Hello again Sud! >From your screen shots I could tell you are running version 6.3.2 of the >software. I think the issue you are seeing might be a solved one in the >latest release 7.1.0. Are you able to update and try the latest version?
Thanks! -David > On Jul 24, 2024, at 7:38 AM, David Shteynberg > <david.shteynb...@isbscience.org> wrote: > > 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 <kumarsuders...@gmail.com > <mailto:kumarsuders...@gmail.com>> 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 <kumarsuders...@gmail.com >> <mailto:kumarsuders...@gmail.com>> 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 >>> <dshteynb...@systemsbiology.org <mailto:dshteynb...@systemsbiology.org>> >>> 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 <kumarsuders...@gmail.com >>>>> <mailto:kumarsuders...@gmail.com>> 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 spctools-discuss+unsubscr...@googlegroups.com >>>>> <mailto:spctools-discuss+unsubscr...@googlegroups.com>. >>>>> 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 spctools-discuss+unsubscr...@googlegroups.com >>>> <mailto:spctools-discuss+unsubscr...@googlegroups.com>. >>>> 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 <http://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 <http://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 <http://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 <http://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 spctools-discuss+unsubscr...@googlegroups.com >> <mailto:spctools-discuss+unsubscr...@googlegroups.com>. >> 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. 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