analytical method that is widely accessible in analytical and phytochemical laboratories.</p><p><br></p><p><strong>Linked R Script</strong></p><p>An R script for PRM data analysis collected with an inclusion list is available in <a href='https://github.com/marneylc/prm' rel='noopener noreferrer' target='_blank'>Github</a>.</p>
Project description:Interventions: We conduct an introduction to the chemotherapy center from diagnosis and treatment department, and, in chemotherapy center, a medical oncologist, a pharmacist or a nurse conducts side effect monitoring using an episode of care sheet (the skin reaction monitoring sheet that we made for the purpose of doing multi-disciplinary cooperation smoothly) at chemotherapy enforcement. By severity of the skin reaction, a tumor physician refers you to a dermatologist, and side effect monitoring, a dermatologist intervene after the next treatment.
Primary outcome(s): Severe skin reaction incidence
Study Design: Single arm Non-randomized
Project description:Development, implementation, and evaluation of a new data acquisition scheme called internal standard triggered-parallel reaction monitoring (IS-PRM) to increase the scale of targeted quantitative experiments while retaining high detection and quantification performance. All the details about the dataset, the associated sample preparation and liquid chromatography coupled to tandem mass spectrometry methods, and the data processing procedures are provided in the manuscript by Gallien et al., entitled "Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring", Molecular and Cellular Proteomics.