Nick Shulman responded: |
2021-02-02 06:51 |
There is a limited set of modifications that Skyline understands when reading a .msp file. You can find that list of modifications here:
https://skyline.ms/announcements/home/support/thread.view?rowId=49257
Where did you get this .msp file?
Could you use a .blib file instead? With .blib files, Skyline does a lot of work to try to figure out what modifications in your document have the same mass as the modifications in your library, but for .msp files, you are limited to the set of modifications in that list.
I am not the expert on .msp files, so I am not sure why Skyline has such a limited list, or what it would take to add things to that list.
-- Nick |
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laura corveleyn responded: |
2021-02-02 07:40 |
Hi Nick,
Thanks for the quick response! This explains a lot. Reading Victor's request, I see we have the same problem. Our .msp file is also created in-house (using predictions) and we can't use a .blib file instead. It would indeed be very helpful if someone else of your team could help us out with this one.
Kind regards,
Laura |
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Brian Pratt responded: |
2021-02-02 08:27 |
It seems like we should be able to do better: "although I also defined it as a modification in the peptide settings" is a perfectly logical thing to expect to work since the MSP reader is built into Skyline, unlike the various blib converters.
I'll open a ticket on this.
Best,
Brian Pratt |
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laura corveleyn responded: |
2021-04-08 06:45 |
Hi,
I was wondering if there are any updates on this issue?
Many thanks!
Kind regards,
Laura |
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Brian Pratt responded: |
2021-04-08 08:57 |
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laura corveleyn responded: |
2021-07-26 08:23 |
Hi Brian,
I see that I don't have access anymore to the issue update. Does this mean this has been resolved or are there any other updates on this? ;)
Thanks!
Kind regards,
Laura |
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Brendan MacLean responded: |
2021-07-26 10:29 |
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Juergen responded: |
2024-02-12 02:03 |
Dear all,
is there any update on this issue?
I am struggeling on the very same issue currently:
To predict the spectra of several unusual cystein modifications used Seq2MS ( https://pubs.acs.org/doi/10.1021/acs.jproteome.3c00180) and wanted to include the generated msp library to my skyline project in order to get an idea of the spectra for PRM measurements. Unfortunately this ends in a complete mess as the peptide sequences are parsed only to the modified residue and thus skyline attempts to merge the spectra for different modification types on the same residue. Is there any way how I could circumvent that issue and still use this library? As we could not synthesise the modified peptides and they are quite low abundant, this seems the best option to develop our PRM assays.
Best regards,
Juergen |
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Brian Pratt responded: |
2024-02-13 11:26 |
That hasn't made it to the top of the development list, but having another request helps set the priority. I'll see what we can do about getting this moving, and I've added you to the notify list so you'll hear about progress.
Best regards,
Brian Pratt |
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Brian Pratt responded: |
2024-02-13 12:48 |
@Juergen I think yours is maybe a different problem than the one originally described here - can you supply an example .msp file so we know what you're dealing with?
Thanks,
Brian |
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Juergen responded: |
2024-02-14 01:03 |
Hi Brian,
Thank you for having a closer look on the issue. I will send you the file by email.
Best regards,
Juergen |
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