ApiDB/EuPathDB Workshop

Expression data II (Proteomics) Exercises

Mark Heiges
Tuesday, June 10th - 3:30 pm

Exercise 1: Mass spec and EST data, Giardia


  • From the EuPathDB site, go to the GiardiaDB site by clicking on the GiardiaDB icon
  • Making use of the available queries and the query history function, where needed, answer the following questions:
    • How many Giardia lamblia genes have evidence of protein expression from mass spectrometry analysis but do not have evidence of transcript expression from ESTs?
    • What are some explanations for why a gene would have expression evidence from MS but not from EST sequencing?

Exercise 2 : Mass spec, CryptoDB and ToxoDB


  • From the EuPathDB site, go to the ToxoDB site or the CryptoDB site by clicking on the icon for that site.
  • Making use of the available queries and the query history function, where needed, answer the following questions:
    • Find examples of mass spectrometry derived peptides in CryptoDB or ToxoDB that support the annotation of intron/exon boundaries.
    • What approach did you take to find them?
    • What other types of experimental evidence contained within CryptoDB or ToxoDB can be used to verify the annotation of intron/exon boundaries?