Chapter 16. Proteomics Informed by Transcriptomics

The choice of protein sequence database used for peptide spectrum matching has a major impact on the extent and significance of protein identifications obtained in a given experiment. Finding a suitable database can be a major challenge, particularly when working with non-model organisms and complex samples containing proteins from multiple species. This chapter introduces the proteomics informed by transcriptomics (PIT) methodology, in which RNA-seq transcriptomics is used to generate a sample-specific protein database against which proteomic mass spectra can be searched. This approach extends the application of proteomics to studies in which it was not previously tractable, and is well suited to the discovery of novel translated genomic elements.