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.  Ion libraries only need to be created once, and are loaded into the SWATH acquisition 2.0 microapp in PeakView software, which performs the extraction of XICs and determination of peak areas for the entire sample set. These peptide and protein peak areas can then be passed automatically to MarkerView software which provides visualization and statistical analysis tools for assessing differential expression information. Other search engines can be used to create ion libraries and then the information can be imported into the SWATH acquisition microapp using the mzIdentML format. Peptide and protein peak areas can also be exported from the software in other formats to integrate with other downstream tools.

Cloud solution:

If you are running larger sample cohorts, it is recommended that you use the SCIEX cloud solution for data processing of your SWATH acquisition datasets, as the cloud is better equipped to handle the speed and scale of today’s proteomics studies. You can learn more about OneOmics suite by listening to the CloudTalks or reading other posts here in the user community.

In addition to SCIEX tools, there are a growing number of publicly available software solutions that can also be used to process SWATH acquisition data.

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