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)

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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

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