I have a big question about some identified proteins by LC-MS/MS from european beech (fagus sylvatica:its genome is not sequenced).
For the identification of proteins two searches were performed:
1. Peptides from ech spot were matched against a populus (which genome is sequenced) database.
2. As we identified a lot of putative and unpredicted proteins in the first search we made a second approach. This time mass spectra were matched against ESTs from Fagus & Quercus. Those ESTs, that are by the way not available in public databases, were blasted against a viridiplantae database (swiss prot) for homolgy search. The blast aims at finding a function to the non-annotated sequences.
My questions regards to the second search, against ESTs. Why are ESTs useful if they are not annotated? Is there a possibility to directly blast mass spectra against a viridiplantae database without using ESTs?
Thank you for your support…
Edited by kern, 16 October 2009 - 05:36 AM.