Re: [spctools-discuss] Crosslink FDR from PeptideProphet

[Lindsey Ulmer]

Thanks! I do have less error tables than I would expect. When I ran
PeptideProphet, I received the warning: "Mixture model quality test failed
for charge (1+)" for multiple charge states.  Would that warning account
for the missing error tables?

On Wed, Sep 16, 2020 at 1:34 PM 'David Shteynberg' via spctools-discuss <
spctools-discuss@googlegroups.com> wrote:

> Hi Lindsey,
>
> PeptideProphet  will generate a separate FDR prediction table for each
> type of Kojak result it analysed, and all three should be in the pepXML
> file.  The three types of Kojak hits are unlinked "n/a", self-linked "loop"
> and cross-linked "xl".PeptideProphet generates a separate model for
> each type of Kojak result.
>
> Thanks for your question!
>
> -David
>
>
> On Wed, Sep 16, 2020 at 12:22 PM Lindsey Ulmer 
> wrote:
>
>> Hi,
>>
>> I'm trying to determine the FDR of crosslinked products from a Kojak and
>> PeptideProphet analysis. There is a second plot in the Predicted
>> Sensitivity and Error Rate chart, which I'm assuming is for the crosslinked
>> products, but I'm having trouble determining which of the error tables
>> correspond to crosslinked results. I've attached a link to the
>> corresponding pepxml below.
>>
>>
>> https://drive.google.com/file/d/1hadnfjsFVCTMVqirdcC2jCeEuUvzVjAt/view?usp=sharing
>>
>> Thanks!
>> Lindsey
>>
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>> 
>> .
>>
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Re: [spctools-discuss] Crosslink FDR from PeptideProphet

['David Shteynberg' via spctools-discuss]

Hi Lindsey,

PeptideProphet  will generate a separate FDR prediction table for each type
of Kojak result it analysed, and all three should be in the pepXML file.
The three types of Kojak hits are unlinked "n/a", self-linked "loop" and
cross-linked "xl".PeptideProphet generates a separate model for each
type of Kojak result.

Thanks for your question!

-David


On Wed, Sep 16, 2020 at 12:22 PM Lindsey Ulmer 
wrote:

> Hi,
>
> I'm trying to determine the FDR of crosslinked products from a Kojak and
> PeptideProphet analysis. There is a second plot in the Predicted
> Sensitivity and Error Rate chart, which I'm assuming is for the crosslinked
> products, but I'm having trouble determining which of the error tables
> correspond to crosslinked results. I've attached a link to the
> corresponding pepxml below.
>
>
> https://drive.google.com/file/d/1hadnfjsFVCTMVqirdcC2jCeEuUvzVjAt/view?usp=sharing
>
> Thanks!
> Lindsey
>
> --
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> "spctools-discuss" group.
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> To view this discussion on the web visit
> https://groups.google.com/d/msgid/spctools-discuss/1352899f-62a4-43fa-8ff1-0d6809251e9dn%40googlegroups.com
> 
> .
>

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[spctools-discuss] Crosslink FDR from PeptideProphet

[Lindsey Ulmer]

Hi,

I'm trying to determine the FDR of crosslinked products from a Kojak and 
PeptideProphet analysis. There is a second plot in the Predicted 
Sensitivity and Error Rate chart, which I'm assuming is for the crosslinked 
products, but I'm having trouble determining which of the error tables 
correspond to crosslinked results. I've attached a link to the 
corresponding pepxml below.

https://drive.google.com/file/d/1hadnfjsFVCTMVqirdcC2jCeEuUvzVjAt/view?usp=sharing

Thanks!
Lindsey

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