Raw spectral library and DIA assay library construction
An O. niloticus kidney spectral library was generated using the peptide-to-spectrum matches and protein annotations generated from DDA data. Data was exported from PEAKS suite X plus in pepxml format and imported into Skyline 20.0 (Pino et al., 2017) to create a non-redundant raw library of MS2 spectra. The initial target list of proteins was then filtered using multiple QC criteria (see results) to reduce the number of transitions, precursors, peptides, and proteins to a unique set that has the highest diagnostic value for quantitation. The final filter steps utilized a sample training set, which was acquired by DIA as described in the next paragraph. The complete assay library including all relevant metadata and corresponding data for the sample training set is available at Panorama Public (Kueltz-Lab_2020-1.url). This assay represents a tier two assay (Abbatiello et al., 2017).