Dear Thibault, This message means that the mass as calculated for your the shuffled peptide with PTMs is not matching to the recorded mass in the pepXML file. Without looking at the file I cannot tell the exact source of the problem. If you can send me a link to your results and data I can take a more in depth look. However, I am currently on vacation and will not be able to take a look at this until Friday. It is possible that the pepXML file from Tandem is not properly encpding static mods, which would explain the large mass differences reported in the error message. If you can send the exact error message and the pepXML snippet for the particular PSM I might be able to say more without having the dataset.
Thanks, -David On Dec 19, 2017 9:45 AM, "Thibault Robin" <[email protected]> wrote: > Dear all, > > I am encountering issues when trying to use PTMProphet on X!Tandem result > files to validate phosphorylation sites. > > Firstly, when converting the X!Tandem result files to pepXML using > Tandem2XML, I get the error that the referred MGF file is not recognized > *"Unknown file type. No file loaded.".*I checked that all the paths were > correct. To overcome this issue I had to convert the original raw files in > mzML for Tandem2XML to work, is it normal that MGF files are not supported ? > > Secondly, I get "*WARNING: Illegal PTM-shuffled peptide detected with > non-matching mass*" warnings when running PTMProphet on the pepXML file. > What I don't understand is that the difference in ppm that are given by the > warnings are quite extreme (80000-150000 ppm). And even if I increase the > MS1 tolerance enough using the PPMTOL parameter, no information is inserted > in the "modification_info" tags in the produced XML file. Am I missing > something obvious ? > > PS: I use command lines and the latest version of the TPP on linux mint > (64 bits). > > Many thanks in advance, > > Thibault > > -- > 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.
