Overview of workflows implemented in Galaxy-P that utilize RNA-Seq data for improved proteomics. The single amino acid polymorphism (SAP) database workflow detects non-synonymous SNPs that yield SAPs. The splice database workflow detects alternatively spliced transcripts and the corresponding novel splice junction polypeptide sequences. The reduced database workflow quantifies the sample’s transcriptome, optionally removes likely unexpressed protein sequences, and allows determination of RNA-protein correlations. Post-search tools filter and annotate novel peptides.