You'll find the latest release candidate (RC4) in: https://sourceforge.net/projects/sashimi/files/Trans-Proteomic%20Pipeline%20%28TPP%29/TPP%20v0.0%20%28Development%29/
Since I don't expect any more changes this should be effectively 4.7. -Joe On Tue, Feb 18, 2014 at 10:28 PM, Robert Jones <[email protected]>wrote: > Bjorn, > > Thank you so very much that was extremely helpful! I'll be well on my way > to finishing my analysis. > > -Robert M Jones > > > On Tuesday, February 18, 2014 6:45:24 AM UTC-7, Bjorn wrote: >> >> Hi, >> As far as I understand it, the TPP uses a mixture model-based approach to >> determine posterior probabilities and it then uses these probabilities to >> estimate the FDR. This can be done with or without the use of a decoy >> database. However, when using some of the more sophisticated options (like >> non-parametric modelling), you will need a decoy database to help the >> modelling algorithms pin down the negative distribution. Also, when the >> data is of not so excellent quality, the decoys can help make a better >> distinction between good and bad identifications. >> >> After the analysis with ProteinProphet, you get something like this in >> the ProteinProphet window: >> >> Prob Sens FPER Corr Incorr >> 0.00 1.000 0.930 217 2874 >> 0.10 1.000 0.337 217 110 >> 0.20 1.000 0.337 217 110 >> 0.30 0.915 0.216 198 55 >> 0.40 0.865 0.152 187 34 >> 0.50 0.816 0.102 177 20 >> 0.60 0.777 0.074 168 14 >> 0.70 0.747 0.058 162 10 >> 0.80 0.647 0.019 140 3 >> 0.90 0.608 0.010 132 1 >> 0.95 0.569 0.005 123 1 >> 0.96 0.547 0.004 119 0 >> 0.97 0.529 0.003 115 0 >> 0.98 0.507 0.002 110 0 >> 0.99 0.470 0.001 102 0 >> 1.00 0.152 0.000 33 0 >> >> The FPER is your FDR, so if you decide to set it at 1%, you notice that >> this corresponds with a probability cut off of 0.90. Now, in your protein >> list, you accept all proteins with a prob. of 0.09 or higher, which is >> estimated to be 132 correct ones and 1 incorrect protein. Everything below >> is discarded. >> >> I found lots of info in the following papers (esp. the last paper). >> Hope this helps! >> Cheers, >> Bjorn >> >> [1] Choi, H., Fermin, D., and Nesvizhskii, A. I. Significance analysis of >> spectral count data in label-free shotgun proteomics. Mol. Cell. Proteomics >> 7, 12 (2008), 2373-2385. >> >> [2] Choi, H., Ghosh, D., and Nesvizhskii, A. I. Statistical validation of >> peptide identifications in large-scale proteomics using the target-decoy >> database search strategy and flexible mixture modeling. J. Proteome Res. 7, >> 1 (2008), 286-292. >> >> [3] Choi, H., and Nesvizhskii, A. I. False discovery rates and related >> statistical concepts in mass spectrometry-based proteomics. J. Proteome >> Res. 7, 1 (2008), 47-50. >> >> [4] Choi, H., and Nesvizhskii, A. I. Semisupervised model-based >> validation of peptide identifications in mass spectrometry-based >> proteomics. J. Proteome Res. 7, 1 (2008), 254-265. >> >> [5] Deutsch, E. W., Mendoza, L., Shteynberg, D., Farrah, T., Lam, H., >> Tasman, N., Sun, Z., Nilsson, E., Pratt, B., Prazen, B., Eng, J. K., >> Martin, D. B., Nesvizhskii, A. I., and Aebersold, R. A guided tour of the >> Trans-Proteomic Pipeline. Proteomics 10, 6 (2010), 1150-1159. >> >> [6] Keller, A., Nesvizhskii, A. I., Kolker, E., and Aebersold, R. >> Empirical statistical model to estimate the accuracy of peptide >> identifications made by MS/MS and database search. Anal. Chem. 74, 20 >> (2002), 5383-5392. >> >> [7] Nesvizhskii, A. I. A survey of computational methods and error rate >> estimation procedures for peptide and protein identification in shotgun >> proteomics. J. Proteomics 73, 11 (2010), 2092-2123. >> > -- > 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 post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/spctools-discuss. > For more options, visit https://groups.google.com/groups/opt_out. > -- Joe Slagel Institute for Systems Biology [email protected] (206) 732-1362 -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
