PITDB

A Resource for Sharing, Annotating and Analysing Translated Genomic Elements

About PITDB


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 July 2018, the PITDB data consist of:

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

Acknowledgements


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.