Hi, David, Can you please also share the comet param version 2024. Or please let me know where i can download it from. Regards Sud
On Thu, Jul 25, 2024 at 12:00 PM sudarshan kumar <[email protected]> wrote: > 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 > > -- ------------------------------------------------------------------- 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/CALZrgHRLB56M-fo-KPQ4AMZEVWg-g-GdfPtn48mBdLS31kzaqQ%40mail.gmail.com.
