Hi David, I tried 7.1.0 also. and I see that the problem is still the same (0 probability to hits returned and that too all with irrelevant proteins) for tandem searched data, and comet searched data both. 1. I see that both the search (comet and tandem) are giving me all good hits. 2. But at peptide prophet it returns me all 0 probability bad hits (undesirable proteins identified).
On Wed, Jul 24, 2024 at 8:08 PM 'David Shteynberg' via spctools-discuss < [email protected]> 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 <[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 > <https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D9Ypc%2Bx1yNj2wCdzDP-YnOzQV1rtNex60HYJSQ5hxJ1qQ%40mail.gmail.com?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/CALZrgHTD5AWyBBXiXokSBMHrB3XgYPEkiFN-hXcue_iGU9y3Mg%40mail.gmail.com.
