A Resource for Sharing, Annotating and Analysing Translated Genomic Elements


PITDB is a publicly available database for sharing of results from PIT (proteomics informed by transcriptomics) experiments. PIT [1] involves the analysis of a given sample by both RNA-seq and proteomic mass spectrometry followed by integration of the acquired data to provide an unprecedented level of information about which genomic elements are being transcribed and translated within a given sample, even if the organism under study does not have an annotated genome. Observed translated genomic elements (TGEs) are BLASTed against reference proteomes using a published workflow [2] to determine whether they are known proteins, protein variants or novel gene products.

Database Statistics

As of August 2018, the PITDB data consist of:

74,253 TGEs
118,649 Transcripts
117,578 Peptides
642,096 PSMs
90,319 Polymorphisms
4 Species


Developed by Shyamasree Saha and Elena Chatzimichali under the supervision of Conrad Bessant (Queen Mary University of London) and David Matthews (University of Bristol). Funded by BBSRC (grants BB/M020118/1 and BB/K016075/1) and Queen Mary University of London.

  1. Evans, V.C., et al., De novo derivation of proteomes from transcriptomes for transcript and protein identification. Nature Methods, 2012. 9(12): p.1207-1211.
  2. Fan, J., eet al., Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics. Mol Cell Proteomics, 2015. 14(11): p.3087-93.