contaminants filtered from TMT-Integrator

[mwfoster]

I have noticed that FragPipe v.18 removes contaminant proteins from the outputs in the TMT-report folder, whereas they were kept in FragPIpe v.17.1. I am using a bovine casein spike-in, so I can fix this by removing "contam" from the .fasta file for these entries. Is there an option in FragPipe to keep contaminants through the reporter ion quantification, or can you make this an option in a future release? Thanks, Matt

• Upload your log file (If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)

[prvst]

@mwfoster I got an internal request to remove the contaminants from all the output tables. If you want to still have them, please add the contaminants to the FASTA file without the contam_ tag.

[mwfoster]

OK, thanks. That is the solution I came up with. Matt

From: Felipe da Veiga Leprevost @.> Sent: Thursday, July 14, 2022 10:21 AM To: Nesvilab/FragPipe @.> Cc: Matthew Foster, Ph.D. @.>; Mention @.> Subject: Re: [Nesvilab/FragPipe] contaminants filtered from TMT-Integrator (Issue #759)

@mwfosterhttps://urldefense.com/v3/__https:/github.com/mwfoster__;!!OToaGQ!tR0Uj01SG_YyLrWDi7CMB_GZMqPgwOkDxmH8La1bSIQq32pmvDkrsVqahbdNSZ-hTElPliKJbNlKqsP162YgrF4EJw$ I got an internal request to remove the contaminants from all the output tables. If you want to still have them, please add the contaminants to the FASTA file without the contam_ tag.

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[fcyu]

@mwfoster I got an internal request to remove the contaminants from all the output tables. If you want to still have them, please add the contaminants to the FASTA file without the contam_ tag.

Hi Felipe @prvst ,

I tested with the latest Philosopher (4.4.0), and see contaminants in the psm.tsv, protein.tsv, and combined_protein.tsv. It does not agree with what you said. Could you double check and confirm? I put my files in https://www.dropbox.com/sh/idnkh4x2ldbnk7h/AABvbwwQOMjN-cFCguvJrCnRa?dl=0

Thanks,

Fengchao

[anesvi]

@mwfosterhttps://github.com/mwfoster – we have a few questions. What version of Philosopher did you use? Did you add contaminants using philosoper? Did you use TMT-Integrator? I think we need a bit more detail

From: Fengchao @.> Sent: Thursday, July 14, 2022 10:54 AM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: Re: [Nesvilab/FragPipe] contaminants filtered from TMT-Integrator (Issue #759)

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@mwfosterhttps://github.com/mwfoster I got an internal request to remove the contaminants from all the output tables. If you want to still have them, please add the contaminants to the FASTA file without the contam_ tag.

Hi Felipe @prvsthttps://github.com/prvst ,

I tested with the latest Philosopher (4.4.0), and see contaminants in the psm.tsv, protein.tsv, and combined_protein.tsv. It does not agree with what you said. Could you double check and confirm? I put my files in https://www.dropbox.com/sh/idnkh4x2ldbnk7h/AABvbwwQOMjN-cFCguvJrCnRa?dl=0

Thanks,

Fengchao

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/759#issuecomment-1184547352, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM65CF723ZD36KTMBEFTVUASZRANCNFSM53NBZN6A. You are receiving this because you are subscribed to this thread.Message ID: @.@.>>

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[mwfoster]

Fengchao is correct that the contaminants are present in those files, but they do not appear in the output in the “tmt-report” folder. I believe this is a change from the previous version of FP, based on my test. I can appreciate both sides of the argument for keeping or excluding from normalization, for example, and I am fine with the workaround that was suggested. The option to keep or exclude contaminants from quantitative reports would be nice in a future version. Matt

From: Alexey Nesvizhskii @.> Sent: Thursday, July 14, 2022 10:59 AM To: Nesvilab/FragPipe @.> Cc: Matthew Foster, Ph.D. @.>; Mention @.> Subject: Re: [Nesvilab/FragPipe] contaminants filtered from TMT-Integrator (Issue #759)

@mwfosterhttps://github.com/mwfosterhttps://urldefense.com/v3/__https:/github.com/mwfoster*3E__;JQ!!OToaGQ!uRv3kDzjqnzWhsg5X1AG8HpwT0I4VggSm8epa_oRMtbwXQJvP4NPHPzgIAJLkxabirGYWiYtyxkz3rm4m2QQL8-ePg$ – we have a few questions. What version of Philosopher did you use? Did you add contaminants using philosoper? Did you use TMT-Integrator? I think we need a bit more detail

From: Fengchao @.mailto:***@***.***> Sent: Thursday, July 14, 2022 10:54 AM To: Nesvilab/FragPipe @.mailto:***@***.***> Cc: Subscribed @.***mailto:***@***.***> Subject: Re: [Nesvilab/FragPipe] contaminants filtered from TMT-Integrator (Issue #759)

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@mwfosterhttps://github.com/mwfosterhttps://urldefense.com/v3/__https:/github.com/mwfoster*3E__;JQ!!OToaGQ!uRv3kDzjqnzWhsg5X1AG8HpwT0I4VggSm8epa_oRMtbwXQJvP4NPHPzgIAJLkxabirGYWiYtyxkz3rm4m2QQL8-ePg$ I got an internal request to remove the contaminants from all the output tables. If you want to still have them, please add the contaminants to the FASTA file without the contam_ tag.

Hi Felipe @prvsthttps://github.com/prvsthttps://urldefense.com/v3/__https:/github.com/prvst*3E__;JQ!!OToaGQ!uRv3kDzjqnzWhsg5X1AG8HpwT0I4VggSm8epa_oRMtbwXQJvP4NPHPzgIAJLkxabirGYWiYtyxkz3rm4m2Tskf5Ijw$ ,

I tested with the latest Philosopher (4.4.0), and see contaminants in the psm.tsv, protein.tsv, and combined_protein.tsv. It does not agree with what you said. Could you double check and confirm? I put my files in https://www.dropbox.com/sh/idnkh4x2ldbnk7h/AABvbwwQOMjN-cFCguvJrCnRa?dl=0https://urldefense.com/v3/__https:/www.dropbox.com/sh/idnkh4x2ldbnk7h/AABvbwwQOMjN-cFCguvJrCnRa?dl=0__;!!OToaGQ!uRv3kDzjqnzWhsg5X1AG8HpwT0I4VggSm8epa_oRMtbwXQJvP4NPHPzgIAJLkxabirGYWiYtyxkz3rm4m2TZ_NaZ6A$

Thanks,

Fengchao

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[anesvi]

@mwfoster did we fix this issue?

[mwfoster]

I did check again today and I don't see contaminants identified in the psm/peptide/protein.txt files passed through to the tmt-report folder. I'm fine with the suggested workaround which is to remove the "contam_" from the protein name if you want to have it appear in the tmt-report files.