Thank you Dr David! That is really great help. I have a couple of follow-up queries:
1) If I use iProphet on these results, does that now use Decoy based FDR estimates or the PeptideProphet statisitcal model only estimates. 2) If I combine multiple PeptideProphet outputs (from fractions of same digest) in iProphet , how does that affect individual PSMs? For example, if a PSM if found in multiple fractions, does it get converted to single PSM in the iProphet output (I just want to make the output compatible to MSStatsTMT - see here https://groups.google.com/g/msstats/c/aINhWMKt2Co) While MSStatsTMT has converters for other SW like Maxquant and PD, I kind of like TPP, so trying to establish a proper workflow for my fractionated TMT data. Thanks again, Debojyoti On Sunday, May 12, 2024 at 10:54:18 PM UTC+5:30 David Shteynberg wrote: > Dear Debojyoti, > > Welcome to the world of TPP! > > If you have a database of targets you can use the following tool in TPP to > generate random (repeat preserving deBruijn) decoys for your targets: > > [image: image.png] > > With the default options this tool will create two independent sets decoys > for each of your targets, prefixed by DECOY0 and DECOY1. > > After you search the data you can analyze it with PeptideProphet in many > different ways. I would suggest you try with the following options to > start: > > [image: image.png] > > This will enable PeptideProphet to use DECOY0 hits as model-decoys and > DECOY1 hits as validation-decoys. > > With these setting the table on the models page will contain model-based > error estimations based on the model trained with DECOY0 ("known" decoys). > > As part of the run with these settings DECOY1 will be used to validate the > PeptideProphet model using the "unknown" decoys. This will be displayed on > the models page "Models Charts" tab near the bottom, for example: > [image: image.png] > > The chart on the right shows both the "DECOY" (DECOY1 "unknown") ROC curve > and the "PREDICTED" (DECOY0 "known" model-based) ROC curve. The error > estimates comparing the model-based error to the unknown/validation > decoy-based error are on the chart on the left. If you want evaluate a > model using a different decoys settings you can run the ProphetModels.pl > decoy validation tool on the following page: > [image: image.png] > > On this page set the decoy proteins to the PeptideProphet "model unknown" > and the excluded decoys to the PeptideProphet "model known' ones (if any) > as follows: > [image: image.png] > > Hopefully this helps you process your dataset. Let us know if you have > additional questions. > > Cheers! > -David > > > > On Sun, May 12, 2024 at 2:38 AM Debojyoti Pal <[email protected]> wrote: > >> Hello everyone >> >> Proteomics newbie here. I am trying to use TPP and peptide prophet but >> really unable to understand the options and outputs. Seeking help of the >> experienced members.[image: peptideprophet.PNG] >> >> What are the options that I need to activate to estimate FDR via the >> target-decoy mode? I am currently generation decoy through comet and >> actuvation "use decoy hits to pin down" option and "known protein names >> begin with" option and "use non parametric model option". What do the >> option "report decoy hits with computed probability do? And the other >> options too? >> >> [image: results.PNG] >> >> How is this decoy based FDR calculated?? I am not asking the principle >> behind it but I can't see a table for the same? And what is the FDR after >> discard? >> >> [image: table.PNG] >> >> The data in this table is not for decoy based FDR, right? This is the >> peptide prophet stattistical model based FDR, correct? >> >> I would be highly obliged if anyone could help me out. >> >> Thanks >> Debojyoti >> PhD Student >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/f3a8af0d-d40d-4ce9-9a99-5a250c5345c9n%40googlegroups.com >> >> <https://groups.google.com/d/msgid/spctools-discuss/f3a8af0d-d40d-4ce9-9a99-5a250c5345c9n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/de8c55e3-2e0a-4af0-809d-13dc88df1a66n%40googlegroups.com.
