specNumHighIntIons

[Nick Carruthers]

Using the PeptideAtlas client, I am swamped by the number of
transitions generated. I want to reduce the number by using only the
most intense ions in the stored spectra- but filling in a value in the
specNumHighIntIons field results in an error.
Has anyone else had this problem?

Regards,
Nick

[Lange Vinzenz]

Hi Nick,
Even though the PeptideAtlas client supports the retrival of
transitions, we have never used it for this purpose. Instead we used it
to retrieve information regarding the proteotypic peptides. To retrieve
the proteotypic peptides you select only the "getPep" option.
To retrieve transitions for yeast I would suggest you to go to
www.MRMAtlas.org
This is based on Q-TRAP data and therefore more reliable than the
iontrap data for predicting the best transitions.
To use the PeptideAtlas client output you would need to perform some
postprocessing selecting only the most abundant fragments and removing
unwanted modifications. Currently, this is not possible since the output
does not contain intensity information. And unfortunately the
specNumHighIntIons is indeed not functional.
Sorry, for this.
Vinz