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PDV: an integrative proteomics data viewer
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a question about exporting b, y ions of selected spectra #61

Closed huiyinc closed 11 months ago

huiyinc commented 1 year ago

Hi,

I try to export the b, y ions of selected spectra using PDV-1.8.1, but the exporting progress is always 0% and no information is written to the file (as shown in the attached figure).

fig

It would be great if you could take a look of it, and let me know if there is anything I miss. Thanks in advance.

Huiyin

KaiLiCn commented 1 year ago

Hi Huiyin,

Sorry for the late reply. If it's ok, could you share your input files with me? I can take a look and test it. You can upload your files here https://www.dropbox.com/request/IDnwH389eOu69VYaXXsx

Best Kai

huiyinc commented 1 year ago

Hi Kai,

Thanks for the reply. I have uploaded the file to dropbox. Please let me know if there is any problem.

Best,

Huiyin

KaiLiCn commented 11 months ago

Hi Huiyin,

Can you try to replace the PDV-1.8.1.jar with this updated one? I am working on other parts of the updates. So it probably needs more time to release the new version. Let me know if it doesn't work. PDV-1.8.1.zip

Thanks, Kai

huiyinc commented 11 months ago

Hi Kai,

Thanks for the help. I have tried the PDV-1.8.1.zip you attached, but it seems that this version doesn't support FragPipe-generated PSM tables (as shown in the figure), and I can't open the PSM tables with it. fig

It would be great if you can let me know if there is anything I miss. Thanks.

Huiyin

KaiLiCn commented 11 months ago

Hi Huiyin,

Can you select your PSM.tsv file in the "identification File" panel? Then there is a "File Type" selection. Selecting "FragPipep". image

Kai

huiyinc commented 11 months ago

Hi Kai,

Sorry for the late reply. I have rerun the PDV you sent me and found out that the software tool is working now. Thank you for all the kind help. PDV is a great visualization tool.

Best wishes,

Huiyin

KaiLiCn @.***> 於 2023年9月25日 上午4:18 寫道：



Hi Huiyin,

Can you select your PSM.tsv file in the "identification File" panel? Then there is a "File Type" selection. Selecting "FragPipep". [image: image] https://user-images.githubusercontent.com/29800230/270189458-b5e22bc5-1010-46f6-a390-4832bfc49773.png

Kai

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