How are peptides and transitions selected for use in quantification, when importing from a ProteinPilot software group file – using SWATH acquisition microapp or Extractor in OneOmics suite?
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...
What software do I need to process my SWATH acquisition data using the desktop or cloud solutions?
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. ...
What is the best way to build spectral ion libraries for use in processing of proteomics SWATH acquisition data?
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...