Re: [spctools-discuss] When to use "Decoy hits to pin down negative distribution" in PeptideProphet

['David Shteynberg' via spctools-discuss]

Dear Soroush,

This option makes use of the TPP's semi-supervised learning mode, which can
be used in conjunction with semi-parametric mode, at the user's
discretion.  Until now, some search engines supported by TPP analysis could
only be modeled by PeptideProphet using semi-parametric and semi-supervised
that required decoys to be used in the search.  Going forward with the new
version of the TPP (pre-release version 6.0.0) this is not going to be
the case as we will be providing both types of models for more search
engine results.  I hope this answers your question.

Cheers,
-David

On Mon, Jan 18, 2021 at 4:02 PM Soroush F  wrote:

> Dear all,
>
> I was wondering when one should use "Use decoy hits to pin down the
> negative distribution" in the Peptide Prophet (run through Petunia)?
>
> If I want to use Target-Decoy approach to estimate FDR in my analysis,
> should I use this box, or it has nothing to do with it?
>
> Thanks,
> Soroush
>
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Re: [spctools-discuss] Error generation while converting raw files

['David Shteynberg' via spctools-discuss]

Dear Giangiacomo,

Thanks for trying the TPP and reporting the problem.  TPP uses the
proteowizard's msconvert tools for this step.  You can remedy the problem
by either upgrading to a newer version of proteowizard's msconvert tool or
use  --ignoreUnknownInstrumentError option with your current version.  On
the generate mzML page you can specify this option in the"Enter
additional options to pass directly to the command-line" text box, just
enter the text  --ignoreUnknownInstrumentError

Hope it works!

Cheers,
-David


On Tue, Jan 19, 2021 at 8:10 AM giangiacomo beretta <
giangiacomo.berett...@gmail.com> wrote:

> Hi, when I try to convert raw files, the conversion tool stops immediately
> reporting the following error:
>
> Reader_Thermo::fillInMetadata] unable to parse instrument model; please
> report this error to the ProteoWizard developers with this information:
> model(Orbitrap Eclipse) name(Orbitrap Eclipse); if want to convert the file
> anyway, use the ignoreUnknownInstrumentError flag
>
> It appears that the system is not recognizing the instrument model that
> produced the raw files. Is there any option to overcome this issue?
>
> Actually I have converted the same files with ProteoWizard without
> troubles.
>
> Thanks in advance!
>
> G
>
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> 
> .
>

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[spctools-discuss] Error generation while converting raw files

[giangiacomo beretta]

Hi, when I try to convert raw files, the conversion tool stops immediately 
reporting the following error:

Reader_Thermo::fillInMetadata] unable to parse instrument model; please 
report this error to the ProteoWizard developers with this information: 
model(Orbitrap Eclipse) name(Orbitrap Eclipse); if want to convert the file 
anyway, use the ignoreUnknownInstrumentError flag 

It appears that the system is not recognizing the instrument model that 
produced the raw files. Is there any option to overcome this issue?

Actually I have converted the same files with ProteoWizard without troubles.

Thanks in advance!

G

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