I would like to add peptides as groups to the document. It seems to work if I use ">" for the group name, e.g.
>biognosys
LGGNEQVTR
GAGSSEPVTGLDAK
VEATFGVDESNAK
is parsed correctly.
However, when I try to do the same with a modification stipulated in square brackets, I get an error:
>biognosys
L[Phenylisocyanate (N-term)]GGNEQVTR
GAGSSEPVTGLDAK
VEATFGVDESNAK
YILAGVENSK
"Unexpected character "[" found on line 2"
At the same time I can simply paste these peptides without the line containing ">", i.e.
L[Phenylisocyanate (N-term)]GGNEQVTR
GAGSSEPVTGLDAK
VEATFGVDESNAK
YILAGVENSK
works as expected with all peptides assigned to "peptides 1".
Is there a way to group peptides in groups like "peptides1" with modifications stipulated in []? |
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| Nick Shulman responded: |
2025-04-03 06:59 |
This will actually work if your protein names start with two greater than signs (">>"):
>>biognosys
L[Phenylisocyanate (N-term)]GGNEQVTR
GAGSSEPVTGLDAK
VEATFGVDESNAK
YILAGVENSK
When the protein name started with one greater than sign, Skyline was interpreting it as a FASTA file. Skyline inserted one protein whose sequence was LGGNEQVTRGAGSSEPVTGLDAKVEATFGVDESNAK and that just happened to have the three tryptic peptides that you wanted.
When the protein starts with two greater than signs, Skyline interprets it as a format that Skyline invented which is "peptide lists". Peptide Lists are allowed to contain peptides with modifications like that and one peptide sequence per line.
Another way to do this would be to insert the peptide sequences using the "Edit > Insert > Peptides" menu item and make sure that the values in the Protein Name column are the same for all of the peptides that you want grouped together.
-- Nick |
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| pavel shliaha responded: |
2025-04-03 07:34 |
Dear Nick,
thanks for the response but it doesn't work. If I paste
>>biognosys
L[Phenylisocyanate (N-term)]GGNEQVTR
GAGSSEPVTGLDAK
VEATFGVDESNAK
YILAGVENSK
I get the same response: "Unexpected character "[" found on line 2". Does it work on your side?
Pavel |
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| Nick Shulman responded: |
2025-04-03 07:59 |
Make sure you are using the latest version of Skyline 24.1.
That's Skyline 24.1.0.414 which was released in February.
If you are using the previous release, 24.1.0.199, from last summer then it does not seem to work, although I am not sure why not.
But, this does work for me in the latest Skyline 24.1 and also Skyline-daily.
-- Nick |
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| pavel shliaha responded: |
2025-04-03 08:55 |
installed new version and it worked. Thanks, Nick! You are the best. Sent my skyline support letter today and told everyone I knew to do it as well! |
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