Hi Jesse, Thanks for helping. Sorry for late reply, as I was out of station with no access to mail. I will step forward with comet search + Peptideprophet.
Regards Ankit On Fri, 15 Feb 2019 at 20:50, Jesse Meyer <[email protected]> wrote: > Hi Ankit, > > Actually I see now it does find peptides from the X!tandem search, it > first tells you: > > Found 676 Decoys, and 834 Non-Decoys > > That is a low number of peptide hits for what I gather from your filenames > is a liver sample. That might be why your models are failing because they > need some minimum per charge to pass. I recommend checking if the X!tandem > search output before PeptideProphet finds a similar number of peptides as > your comet search. > > In my experience, you should get similar results with msconvert vs sciex > converter. You can rule this out by converting with the other one and > comparing. You will get a slight improvement using msconvert with the > qtofpeakpicker flag compared to sciex or normal msconvert. The conversion > will only influence PeptideProphet indirectly by changing your number of > hits because although it tries to look for your raw data I don't think it > actually needs to unless you want the TPP GUI to associate the two for > viewing spectra in your browser. > > In the end, if your comet search + PeptideProphet works you might just go > with that. You do get more by combining searches but for most projects I'm > left with more changes than I can interpret anyway. > > Good luck and best regards, > Jesse > > > 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 2:00 PM Ankit Balhara <[email protected]> > wrote: > >> 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. >> 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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