This short video walks through the use of the automated MRM optimization feature in SCIEX OS software for optimizing the compound dependent parameters for an MRM experiment using an infusion approach. Here, we infuse reserpine to demonstrate the key elements of MRM...
This short video walks through the use of the automated compound optimization feature in SCIEX OS Software for optimizing the parameters for an MRM3 experiment. Here, we use reserpine and walk through the elements of MRM3, highlighting the key steps of optimization...
For 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...
When 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...
If 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...
With 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...
In 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...
When 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...
The 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...
The 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...
The “Intensity (Peptide)” values come from LCMSReconstruct, in ProteinPilot software 5.0. It maps the RT, m/z, intensity MS1 surface to find the peak information for the peptide. The Intensity (Peptide) is a weighted sum of the heights of the isotope series at the...
When setting up your search in ProteinPilot software, you select either a Rapid Search or a Thorough Search in the Search Effort section. This setting determines which parts of the algorithm will be invoked and effectively how deep into your sample you will search to...