TMT channel interference problem!

[seongminlab]

Dear developers!

In our TMTPro-16plex labeling data, 126 and 134N channels without peptides, other channels labeled with HEK and HeLa peptide.

in this case, we found more than 5% of channel interference from 127 to 126!

So, how can we use isotope distribution (from Thermo, TMT kit with each Lot Number) for peptide quantification?

and can we use protein quantification without TMT-integrator on FragPipe?

Thank you

[anesvi]

FragPipe/TMT-Integrator does not have the isotope impurity correction. We used to have it but removed because it was creating some new problems.

When you have empty channels, annotate them as None in the annotation.txt file

You can use PSM.tsv to do your own quantification in any way you want

There is also quantification in protein.tsv files that is from Philosopher quant, not TMT-Integrator. And it is based on summing reporter ion intensities, more like in PD.

Best Alexey

From: Seongmin Cheon @.> Sent: Thursday, October 20, 2022 9:27 PM To: Nesvilab/FragPipe @.> Cc: Subscribed @.***> Subject: [Nesvilab/FragPipe] TMT channel interference problem! (Issue #868)

External Email - Use Caution

Dear developers!

In our TMTPro-16plex labeling data, 126 and 134N channels without peptides, other channels labeled with HEK and HeLa peptide.

in this case, we found more than 5% of channel interference from 127 to 126!

So, how can we use isotope distribution (from Thermo, TMT kit with each Lot Number) for peptide quantification?

and can we use protein quantification without TMT-integrator on FragPipe?

Thank you

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/868, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM644H635JUTSQYB75PDWEHWO7ANCNFSM6AAAAAARKWDJXQ. You are receiving this because you are subscribed to this thread.Message ID: @.**@.>>

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[lbwfff]

FragPipe/TMT-Integrator does not have the isotope impurity correction. We used to have it but removed because it was creating some new problems. When you have empty channels, annotate them as None in the annotation.txt file You can use PSM.tsv to do your own quantification in any way you want There is also quantification in protein.tsv files that is from Philosopher quant, not TMT-Integrator. And it is based on summing reporter ion intensities, more like in PD. Best Alexey From: Seongmin Cheon @.> Sent: Thursday, October 20, 2022 9:27 PM To: Nesvilab/FragPipe @.> Cc: Subscribed @.> Subject: [Nesvilab/FragPipe] TMT channel interference problem! (Issue #868) External Email - Use Caution Dear developers! In our TMTPro-16plex labeling data, 126 and 134N channels without peptides, other channels labeled with HEK and HeLa peptide. in this case, we found more than 5% of channel interference from 127 to 126! So, how can we use isotope distribution (from Thermo, TMT kit with each Lot Number) for peptide quantification? and can we use protein quantification without TMT-integrator on FragPipe? Thank you — Reply to this email directly, view it on GitHub<#868>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM644H635JUTSQYB75PDWEHWO7ANCNFSM6AAAAAARKWDJXQ. 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

Hi Alexey,

I have some doubts about the tmt process of fragpipe, as you said TMT-Integrator does not perform isotope impurity correction, will this affect the quantification? Then I noticed that the default tmt process does not use MSBooster for further evaluation, is there a reason for this?

Thanks, LeeLee

[anesvi]

Hi LeeLee,

Our tests showed that performing isotope correction did not improve the quantification noticeably

You can turn MSBooster on. There will be a gain, but quite small. We may turn it on in the next release for TMT workflows.

Best Alexey

From: LeeLee @.> Sent: Thursday, November 10, 2022 10:34 PM To: Nesvilab/FragPipe @.> Cc: Nesvizhskii, Alexey @.>; Assign @.> Subject: Re: [Nesvilab/FragPipe] TMT channel interference problem! (Issue #868)

External Email - Use Caution

FragPipe/TMT-Integrator does not have the isotope impurity correction. We used to have it but removed because it was creating some new problems. When you have empty channels, annotate them as None in the annotation.txt file You can use PSM.tsv to do your own quantification in any way you want There is also quantification in protein.tsv files that is from Philosopher quant, not TMT-Integrator. And it is based on summing reporter ion intensities, more like in PD. Best Alexey From: Seongmin Cheon @.> Sent: Thursday, October 20, 2022 9:27 PM To: Nesvilab/FragPipe @.> Cc: Subscribed @.> Subject: [Nesvilab/FragPipe] TMT channel interference problem! (Issue #868https://github.com/Nesvilab/FragPipe/issues/868) External Email - Use Caution Dear developers! In our TMTPro-16plex labeling data, 126 and 134N channels without peptides, other channels labeled with HEK and HeLa peptide. in this case, we found more than 5% of channel interference from 127 to 126! So, how can we use isotope distribution (from Thermo, TMT kit with each Lot Number) for peptide quantification? and can we use protein quantification without TMT-integrator on FragPipe? Thank you — Reply to this email directly, view it on GitHub<#868https://github.com/Nesvilab/FragPipe/issues/868>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM644H635JUTSQYB75PDWEHWO7ANCNFSM6AAAAAARKWDJXQ. 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

Hi Alexey,

I have some doubts about the tmt process of fragpipe, as you said TMT-Integrator does not perform isotope impurity correction, will this affect the quantification? Then I noticed that the default tmt process does not use MSBooster for further evaluation, is there a reason for this?

Thanks, LeeLee

— Reply to this email directly, view it on GitHubhttps://github.com/Nesvilab/FragPipe/issues/868#issuecomment-1311188318, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIIMM6336IND4CGTIDQBZNTWHW5ELANCNFSM6AAAAAARKWDJXQ. You are receiving this because you were assigned.Message ID: @.**@.>>

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