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Summary
Proteomic data of whole brain in HXB/BXH rat strains using LC/LC-MS/MS
A total of 31 HXB/BXH strains were used for profiling rat brain proteome. 8,124 proteins were quantified across all 5 batches. By using 3 batches of 16-plex tandem mass tag (TMT)-based LC/LC-MS/MS, 42 samples (21 strains; both male and female) were analyzed. By using 2 batches of 11-plex tandem mass tag (TMT)-based LC/LC-MS/MS, an additional 20 samples (10 strains; both male and female) were analyzed. TMT report ion intensities are corrected, normalized, and summarized for each protein. The intensities were transformed by log2. We used the limma R package to correct the batch effect across 5 batches. Expression values in each batch were further normalized by z-score. Gene names: extracted from Swissprot and UCSC database and manually annotated; protein accession: from the UniProt database. A small proportion of genes have two or more protein isoforms although we used the "unique" protein.