few Lipids from Lipimatch are not getting convrted #13
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Hi @yashwantkumar ! The Cer class has generally more issues since there are many different additional markers. I hope we can find a more generic solution for this kind of issues and fix it in the next release. Best, Zhixu Ni |
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I am using lipidmatch flow (http://secim.ufl.edu/secim-tools/lipidmatchflow/).
I have also attached the list of lipids that can be identified from
lipidmatch flow (with all possible unusual names). Please check that.I am
using http://lipidmaps.org/lipidlynxx/ for conversion. lipidR 2.2.0 version
of lipidR has been installed.
…On Mon, Oct 19, 2020 at 4:49 PM Zhixu Ni ***@***.***> wrote:
Hi @yashwantkumar <https://github.com/yashwantkumar> !
Thank you very much for submitting this issue!
The Cer class has generally more issues since there are many different
additional markers.
We are making an upgrade of the nomenclature decode module with special
focus on Cer, HexCer, SM, and SPB.
Can you tell me which version of Lipidmatch are you using now, and which
distribution of LipidLynxX are you using (e.g. Source code, exe, or online
version on LIPID MAPS)? I will have a more closer look.
I hope we can find a more generic solution for this kind of issues and fix
it in the next release.
Best,
Zhixu Ni
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Many thanks for the information!
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I could not attach the file on Github. Please find the attachment to this
email.
…On Mon, Oct 19, 2020 at 5:05 PM Zhixu Ni ***@***.***> wrote:
Many thanks for the information!
I'm not able to get the attached file you mentioned through email reply.
Can you please use the GitHub native reply and upload attach files again?
Instructions here:
https://github.blog/2015-09-25-attach-files-to-comments/
Thanks!
I am using lipidmatch flow (
http://secim.ufl.edu/secim-tools/lipidmatchflow/). I have also attached
the list of lipids that can be identified from lipidmatch flow (with all
possible unusual names). Please check that.I am using
http://lipidmaps.org/lipidlynxx/ for conversion. lipidR 2.2.0 version of
lipidR has been installed.
… <#m_-1168419414138060836_>
On Mon, Oct 19, 2020 at 4:49 PM Zhixu Ni *@*.***> wrote: Hi @yashwantkumar
<https://github.com/yashwantkumar> https://github.com/yashwantkumar !
Thank you very much for submitting this issue! The Cer class has generally
more issues since there are many different additional markers. We are
making an upgrade of the nomenclature decode module with special focus on
Cer, HexCer, SM, and SPB. Can you tell me which version of Lipidmatch are
you using now, and which distribution of LipidLynxX are you using (e.g.
Source code, exe, or online version on LIPID MAPS)? I will have a more
closer look. I hope we can find a more generic solution for this kind of
issues and fix it in the next release. Best, Zhixu Ni — You are receiving
this because you were mentioned. Reply to this email directly, view it on
GitHub <#13 (comment)
<#13 (comment)>>,
or unsubscribe
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.
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please check |
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I got his file, thanks! Thanks! |
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.csv file contains MSMS id information. Should I sent that to you? I would
like to use lipidR without missing any lipid so any format is fine.
…On Mon, 19 Oct 2020 at 17:16, Zhixu Ni ***@***.***> wrote:
names_lipids.xlsx
<https://github.com/SysMedOs/LipidLynxX/files/5401463/names_lipids.xlsx>
I got his file, thanks!
Can you send me Cer_H.csv, CerP_H.csv and PlasmenylTG_NH4.csv as well?
Which export format you want to use?
e.g.
Shorthand @ Molecular species level
COMP_DB @ Bulk level
Thanks!
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Can you send me these csv file via Google Drive / One Drive? Thanks! |
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shared on your email ID. zhixu.ni@uni-leipzig.de
…On Mon, Oct 19, 2020 at 5:30 PM Zhixu Ni ***@***.***> wrote:
.csv file contains MSMS id information. Should I sent that to you? I would
like to use lipidR without missing any lipid so any format is fine.
… <#m_-5280553649649377111_>
On Mon, 19 Oct 2020 at 17:16, Zhixu Ni *@*.***> wrote: names_lipids.xlsx
https://github.com/SysMedOs/LipidLynxX/files/5401463/names_lipids.xlsx I
got his file, thanks! Can you send me Cer_H.csv, CerP_H.csv and
PlasmenylTG_NH4.csv as well? Which export format you want to use? e.g.
Shorthand @ Molecular species level COMP_DB @ Bulk level Thanks! — You are
receiving this because you were mentioned. Reply to this email directly,
view it on GitHub <#13 (comment)
<#13 (comment)>>,
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Can you send me these csv file via Google Drive / One Drive.
You can send the link to my email: zhixu.ni <#at> uni-leipzig.de
Thanks!
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Many thanks @yashwantkumar ! Best, Zhixu Ni |
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Hi,
Hope you have resolved the file format issue, I requested.
Best regards,
Yashwant
…On Mon, Oct 19, 2020 at 5:54 PM Zhixu Ni ***@***.***> wrote:
shared on your email ID. ***@***.***
Many thanks!
I've downloaded these files and will have a look soon.
I'll update you when the fixed version is available.
Best,
Zhixu Ni
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Hi @yashwantkumar ! I've fixed it on a develop branch using a lite collection of the names you provided, but still no GUI available. Thank for the feedback again, I will notify you again when the fix is online. Best, |
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Thank you so much.
…On Wed, 9 Dec 2020 at 18:13, Zhixu Ni ***@***.***> wrote:
Hi @yashwantkumar <https://github.com/yashwantkumar> !
I've fixed it on a develop branch using a lite collection of the names you
provided, but still no GUI available.
Due to the current plans, this fix will be tested with other improvement
including speed upgrade and will be released in January I hope.
Once this upgrade is ready it will be available with GUI and the version
on LIPID MAPS will be upgraded as well.
Thank for the feedback again, I will notify you again when the fix is
online.
Best,
Zhixu Ni
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unconverted.txt |
Cer-NDS(d20:0/18:0)
Cer-NS(d18:2/22:0)
HexCer-NS(d18:1/23:0)
plasmanyl-TG(O-20:0_14:0_18:2)
These lipids identification is the output of lipidmatch. Software could not convert into lipidlynx format.
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