Additional file 1 of Quantitative proteome profiling reveals molecular hallmarks of egg quality in Atlantic halibut: impairments of transcription and protein folding impede protein and energy homeostasis during early development

Additional file 1: Fig. S1. Correlation of reproductive parameters with embryo survival and egg quality in halibut. Fig. S2. TMT labeling based LC-MS/MS quantification for candidate marker proteins. Fig. S3. TaqMan qPCR based relative quantification of gene expression for candidate marker proteins. Fig. S4. PRM based LC-MS/MS quantification of protein abundances for candidate marker proteins. Fig. S5. Results of counts and measurements of some mitochondrial parameters based on TEM imaging. Fig. S6. Some examples of mitochondrial observations in halibut eggs. Fig. S7. Biological samples and egg quality assessment procedure used in this study. Fig. S8. Experimental design. Fig. S9. Quantification of heavy peptides selected for use in PRM based LC-MS/MS. Table S1. List of females used in this study. Table S2. Differentially abundant proteins between good and poor quality halibut eggs based on peak area intensities obtained from the TMT based LC-MS/MS. Table S3. STRING protein-protein interaction networks enrichment analysis. Table S4. List of primers and probes used for relative quantification of gene expression and mtDNA quantification using TaqMan based qPCR. Table S5. List of reference peptides used for PRM based LC-MS/MS.