Comments (9)
KaiLiCn
commented on June 18, 2024
Hi, may I ask which format of result file you used? If it's ok, could you share your input files with me? Including result file and mgf file(s).
Kai
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marielclores
commented on June 18, 2024
Hi,
Yes, I used pepXML and mgf from Fragpipe. The ones I am using at the moment
are labeled with 20220909_BR.
https://uconn-my.sharepoint.com/:f:/g/personal/mariel_clores_uconn_edu/Ej-DQWx5J6NIgV_fCZzz6p8BzqJ1ubdhq1vbsNEurXsfXw?e=eyi5zO
I installed PDV on a different computer and encountered the same problem. I
even used the old data I used before when it was working well and still
encountered the same problem. One of these data is labeled with
20220530_OldNHSSamples.
I would really like to use PDV to analyze more samples. Thank you so much
for helping me!
Mariel
…On Mon, Sep 26, 2022 at 8:11 PM KaiLiCn ***@***.***> wrote:
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Hi, may I ask which format of result file you used? If it's ok, could you
share your input files with me? Including result file and mgf file(s).
Kai
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KaiLiCn
commented on June 18, 2024
Hi Mariel,
Thanks for your quick reply. I will take a look tomorrow.
By the way, if you run Fragpipe, it supports opening PDV inside Fragpipe directly after V18.0. I also added a few new features. And I am a little busy updating this standalone version. But I will push an update once I have time to summarize my codes.
Let me know if you have any questions about running PDV inside Fragpipe.
Kai
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marielclores
commented on June 18, 2024
Hi Kai,
Thank you very much! Is there a tutorial or instructions on how to open PDV
inside Fragpipe?
Mariel
…On Mon, Sep 26, 2022 at 8:45 PM KaiLiCn ***@***.***> wrote:
*Message sent from a system outside of UConn.*
Hi Mariel,
Thanks for your quick reply. I will take a look tomorrow.
By the way, if you run Fragpipe, it supports opening PDV inside Fragpipe
directly after V18.0. I also added a few new features. And I am a little
busy updating this standalone version. But I will push an update once I
have time to summarize my codes.
Let me know if you have any questions about running PDV inside Fragpipe.
Kai
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KaiLiCn
commented on June 18, 2024
Once you have done your run in Fragpipe after V18.0, there is a button over there:
If you want to open the existing result, please direct the "Output dir" to your result folder. Make sure the path of your raw files is correct.
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KaiLiCn
commented on June 18, 2024
Hi Mariel,
Does it work for you?
Kai
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marielclores
commented on June 18, 2024
Hi Kai,
It didn't work for me still.
Sincerely,
Mariel
…On Wed, Sep 28, 2022 at 1:14 PM KaiLiCn ***@***.***> wrote:
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Hi Mariel,
Does it work for you?
Kai
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KaiLiCn
commented on June 18, 2024
Hi Mariel,
I tried the files you shared with me last time. A few spectra can not be found inside the mgf file. There are some suggestions:
- Try to input "psm.tsv" into PDV and select "Philosopher(FragPipe)" as file type.
- Try to open PDV directly after finishing your search inside FragPipe. It would be helpful if you could share your FragPipe result folder and raw files with me. I can take a closer look about your search.
Kai
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marielclores
commented on June 18, 2024
Hi Kai,
I try to use the PDV from FragPipe and I am encountering a problem (picture
attached to this email). I didn't have a TMT mass in my modification and
the PDV shows this several times. The modification masses I have are
Dimethylation-D0: 28.0313 (both N-term and K)
Dimethylation-D6:34.06896 (both N-term and K)
Desthiobiotin Probe:196.20625 (on K)
Will you be able to help me with this?
Thank you,
Mariel
…On Tue, Oct 4, 2022 at 2:52 PM KaiLiCn ***@***.***> wrote:
*Message sent from a system outside of UConn.*
Hi Mariel,
I tried the files you shared with me last time. A few spectra can not be
found inside the mgf file. There are some suggestions:
1. Try to input "psm.tsv" into PDV and select "Philosopher(FragPipe)"
as file type.
2. Try to open PDV directly after finishing your search inside
FragPipe. It would be helpful if you could share your FragPipe result
folder and raw files with me. I can take a closer look about your search.
Kai
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Related Issues (20)
- visualization for fractionated samples HOT 8
- PDV Gui HOT 4
- Table not instantiated HOT 10
- mass error plot
- No spectrum found despite correct scan title HOT 5
- vulnerable log4j.jar file HOT 2
- Please increase JVM memory HOT 4
- How to add custom ions for spectrum annotation HOT 3
- Incompatible with Windows 11? HOT 2
- How does the author use the graphical user interface? HOT 1
- PEAKS Studio Peptide Mapping issue HOT 1
- Want to visualize results of XRNAX protocol HOT 1
- Export failed HOT 18
- Cannot navigate to subdirectory on MacOS HOT 4
- Can't parse Tide file HOT 4
- Feature request: specify scan number in one-PSM mode HOT 1
- Fail to parse Tide pepXML HOT 9
- Issue with coloring of i* and r* ions. HOT 2
- batch export modification spectra HOT 3
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