Hi David, thanks for your answer. It is very weird because I have like 2858 proteins and 10501 unique peptides. I believe there are enough IDs. It might be the PeptideProphet parameters: PeptideProphet probability:0.05 Force the fitting of the mixture model (bypass automatic mixture model checks) Use decoy hits to pin down the negative distribution. Decoy protein names begin with: (whitespace not allowed) I tried with and without the second one, but without it gives this error: *Command FAILED* RETURN CODE:65280
WARNING: Mixture model quality test failed for charge (1+). model complete after 22 iterations command completed in 16 sec running: "C:/TPP/bin/ProphetModels.pl -i /tmp/a06284/Results_SpectraST_Search_3lib/interact.pep.xml -d "DECOY""Analyzing /tmp/a06284/Results_SpectraST_Search_3lib/interact.pep.xml ... Parsing search results "c:/TPP/data/Results_SpectraST_Search_3lib/041117_DDA_Rep1 (SpectraST)"... => Found 0 hits. (0 decoys, 0 excluded) => Total so far: 0 hits. (0 decoys, 0 excluded) Parsing search results "c:/TPP/data/Results_SpectraST_Search_3lib/041117_DDA_Rep4 (SpectraST)"... => Found 0 hits. (0 decoys, 0 excluded) => Total so far: 0 hits. (0 decoys, 0 excluded) Parsing search results "c:/TPP/data/Results_SpectraST_Search_3lib/041117_DDA_Rep5 (SpectraST)"... => Found 0 hits. (0 decoys, 0 excluded) => Total so far: 0 hits. (0 decoys, 0 excluded) command completed in 0 sec running: "C:/TPP/bin/InterProphetParser /tmp/a06284/Results_SpectraST_Search_3lib/interact.pep.xml /tmp/a06284/Results_SpectraST_Search_3lib/interact.ipro.pep.xml"Running NSS NRS NSE NSI NSM NSP FPKM Model EM: Computing NSS values ... done Computing NRS values ... done Computing NSE values ... done Computing NSI values ... done Computing NSM values ... done Computing NSP values ... Creating 1 threads Wait for threads to finish ... 0--------------------------------------------------50------------------------------------------------100% done FPKM values are unavailable ... Iterations: .done command completed in 0 sec running: "C:/TPP/bin/ProphetModels.pl -i /tmp/a06284/Results_SpectraST_Search_3lib/interact.ipro.pep.xml -d "DECOY""Analyzing /tmp/a06284/Results_SpectraST_Search_3lib/interact.ipro.pep.xml ... Reading NSP model ... Parsing search results "c:/TPP/data/Results_SpectraST_Search_3lib/041117_DDA_Rep1 (SpectraST)"... => Found 0 hits. (0 decoys, 0 excluded) => Total so far: 0 hits. (0 decoys, 0 excluded) Parsing search results "c:/TPP/data/Results_SpectraST_Search_3lib/041117_DDA_Rep4 (SpectraST)"... => Found 0 hits. (0 decoys, 0 excluded) => Total so far: 0 hits. (0 decoys, 0 excluded) Parsing search results "c:/TPP/data/Results_SpectraST_Search_3lib/041117_DDA_Rep5 (SpectraST)"... => Found 0 hits. (0 decoys, 0 excluded) => Total so far: 0 hits. (0 decoys, 0 excluded) command completed in 0 sec moving tempfile /tmp/a06284/Results_SpectraST_Search_3lib/interact.ipro.pep.xml to interact.ipro.pep.xml running: "C:/TPP/cgi-bin/PepXMLViewer.cgi -I /tmp/a06284/Results_SpectraST_Search_3lib/interact.ipro.pep.xml.a06284" command "C:/TPP/cgi-bin/PepXMLViewer.cgi -I /tmp/a06284/Results_SpectraST_Search_3lib/interact.ipro.pep.xml.a06284" failed: Unknown error command "C:/TPP/cgi-bin/PepXMLViewer.cgi -I /tmp/a06284/Results_SpectraST_Search_3lib/interact.ipro.pep.xml.a06284" exited with non-zero exit code: 255 QUIT - the job is incomplete So I needed to include the second parameter. With the DECOY option, not sure which option to pick, I tried all of them, but I got negative prob with all. Thank a lot for your help El martes, 13 de junio de 2017, 8:07:12 (UTC-7), David Shteynberg escribió: > > Negative probabilities are output as place holders when there aren't > enough IDs to estimate a valid mixture model. When PeptideProphet cannot > compute a probability but based on other models thinks the ID is correct it > reports it with a negative probability equal to the absolute charge. It > would be helpful to know your PeptideProphet parameters to help > troubleshoot the failure to report a mixture model probability. > > -David > > On Mon, Jun 12, 2017 at 5:15 PM, Carolina <[email protected] > <javascript:>> wrote: > >> Hello, >> I built a library with decoys with SpectraST, and then, performed the >> search of raw files also with SpectraST against that library. The results >> were analyzed with peptide prophet but the probabilities are all negative, >> from -2 to -7. My intention is to get a FDR on my results, and that >> probability can not be right. Would you know what it might be going on? >> Thanks, Carolina >> >> -- >> 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] <javascript:>. >> To post to this group, send email to [email protected] >> <javascript:>. >> Visit this group at https://groups.google.com/group/spctools-discuss. >> For more options, visit https://groups.google.com/d/optout. >> > > -- 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 https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
