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).