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...
What is the Most likely ratio normalization strategy? by Christie Hunter | Aug 7, 2021 | Algorithms, Life Science Research, MarkerView, Metabolomics, OneOmics, Proteomics, QTOF, SCIEX information, ZenoTOF 7600 systemWhen performing LC-MS quantitation, there are numerous sources of experimental variance that can confound the quality of your results (variation in the starting amount of sample, variation in the LC-MS measurements, etc.). Having a robust normalization strategy that...
What is the difference between the gobal and the local FDR rates in ProteinPilot software? by Christie Hunter | Aug 6, 2021 | Data processing, Life Science Research, ProteinPilot, Proteomics, QTOF, SCIEX information, ZenoTOF 7600 systemThe main idea of the target-decoy approach to compute false discovery rates is to feed the search engine answers that you know are wrong. These are referred to as ‘decoys’, typically generated by reversing, randomizing, or scrambling real protein sequences. You then...
Protein alignment template for results comparisons across multiple group files from ProteinPilot software database searches by Christie Hunter | Aug 6, 2021 | Data Visualization, Life Science Research, ProteinPilot, Proteomics, QTOF, SCIEX information, ZenoTOF 7600 systemThe key challenge in aligning protein level results is flexible matching by making use of the accession ambiguity in reported protein groups. The better this task is done, the more complete will be the protein matching across multiple results. For quantitative work, a...