Can I merge multiple ion libraries within OneOmics suite for my SWATH acquisition proteomics analysis? by Christie Hunter | Aug 7, 2021 | Data processing, Life Science Research, OneOmics, Proteomics, QTOF, SCIEX information, ZenoTOF 7600 systemFor targeted processing of SWATH acquisition proteomics data, ion libraries are used to provide the information on the proteins, peptides, fragment ions and retention time to be used. To get the most out of your SWATH acquisition data, it is often required to build...
How do I add a retention time calibration protein to my SWATH acquisition ion library? by Christie Hunter | Aug 7, 2021 | Data processing, Life Science Research, OneOmics, Proteomics, QTOF, SCIEX information, ZenoTOF 7600 systemWhen processing SWATH acquisition data, you want to use a reasonably narrow time window to reduce the chance of incorrect peak integrations and to reduce data processing time. There are currently two strategies being employed today to adjust for differences between...
How do I calibrate my retention times when I plan to process my proteomics data with OneOmics suite? by Christie Hunter | Aug 7, 2021 | Data processing, Life Science Research, OneOmics, Proteomics, QTOF, SCIEX information, ZenoTOF 7600 systemIf the retention times (RT) within the ion library to be used differ from the retention times that will be observed in the SWATH acquisition data to be processed, it is important to recalibrate the retention times within the ion library. If a Retention Time...
How is the protein level fold-change computed on proteomics data using Assembler app? by Christie Hunter | Aug 7, 2021 | Algorithms, Life Science Research, OneOmics, Proteomics, QTOF, SCIEX information, ZenoTOF 7600 systemWith bottom-up proteomics, we quantify peptides in the sample and then infer the protein level quantitation from that data. However, due to post-translational modifications, different protein isoforms, etc. we don’t always expect that all peptides associated with the...
How do I define the experimental design (the metadata) for my SWATH acquisition study within the OneOmics suite? What are the requirement for replicates? by Christie Hunter | Aug 7, 2021 | Data processing, Life Science Research, Metabolomics, OneOmics, Proteomics, QTOF, SCIEX information, ZenoTOF 7600 systemIn quantitative Omics research, the goal is to understand which analytes (protein or metabolite) are perturbed between experimental conditions; therefore we carefully design our studies to explore these questions. The algorithms used within the Assembler application...