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.
Project description:Women are vulnerable to cervical diseases including normal control, HSIL and early stage cervical carcinoma . The parallel reaction monitoring mass spectrometry (PRM-MS) were used to qualitatively and quantitatively analyze the candidate differential proteins identified in our previous studies and to link them with HPV status. The integration of HPV status with candidate serum markers is expected to efficiently narrow down the high risk population and provide sufficient clinical information for early diagnosis and effective therapy.
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: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.
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:To examine the properties of 14N and 15N labeled peptides from 15 metabolic labeling samples, we set up targeted quantification using Parallel Reaction Monitoring (PRM) on a high resolution, high accuracy mass spectrometer. We first examined the co-elution of light and heavy peptide forms. Furthermore, we examined the fragment spectra of the light and heavy peptides and compared the pattern of the fragments.
Project description:The objective of this study was to identify and evaluate the performance of target peptide for the detection of soy protein in a cookie matrix using parallel reaction monitoring.
Project description:In this study, we have developed a parallel reaction monitoring (PRM)-based assay for quantitative profiling of 83 PTKs. The assay detects 308 proteotypic peptides from 54 receptor tyrosine kinases and 29 nonreceptor tyrosine kinases in a single run. We used this assay to determine PTKs in lung cancer cell lines with either susceptibility (11-18) or acquired resistance (11-18R) to the epidermal growth factor receptor tyrosine kinase inhibitor erlotinib. We also performed label free shotgun proteome analyses of the 11-18 and 11-18R cells and iTRAQ comparisons of phosphotyrosine peptides from 11-18 and 11-18R cells.
Project description:Parallel reaction monitoring (PRM) analysis was used to confirm changes in abundance of the target proteins (AceF, SodA, YopD, YopE, GroEL, TerE, and OsmY2),. Equal amounts of proteins from the culture supernatants and cell pellets were separated by SDS-PAGE, and bands corresponding to each of the target proteins were subjected to in-gel digestion. The peptide samples for the target proteins were then analyzed by mass spectrometry, and three peptides from each target protein were selected for the PRM analysis. The selection criterion for the peptides was a sequence length of 6–15 amino acids, while peptides with any modifications or missed cleavage sites were excluded. The peak area of three b-/y-ions from each peptide was used to calculate the peptide ratio, and the ratios of three peptides were used to determine the target protein ratio in different samples.