One more question. I am using COMET prior to the peptide prophet steps. COMET is already generating decoy database (concatenated search), do I need to turn the decoy search off in COMET?
On Tuesday, May 14, 2024 at 2:38:00 PM UTC+5:30 Debojyoti Pal wrote: > 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/164dec33-2bcb-4ead-8326-603be2f38f6an%40googlegroups.com.
