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 jessegme...@gmail.com On Thu, Feb 14, 2019 at 12:27 PM Ankit Balhara <ankit1517.ni...@gmail.com> 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 spctools-discuss+unsubscr...@googlegroups.com. > To post to this group, send email to spctools-discuss@googlegroups.com. > 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
