Appendix S1 Materials and methods.

Fig. S1 The significant (< 0.01) protein-protein interaction models found in the (A) freshwater and (B) brackishwater whitefish, based on the observed proteomic responses to salinity.

Fig. S2 The highest scoring IPA networks for the (A) freshwater (IPA score = 70) and (B) brackishwater (IPA score = 81) whitefish.

Table S1 The protein IDs, human orthologs, peptide counts, sequence coverage and label-free quantification (LFQ) intensities before and after normalization for the 1500 proteins and protein groups that have been identified and quantified in the studied freshwater (FW) and brackishwater (BW) whitefish.

Table S2 The IDs, descriptions and P-values of the GO terms that were found enriched (P < 0.05) for the lists of significant proteins in freshwater and brackishwater whitefish.

Table S3 The calculated degree and radiality indices for the proteins of the freshwater- and brackishwater-whitefish networks that were generated with the IPA software.

Table S4 Molecule and interaction information of the freshwater and brackishwater whitefish networks that were generated with the IPA software.

Table S5 Length of hatched whitefish of brackishwater and freshwater origin.

Table S6 Stage-specific survival of brackishwater and freshwater whitefish.

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