Hi Mike and David,
first of all: thanks for your effort!
I have used the same database for both searches. If I look on the xml
result file of the 1.6.1 search, I see reverse hits. The database is fine,
all reverse hits start with REVERSE_
I did not enable accurate mass binning because I just wanted to try the
default setting first, but if it's better for high res. data then I will
switch it on in the future.
Thank you! Thomas
Am Donnerstag, 19. September 2019 19:37:23 UTC+2 schrieb David Shteynberg:
>
> 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...@googlegroups.com <javascript:>> 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.go...@gmail.com <javascript:>> 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
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
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