Hi John,
I didn't implement this part of the code but I can check for you what
is actually being computed as to why I am not as certain. The
relevant code is in the file MascotScoreParser.cxx in the parse
function. By reading the code it appears that PeptideProphet on
Mascot compute a linear correlation between:
(ionscore - homologyscore) and (ionscore-identityscore) , using
those results where ionscore > homologyscore
lets call this function
IH(II)
When computing the f-value to model with a mixture distribution for
each spectrum the (ionscore - identityscore) score for a given
spectrum is then computed as MAX { IH(II), II } . This value is then
linearly scale to get within the range that PeptideProphet models. It
would be wise on our part to make the output messages less cryptic and
more informative.
Cheers,
-David
On Tue, Feb 8, 2011 at 8:53 AM, John Damask <[email protected]> wrote:
> Hi David,
> I've been meaning to ask, what's being calculated in this part of
> PeptideProphet:
>
> results for charge 2: -7.19405 adj_ion_mean and 15.0557 adj_ion_hom
> mean
> 62.9988id mean0.906181 correlation (r)
> 2+ ion - id = 0.965428*(ion - hom) + -21.7292 with error = 5.12625
>
> Best,
> John
>
>
> On Feb 8, 1:32 am, Jagan Kommineni <[email protected]> wrote:
>> David,
>>
>> I have updated our installation version of TPP with the latest version of
>> the TPP. This bug has disappeared.
>>
>> Thanks for your suggestion.
>>
>> with regards,
>>
>> Jagan
>>
>> On Tue, Feb 8, 2011 at 6:06 AM, David Shteynberg <
>>
>> [email protected]> wrote:
>> > Hi Jagan,
>>
>> > Thanks for the thorough bug report. Have you tried the latest version? The
>> > RT or PI models had bug that have been fixed since July. Also if you want
>> > to upload these search results I can try tracing the latest code on it.
>>
>> > Cheers,
>> > -David
>
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