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Nesvilab / TMT-Integrator

A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.
http://tmt-integrator.nesvilab.org
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TMT Quantification Question #28

Closed barny116 closed 11 months ago

barny116 commented 1 year ago

Hi, I am new to using MSFragger, but I am really excited about its capabilities. I typically use PD to search my TMTPro 16-plex labeled peptide samples. However, I am trying a new application that PD is not suited for. Can you provide me with more information on the "min intensity (percent)" option? In my PD searches with TMT labels, I usually require a reporter ion S/N ratio of 10/1. Thanks, Lea

anesvi commented 1 year ago

It is similar to the PD SN filter option. We remove PSMs with the intensity values falling in the lowest 5% (2.5% for PTM data). You can change these values, but what we set as defaults is what worked well for us in our tests.

barny116 commented 1 year ago

Thank you so much for your prompt response. Also, is there anyway to add correction values for the individual TMT labels in MSFragger? Typically, I set the co-isolation threshold to 25% in PD. I believe that would be 75% in MSFragger's "min purity" option, as it is flipped? Is that correct? Thanks, Lea

On Wed, Mar 29, 2023 at 3:37 PM Alexey Nesvizhskii @.***> wrote:

It is similar to the PD SN filter option. We remove PSMs with the intensity values falling in the lowest 5% (2.5% for PTM data). You can change these values, but what we set as defaults is what worked well for us in our tests.

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/TMT-Integrator/issues/28#issuecomment-1489275370, or unsubscribe https://github.com/notifications/unsubscribe-auth/A62XJWH32DOL2TPUHFDBIRTW6SMQTANCNFSM6AAAAAAWMMFYMU . You are receiving this because you authored the thread.Message ID: @.***>

anesvi commented 1 year ago

We do not have the correction option. As far as Purity, yes it is flipped (so PD's 75% filter is Purity 25%. We recommend 50%, our default)

barny116 commented 1 year ago

Awesome, thanks. Can you give me some insight on why your team chose not to include the correction step? -Lea

anesvi commented 1 year ago

We extensively tested it as part of CPTAC consortium benchmarking, and it was not helping and even creating occasional problems. We disabled that option a while back. At any rate, we do not plan to add it back any time soon as we have other priorities.