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The most important consideration in adding a new RT calibration protein to your library is making sure you are getting the retention time for both into the same retention time or chromatographic frame. Below is a list of steps that walks you through how to do this....
Similar extraction processes are used in both the SWATH acquisition microapp in PeakView software on the desktop and the Extractor app in OneOmics suite. After the fragment ions have been selected for each peptide, the extracted ion chromatograms are generated and the...
Similar selection processes are used in both the SWATH acquisition microapp in PeakView software on the desktop and the Extractor app in OneOmics suite. During the protein grouping process in ProteinPilot software, there is an extensive analysis that is done on the...
Desktop solution: If you are processing your SWATH acquisition data using the SCIEX pipeline, there are a 3 software packages that work together seamlessly for processing. First, you would process your IDA data using ProteinPilot software to create an ion library. ...
The information needed for targeted data extraction in our current SWATH acquisition workflow is relatively simple. You need the parent ion m/z; you need the m/z and relative intensities of the major fragment ions that are produced during MS/MS; and you need to know...
To continue to improve the quality of the SWATH acquisition data that one can achieve in complex matrices, we are working on ways that we can decrease the size of the Q1 window, while still maintaining full mass range coverage and optimal cycle times. One great way...
In data-independent acquisition strategies like SWATH acquisition, an expanded mass isolation window is stepped across a mass range covering the mass-to-charge (m/z) distribution of peptides and a full scan MS/MS spectrum is collected at each step. Post-acquisition,...
Results workspaces in the OneOmics suite contain a variety of figures, all available for download as SVG (scalable vector graphic) files. To download your figures, select the orange arrow icon located in the upper right-hand corner of each plot. Download will...
As multi-omics research is often highly collaborative, tools for rapidly sharing important results files are needed to drive scientific progress. The SCIEX Data Store in the OneOmics suite enables you to not only organize your uploaded multi-omics data files into...
To share your results stored in BaseSpace, login into your BaseSpace account and select the project you wish to share. Note that your collaborator must already have a BaseSpace account. 2. There are a number of options for how to share a BaseSpace project: Share...
Download this library for use with the SWATH acquisition performance kit Human2D_SOP_PepCalMix_ Jan2016.txt Note: This is a small library that was generated using the K562 human leukemia cell line and may not be appropriate for use on your other biological studies....
Download your specific instrument tracker to track your instrument performance over time. Compare your results from the SWATH acquisition performance kit against suggested performance guidelines. Guidelines provided for each of the 4 tests in the SWATH acquisition...
To set up a SCIEX high flow source for microflow LC (Turbo V ion source, DuoSpray source or IonDrive Turbo V ion source), first you must replace the wider bore electrodes with more narrow bore hybrid electrodes. Note with the OptiFlow Turbo V ion sources, there are...
Symptom: LC-MS peptide peak are is smaller than expected in PepCalMix Test Test: Use PepCalMix Infusion tests to determine if it is a problem with LC or MS Solution: First perform the SCIEX recommended performance tests using infusion on your MS system. If these...
Symptom: The elution of peptides is delayed, appearing later than expected. Example LC-MS traces are shown in the that represents a typical elution range for PepCalMix using the standard recommended tubing. Test: Use PepCalMix LC-MS test to check the peptide elution...
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