SWATHXtend - APAF developed software to extend peptide assay libraries for SWATH mass spectrometry analysis. Use this to merge a local IDA data with spectral libraries from external sources such as large repositories. The script can be downloaded from BioConductor and can be found at this link.
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Wu et al. SWATH mass spectrometry performance using extended peptide MS/MS assay libraries. Mol. Cell Proteomics mcp.M115.055558. First published online on May 9, 2016