Here are step by step instructions to get started using the OneOmics applications in BaseSpace. Click on the embedded links for more detailed information.
- Download and install Cloud Connect
- Use CloudConnect to upload data files and ion libraries to BaseSpace. Download the CloudConnect User Guide for help >
- Use Protein Expression Extractor in BaseSpace to extract quantitative information from SWATH data (equivalent to SWATH 2.0 processing in PeakView® Software)
- Visualize your results via the Protein Expression Workflow beta* app.
- The Experiment Manager application allows you to define the study level meta data and experiment groups
- Next, use Protein Expression Assembler to normalize data and compute protein expression differences using study level meta data. (Note, do not use the Assembler application on the main app page, use the one inside Protein Expression Workflow app.)
- The Browser application allows you to view your differential protein expression data across experiment groups, from a biological perspective
- The Analytics application allows you to assess the data quality: %CV, FDRs, normalization, etc.
*Look for these icons while using the SCIEX apps in BaseSpace to instantly provide your feedback and ideas to our software developers and help us as we continue to improve the OneOmics experience!