Hi Jesse, Thanks for helping. I also tried the same data on comet also, it is showing no errors. And I am using same fasta and mass tolerances for comet search also, and its peptideprophet results are showing no errors. As I have mentioned that I am using msconvert directly but not AB Sciex converter for data conversion, could this be the reason of it. Also, I have attached the tandem parameters file, could you please have a look into that also.
Thanks Ankit On 15-Feb-2019 00:43, "Jesse Meyer" <[email protected]> wrote: > Hi Ankit, > > I've seen this before when my search doesn't produce any hits - usually > the mixture model fails for only charge 1+, 6+, 7+ because I set the > instrument to not fragment those charge states, but your model failed all > of them. Either there are no peptides in your samples, or your search > settings were very wrong and that prevented you from finding any hits. > > I suggest checking your raw data's chromatogram for the presence of > peptide peaks and also rich MS/MS spectra, and if you have those, then > double check that you used the correct search settings (e.g. correct fasta, > correct precursor/fragment tolerances, etc). > > > Best, > > Jesse G. Meyer, Ph.D. > Postdoctoral Fellow > Coon Lab > Department of Chemistry > Department of Biomolecular Chemistry > National Center for Quantitative Biology of Complex Systems > University of Wisconsin - Madison > [email protected] > > > On Thu, Feb 14, 2019 at 12:27 PM Ankit Balhara <[email protected]> > wrote: > >> Hi, >> >> I am using peptideprophet for the statistical validation of X!Tandem >> results. I am using the options: Use accurate mass binning, using ppm, Use >> Hydrophobicity / RT information, Use decoy hits to pin down the negative >> distribution. Decoy protein names begin with'rev_', Use Non-parametric >> model (can only be used with decoy option) and Report decoy hits with a >> computed probability (based on the model learned). I have acquired the data >> on AB Sciex system but I used msconvert for conversion of .wiff files to >> mzXML format. >> But I am getting the following error message: >> >> Found 676 Decoys, and 834 Non-Decoys >> Iterations: .........10.........20.....Estimating Retention Time Model ... >> please wait ... WARNING: Not enough IDs in run index c:/TPP/data/liver_DDA_1 >> to generate RT Gradient Correction.WARNING: Not enough high probability IDs >> in run index c:/TPP/data/liver_DDA_1 to generate RT model. RT Model has been >> disabled. >> Run Index: c:/TPP/data/liver_DDA_1, slope=nan, intercept=nan, >> r_sq=nanWARNING: Not enough IDs in run index c:/TPP/data/liver_DDA_2 to >> generate RT Gradient Correction.WARNING: Not enough high probability IDs in >> run index c:/TPP/data/liver_DDA_2 to generate RT model. RT Model has been >> disabled. >> Run Index: c:/TPP/data/liver_DDA_2, slope=nan, intercept=nan, >> r_sq=nanWARNING: Not enough IDs in run index c:/TPP/data/liver_DDA_3 to >> generate RT Gradient Correction.WARNING: Not enough high probability IDs in >> run index c:/TPP/data/liver_DDA_3 to generate RT model. RT Model has been >> disabled. >> Run Index: c:/TPP/data/liver_DDA_3, slope=nan, intercept=nan, >> r_sq=nanWARNING: Not enough high probability IDs in run index >> c:/TPP/data/liver_DDA_1 to generate RT model. RT Model has been disabled. >> Run Index: c:/TPP/data/liver_DDA_1, slope=nan, intercept=nan, >> r_sq=nanWARNING: Not enough high probability IDs in run index >> c:/TPP/data/liver_DDA_2 to generate RT model. RT Model has been disabled. >> Run Index: c:/TPP/data/liver_DDA_2, slope=nan, intercept=nan, >> r_sq=nanWARNING: Not enough high probability IDs in run index >> c:/TPP/data/liver_DDA_3 to generate RT model. RT Model has been disabled. >> Run Index: c:/TPP/data/liver_DDA_3, slope=nan, intercept=nan, r_sq=nan >> >> WARNING: Mixture model quality test failed for charge (1+).WARNING: Mixture >> model quality test failed for charge (2+).WARNING: Mixture model quality >> test failed for charge (3+).WARNING: Mixture model quality test failed for >> charge (4+).WARNING: Mixture model quality test failed for charge >> (5+).WARNING: Mixture model quality test failed for charge (6+).WARNING: >> Mixture model quality test failed for charge (7+). >> model complete after 26 iterations >> command completed in 4 sec >> >> >> Could anyone help me out to resolve this problem? >> >> I am also attaching the tandem parameter file also. Also the X!Tandem >> results showed that the valid models for first data = 0, while 2 and 4 >> models for two other data. >> >> -- >> 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. >> > -- > 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. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. 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