idotp filtering

idotp filtering lisa walrond  2022-04-26

I am trying to filter my data based on idotp threshold (0.8). It appears when I apply this filter that peptides from all samples are deleted if peptides from any of the samples do not meet the idotp threshold. As opposed to just filtering out the specific samples that do not meet the threshold and leaving the good result. I am looking for a faster way to remove peaks from peptides that aren't real. I hope that is clear.
Thank you

Nick Shulman responded:  2022-04-26
You can use the Document Grid to remove peaks which match particular criteria.
After you have selected rows in the Document Grid, there is a "Actions" dropdown at the top of the Document Grid which has "Remove Peptide Peaks" and "Remove Precursor Peaks" menu items.
-- Nick
lisa walrond responded:  2022-04-28
Thank you. I was hoping to be able to do this in an automated fashion. What I was referring to is in the main document. Refine - Advanced - Results - Expected relative intensity correlation - Min idotp. When I set this to 0.8, I lose good (real) results that are 0.99 if some samples in the dataset I am analyzing have idotp values under the threshold.