LFQ-phospho - sequence

[nishimuy]

Will you be able to extract the sequence window more flexibly? Could you get the predicted phosphosite in the middle of the window, so we can get the sequence of both the N and C terminus sides? I am using combined_site_STY_79.9663.tsv, and the Peptide column provides sequence, but the the length of the sequence varies between sites too.

[fcyu]

What if there are two phospho in the peptide?

Thanks,

Fengchao

[nishimuy]

Hi Fengchao,

I am working on PhosR to examine kinase-substrate relationship using combined_site_STY_79.9663.tsv. I thought we still know which site based on the localization score even if you have two phospho in the peptide?

They said; "Sequence window: A character vector denoting the sequence window, typically of 15–31 in
length. The residues in the sequence window should be capitalized. Note that the predicted phosphosite should reside in the middle of the window. Any phosphosites that are found near the N or C terminus of the protein will require a placeholder (i.e., add ‘‘_’’ to either side of the flanking sequence) to position the phosphosite in concern at the middle of the sequence win- dow (Most processing software will do this for you automatically)."

The sequence window shown in combined_site_STY_79.9663.tsv might not be suitable for this analysis.