Can you compress the mzML file, the search database and your search together and reshare? I will need at least those file to try to reproduce your process.
Cheers! On Wed, Jul 24, 2024, 2:19 AM sudarshan kumar <[email protected]> wrote: > > 20240417_AN_171_POS_LCMSMS_00.mzML > <https://drive.google.com/file/d/1qNf8C08bcg0KwF56HmonihILxh3uVqyU/view?usp=drive_web> > please find the mzml file shared through drive > > On Wed, Jul 24, 2024 at 12:40 AM sudarshan kumar <[email protected]> > wrote: > >> Thank you so much David, >> Please find the screenshot of what I am getting. >> I am sharing the file also for you to check please. >> Best regards, >> Sud >> >> >> 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 >> >> > > -- > ------------------------------------------------------------------- > 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/CALZrgHTC2%2BQ5XagQASK5OL5zHRhaykxHYY83%2B0L%3DbHE9FkN%3DRg%40mail.gmail.com > <https://groups.google.com/d/msgid/spctools-discuss/CALZrgHTC2%2BQ5XagQASK5OL5zHRhaykxHYY83%2B0L%3DbHE9FkN%3DRg%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%3D9Ypc%2Bx1yNj2wCdzDP-YnOzQV1rtNex60HYJSQ5hxJ1qQ%40mail.gmail.com.
