The authors used a mass spectrometry approach coupled with retention time shift software to measure the peptide abundances between the BY and RM strains and their segregants. Replicating a sample via quantitative western blot they found that they could reliably measure peptides as a quantitative trait, and that the levels showed inheritance patterns similar to transcript data from a previous study. A number of peptide levels differ significantly between the two parents and a linkage analysis found four major hotspots responsible for many of these linkages. Two of these hotspots were enriched for peptide synthesis, one being on LEU2, the other two were not enriched for any particular term. Almost all the peptides showed trans linkage. Only three of the four hotspots overlap to hotspots generated by transcript data of the 278 measurable peptides, and only rarely do these hotspots link to both a peptide and its corresponding transcripts. Interestingly, the 278 transcripts find the same hotspots as the total transcript database, suggesting a limited number of polymorphism control the whole proteome, thus the small sample size of proteins may still find the proteome hotspots.
•Other notes:
-weak correlation between transcript and peptide levels, suggesting post-transcriptional regulation acts as a buffer
-BY and RM differ at ~0.6% of genome
-if a representative sample this means 1/3 of all proteins differ between BY and RM
-221 peptides for 278 proteins
-heritability average was 62%
-expanded to 0.17 to get 85 proteins, 109 linkages
=only 7% of peptides map to a marker within 20kb of their ORF
-average correlation between protein and transcript abundance is 0.186
-3 of 4 hotspots overlap
=shared hotspots do not always overlap the same gene’s transcript and protein
=same polymorphism causes changes at different stages for different genes
