Hi Mike and Thomas,
I am not sure where Kojak search went wrong, but somehow the 1.6.1 search
contains 0 decoys ("REVERSE") tagged hits and the 1.5.5 search has many.
Can you check your database and search parameters? Also is there any
reason your are not enabling the ACCMASS option that will help the
classification?
Thanks,
-David
On Thu, Sep 19, 2019 at 4:48 AM 'Michael Hoopmann' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:
> Hi Thomas,
> Sorry for the slow response, but HUPO is over now. I'll help take a look
> and find the problem.
> Cheers,
> Mike
>
> On Sun, Sep 15, 2019 at 11:56 PM Thomas Gossenreiter <
> thomas.gossenrei...@gmail.com> wrote:
>
>> Please find the links to the files below:
>>
>> https://drive.google.com/open?id=1bO2E0duY8gr3UCoMRClKhKlEBiLqG88D
>> https://drive.google.com/open?id=15BKZkfBfPsMROSvrxBOK9XtCivHG7nHk
>>
>>
>> Am Freitag, 13. September 2019 16:27:47 UTC+2 schrieb David Shteynberg:
>>>
>>> It would be very helpful to see your Kojak pepxml results.
>>>
>>> Thanks,
>>> David
>>>
>>>
>>> On Fri, Sep 13, 2019, 12:01 AM Thomas Gossenreiter <
>>> thomas.go...@gmail.com> wrote:
>>>
>>>> Hi David,
>>>>
>>>> thanks for your quick response. Here is the link to the zipped pep.xml
>>>> files. Is this enough or do you also need the pep.xmls from the kojak
>>>> search?
>>>>
>>>> https://drive.google.com/open?id=1zKW0JVfVL_LME0gmt_L6AI7j8AymUmD1
>>>>
>>>>
>>>> Am Donnerstag, 12. September 2019 18:02:07 UTC+2 schrieb David
>>>> Shteynberg:
>>>>>
>>>>> Hi Thomas,
>>>>>
>>>>> I am not sure what is happening but if you could provide the dataset
>>>>> files for the two search results I can investigate. PeptideProphet does
>>>>> calculate different models for the different crosslink types.
>>>>>
>>>>> Thanks,
>>>>> -David
>>>>>
>>>>> On Thu, Sep 12, 2019 at 8:59 AM Thomas Gossenreiter <
>>>>> thomas.go...@gmail.com> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I have used Kojak 1.6.1 in the TPP pipeline and got some strange
>>>>>> results (very similar ms2 spectra from one peptide with similar Kojak
>>>>>> scores got very different probabilities when running peptide prophet). I
>>>>>> have plotted the Kojak score vs. the peptide prophet probability for
>>>>>> target
>>>>>> and decoy hits and there is hardly any correlation between the kojak
>>>>>> score
>>>>>> and the probability.
>>>>>>
>>>>>> I have repeated the search Kojak version that comes along with TPP
>>>>>> (1.5.5) using the same settings except for the top_count parameter. I
>>>>>> think
>>>>>> this looks how it should, except for the cross-links which are scored
>>>>>> very
>>>>>> well by Kojak but get a bad peptide prophet probability. Is this the case
>>>>>> when one peptide has a very good Kojak sub score and the other one a very
>>>>>> bad score?
>>>>>>
>>>>>> Does version 1.6.1 work for you or do you have any idea what is
>>>>>> happening here? I attached a ppt file with the figures.
>>>>>>
>>>>>> I also got a general questions: Is peptide prophet calculating FDRs
>>>>>> separately for cross-linked, loop-linked and normal peptides?
>>>>>>
>>>>>> Kind regards,
>>>>>> Thomas
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> 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...@googlegroups.com.
>>>>>> To view this discussion on the web visit
>>>>>> https://groups.google.com/d/msgid/spctools-discuss/12f12195-f115-41e5-a196-b53e18e170df%40googlegroups.com
>>>>>> <https://groups.google.com/d/msgid/spctools-discuss/12f12195-f115-41e5-a196-b53e18e170df%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...@googlegroups.com.
>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/spctools-discuss/abe43fc7-eb03-4411-a6ac-c5ca4a5c326a%40googlegroups.com
>>>> <https://groups.google.com/d/msgid/spctools-discuss/abe43fc7-eb03-4411-a6ac-c5ca4a5c326a%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.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/spctools-discuss/71e9da68-1b77-4913-b2f0-049275e04709%40googlegroups.com
>> <https://groups.google.com/d/msgid/spctools-discuss/71e9da68-1b77-4913-b2f0-049275e04709%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.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/CANMWFMNVu2gfVxcUq_Pbttrx7WZOJHCsOtk6VOZb-H6THUtLTA%40mail.gmail.com
> <https://groups.google.com/d/msgid/spctools-discuss/CANMWFMNVu2gfVxcUq_Pbttrx7WZOJHCsOtk6VOZb-H6THUtLTA%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 spctools-discuss+unsubscr...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/spctools-discuss/CAGJJY%3D86bvivkoFJGAsQn6xvdDLfraULp%2B%3DNLvsjLHcqZ7n19Q%40mail.gmail.com.
