paste modified peptides into skyline to generate a target list

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paste modified peptides into skyline to generate a target list YZ  2014-08-04
 
Good Morning!

I am wondering if it is possible to import the information of peptide modification when I am directly coping and pasting peptide sequence into skyline to generate a target list. Right now the way I am importing modified peptides is that right clicking the pasted peptide sequence, selecting "modify" and editing modifications. Since the number of my targeted peptides is large (around 300-600), I am incapable of editing all modifications individually. It would be great if there is a faster way to generate the list of modified peptides.

Thank you very much for your help!

Jojo Zhu
 
 
Brendan MacLean responded:  2014-08-04
Hi Jojo,
Yes, this is supported. In Skyline 2.5, three formats are supported:

PEPT[+80]IDER
PEPT[Phospho (ST)]IDER
PEPT(unimod:21)IDER

In a future version, we expect also to support the AB SCIEX 3-letter abbreviations:

PEPT[Pho]IDER

Give any of the first three a try. Thanks for posting your question.

--Brendan