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[marielclores]

I've been trying to use PDV using two different computers and they keep giving me the same issue:

I tried selecting the files I used before when it was working still. This time, it didn't work and gave the same error. Can someone help me?

[KaiLiCn]

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

[marielclores]

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

— Reply to this email directly, view it on GitHub https://github.com/wenbostar/PDV/issues/36#issuecomment-1258807943, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3ITXAWVAEB3DB7D4SAQ3VLWAI3Q7ANCNFSM6AAAAAAQVMGKKU . You are receiving this because you authored the thread.Message ID: @.***>

[KaiLiCn]

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

[marielclores]

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

— Reply to this email directly, view it on GitHub https://github.com/wenbostar/PDV/issues/36#issuecomment-1258828407, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3ITXASA2UNR6EPKSBQHTFLWAI7SRANCNFSM6AAAAAAQVMGKKU . You are receiving this because you authored the thread.Message ID: @.***>

[KaiLiCn]

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.

[KaiLiCn]

Hi Mariel,

Does it work for you?

Kai

[marielclores]

Hi Kai,

It didn't work for me still.

Sincerely, Mariel

On Wed, Sep 28, 2022 at 1:14 PM KaiLiCn @.***> wrote:

Message sent from a system outside of UConn.

Hi Mariel,

Does it work for you?

Kai

— Reply to this email directly, view it on GitHub https://github.com/wenbostar/PDV/issues/36#issuecomment-1261216293, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3ITXARDEHCMMTYI74MHXX3WAR4H7ANCNFSM6AAAAAAQVMGKKU . You are receiving this because you authored the thread.Message ID: @.***>

[KaiLiCn]

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

[marielclores]

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

— Reply to this email directly, view it on GitHub https://github.com/wenbostar/PDV/issues/36#issuecomment-1267446214, or unsubscribe https://github.com/notifications/unsubscribe-auth/A3ITXAX3GM4GYMEDBGKCWATWBR4FJANCNFSM6AAAAAAQVMGKKU . You are receiving this because you authored the thread.Message ID: @.***>