Export failed

[perhag972]

I fail to export spectra from a MS fragger search of TIMS TOF data as PNG file. Any suggestion how this could be resolved?

[KaiLiCn]

Sorry, I can't see you picture. Could you share it again?

[perhag972]

[KaiLiCn]

Hi there,

Here is a bug to export batch spectra. I will fix it in next version.

I noticed you only need one spectra. Could you please try this way to export it? Click the Export in the toolbar.

Please let me know if it doesn't works.

Kai

[KaiLiCn]

By the way, you can open PDV directly inside FragPipe right now. It will provide more information than standalone version.

[perhag972]

Hi,

It worked when i exported a single spectrum according to your instructions, but i actually wanted to export the whole batch so it would be really great if you could fix the bug. And thanks for the tip about Fragpipe, will try it out.

BR Per

I actually wanted to export the whole batch

[KaiLiCn]

OK. I will try to fix it this week. Will let you you after updating the release.

[perhag972]

Great, thanks, Btw, i have noticed that it can take very long time to load big datasets. Any tips on how to speed this up?

[KaiLiCn]

I optimized some steps in FragPipe version, but I don't have time to update the codes here. Could you try if it helps? And the batch export function in FragPipe is locked. I will test and open it soon.

[perhag972]

OK, I will try.

[KaiLiCn]

Hi,

I just updated the package. Could you try it?
https://www.dropbox.com/s/d0qmm08luix0gcv/FP-PDV-1.0.3.jar?dl=0

Enter FragPipe folder and replace FP-PDV-1.0.3.jar with this new one:

There is a button to export selected spectra:

This function is still under testing. Please let me know if you have any issues. Or you can open a new issue under FragPipe respositry.

Kai

[perhag972]

It takes VERY long time to load big datasets into PDV (for example psm.tsv from fragpipe). Any tips on how this can be speeded up?

[KaiLiCn]

As I showed in the previous post, you could try to open PDV inside FragPipe using the new package I shared with you. You don't need to import psm.tsv by yourself. After searching, click the button.

https://www.dropbox.com/s/d0qmm08luix0gcv/FP-PDV-1.0.3.jar?dl=0
It will increase 5-10X speed. Let me know if you have difficulty running it.

Kai

[perhag972]

I have tested also to use PDV inside Fragpipe with the file you sent to me. It works for small datasets but it still takes very long time to open big datasets.

[KaiLiCn]

What's the raw file type? And how many raw files do you have?

[anesvi]

Maybe PDV can open just some files, not all, when starting. Then have an option to load the remaining data. What one would want to see if the number of files huge? It’s not that useful to look at data using a viewer if the dataset is huge. Alexey From: KaiLiCn ***@***.***> Sent: Tuesday, October 11, 2022 3:15 PM To: wenbostar/PDV ***@***.***> Cc: Subscribed ***@***.***> Subject: Re: [wenbostar/PDV] Export failed (Issue #38) External Email - Use Caution What's the raw file type? And how many raw files do you have? — Reply to this email directly, view it on GitHub<#38 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIIMM65Q2JWF4H5265V5Y4TWCW4B7ANCNFSM6AAAAAAQ4ZGA2Q>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.******@***.***>> ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[KaiLiCn]

Thanks, @anesvi! After changing mgf to mzml in the next version, we could open it much faster. I am testing that part. @perhag972 sorry for the inconvenience. I will send you a pre-release version once I finish testing.

[perhag972]

It is 42 rawfiles from timstof data converted to mgf file of ca 5 GB each processed in fragpipe

[KaiLiCn]

I see. Will let you know if I have any updates.