also required are your search params and db On Thu, Jul 25, 2024, 5:14 AM sudarshan kumar <[email protected]> wrote:
> 20240417_AN_171_POS_LCMSMS_00.shrunken.mzML > <https://drive.google.com/file/d/16xvJYrOzHzb0jjXse-XY50gHGs7YGJFW/view?usp=drive_web> > > > On Tue, Jul 23, 2024 at 10:16 AM David Shteynberg < > [email protected]> wrote: > >> Hello Sudarshan, >> >> Although it is not possible to tell exactly what happened here without >> more information, the usual suspects are: >> >> 1. Data Quality >> 2. Incorrect Database >> 3. Incorrect Parameters >> >> I just ran a test of X!Tandem locally on the ISB18 dataset. The search >> ran and the TPP validation generated PSMs with positive probability >> values. If you are able to provide more information about your specific >> analysis or post your dataset online for download I would be happy to take >> a closer look. >> >> Cheers! >> -David >> >> >> >> >> On Jul 23, 2024, at 4:56 AM, sudarshan kumar <[email protected]> >> wrote: >> >> Hi, >> Can you please explain why? >> When I searched with tandem, IT shows all good hits as I expected from >> the sample. >> But when I used peptide prophet, The result is all 0 probability? >> I tried merging 4 files and individually also. But in all cases the >> probability comes to 0. >> >> where is the problem> >> >> Best >> >> -- >> 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/e74da627-d489-453c-b480-96453fbdc6a5n%40googlegroups.com >> <https://groups.google.com/d/msgid/spctools-discuss/e74da627-d489-453c-b480-96453fbdc6a5n%40googlegroups.com?utm_medium=email&utm_source=footer> >> . >> >> >> -- >> 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 view this discussion on the web visit >> https://groups.google.com/d/msgid/spctools-discuss/4E5196E2-E7D9-4B46-91CB-462A19AEFAAC%40systemsbiology.org >> <https://groups.google.com/d/msgid/spctools-discuss/4E5196E2-E7D9-4B46-91CB-462A19AEFAAC%40systemsbiology.org?utm_medium=email&utm_source=footer> >> . >> > > > -- > ------------------------------------------------------------------- > The real voyage of discovery consists not in seeking new lands but seeing > with new eyes. — Marcel Proust > > Dr. Sudarshan Kumar > (Fulbright-Nehru Fellow) > (B.V.Sc.& A.H., M.V.Sc., PhD.) > Sr. Scientist > Animal Biotechnology Center > (Proteomics and Cell Biology Lab.) > National Dairy Research Institute Karnal, 132001 > Haryana, India > Contact No 09254912456 > URL www.ndri.res.in > Orcid Id: https://orcid.org/0000-0002-9816-4307 > > -- > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/spctools-discuss/CALZrgHRLCSdsG5uEPbsrtUGzV5_6iephhY8GofZa3ZwVfoyohA%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CALZrgHRLCSdsG5uEPbsrtUGzV5_6iephhY8GofZa3ZwVfoyohA%40mail.gmail.com?utm_medium=email&utm_source=footer> > . > -- 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 view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D-%2Bi0kHvQJB8UOuaLHtObppXBo1fZsZhkG8VfMx1GXoMQ%40mail.gmail.com.
