Shaun, The latest TPP supports CRUX output. It has been awhile since I implemented this support but it appears that the Crux function is very similar to TPP sequest discriminant but only using Xcorr and delta Cn.
Pumuta, I have not yet tried the Q-ranker code, but the PeptideProphet paper you site is the original from 9 years. Since then there have been a number of improvements to the algorithm. Perhaps the paper you should be citing is the iProphet paper that show using the TPP on the the results of a single search engine or on combining multiple search engines the paper can be found here http://mcponline.org/content/early/2011/08/29/mcp.M111.007690.abstract?sid=a82bdd5e-a70e-464a-a5e5-292c8a00a3f7. Perhaps we will integrate the Q-ranker algorithm into the TPP in the future, in fact I am currently trying to install this software on my systems. Until then however, I will offer that instead of trying to Jerry-rig tools not yet integrated with the TPP to the ProteinProphet algorithm is awkward, likely to cause you more potential problems and headaches, than if you simply: 1. download and install the latest TPP version from here: http://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v4.5%20%28rapture%29%20rev%200/ 2. run your Crux data through the pipeline Good luck, -David On Mon, Oct 3, 2011 at 11:55 PM, Putuma Gqamana <[email protected]> wrote: > Peptide Prophet and post-search algorithms like Q-ranker, Percolator > and Q value all treat SEQUEST output data and create discriminants > from it, i.e., Prophet discriminant has 4 SEQUEST terms compared to > Percolator's 17 terms of which 10 are SEQUEST based and Q-ranker's 34 > terms. So I take it that Peptide Prophet cannot treat CRUX outputs > which are already post-search statistically treated outputs, but it > definitely treats SEQUEST outputs. Of course, you already know that > Q-ranker > Percolator > Prophet, so what you are trying to do is kinda > awkward or retrogressive here. You'd rather subject a CRUX Qranker > pepXML output or percolator.pepXML to Protein Prophet instead. > > On Mon, Oct 3, 2011 at 12:12 PM, naturofix <[email protected]> wrote: >> Does anyone know how PeptideProphet generates the discriminant score >> when it gets an input from Crux, for instance the >> qranker.target.pep.xml output. These files contain a q-ranker_score >> and a q_ranker_q_value as well as delta_cn and Xcorr_score. >> >> Which of these statistics are used to generate the probability score >> in the interact.pep.xml output. >> Where can I find a formula for this calculation. Does the same hold >> for percolator? >> >> >> -- >> You received this message because you are subscribed to the Google Groups >> "spctools-discuss" group. >> To post to this group, send email to [email protected]. >> To unsubscribe from this group, send email to >> [email protected]. >> For more options, visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> >> > > > > -- > Putuma P. Gqamana, Ph.D. - Wellcome Trust - CIDRI Postdoctoral Research Fellow > University of Cape Town Faculty of Health Sciences > c/o Blackburn Group - Division of Medical Biochemistry > N3.06.4 Wernher and Beit Building North > Anzio Road, > Observatory, 7925 > > Email : [email protected], [email protected], [email protected] > Phone: ++27-21-406-6453 (w) > Phone: ++27-73-764-7825 (cell) > Skype: Putuma.Gqamana > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
