Some proteins appearing in protein file but not peptide file

[ndtivendale]

Describe the bug In my output files, the protein.tsv file contains some proteins that are not present in the peptide.tsv file or the [filename].tsv file. Can you explain to me what is going on?

Also, can you explain the difference between the peptide.tsv file and the [filename].tsv file? I understand they have different headers, but what is the difference apart from that?

---

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• or just copy text from the output console on Run tab to a text file.

[ndtivendale]

Still waiting for the file request.

[prvst]

@ndtivendale

It looks like you did not receive the email with the request. Please try with the link instead

https://www.dropbox.com/request/v7wonNJEWsRyb2Lk91b5

[ndtivendale]

@prvst It must have been caught by the spam filter.

[ndtivendale]

Can you re-send the link please? My files didn't upload before the request expired.

From: Felipe da Veiga Leprevost @.> Sent: Friday, 1 July 2022 10:27 PM To: Nesvilab/FragPipe @.> Cc: Nathan Tivendale @.>; Mention @.> Subject: Re: [Nesvilab/FragPipe] Some proteins appearing in protein file but not peptide file (Issue #646)

@ndtivendalehttps://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fndtivendale&data=05%7C01%7Cnathan.tivendale%40uwa.edu.au%7Cfe9f1a5bf8914bd7186208da5b6dbe81%7C05894af0cb2846d8871674cdb46e2226%7C0%7C0%7C637922824156295115%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Ui4%2BWtIY6Dqzqqlr%2FWI0FlNe0vj%2BpU5Z%2FXdNpqjeYo0%3D&reserved=0

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[prvst]

https://www.dropbox.com/request/1SGPs8Dy19tA12eX1zMh

[prvst]

@ndtivendale You need to send me all your files, not the mzML. I need to see your run logs, peptide inference, validation, output tables, and the database. Send me all files from your analysis folder.

[ndtivendale]

@prvst sorry, I didn't understand. Will do.

[prvst]

@ndtivendale I ran ProteinProphet, and filtered your files using the sequential and the 2D filter. In both cases, all proteins that you mentioned above were present or absent in all output files. Because I cannot reproduce your issue, I believe they might relate it to files being reprocessed. Have you tried cleaning all folders from temporary and intermediary files before trying again?

[ndtivendale]

I will try that.

[danielgeiszler]

We have a comprehensive list of output files and explanation of them here:

https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_outputs.html#psmtsv

On Apr 20, 2022, at 20:08, Nathan @.***> wrote:  @prvst OK, I'll try that. In the meantime, here are three examples of proteins that are in the protein file but not the psm file for the replicate that I posted at the beginning of the thread. There are 175 more examples of such proteins in this replicate. AT1G12010.1 AT1G47500.1 AT2G29470.1

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