Hi Philipp,
The most recent development version of TPP works with pepxml annotations
from MS-GF+ searches. The tool "idconvert.exe" from Proteowizard
(version 3.0.4388) is able to convert .mzid to pepxml for this purpose.
Although this works, the PeptideProphet output states that the
discriminant function for MS-GF+ data is not yet optimized. I look
forward to the official release.
Best,
Jesse
On 3/20/2013 9:12 AM, philipp (Overall Lab / UBC Vancouver) wrote:
Hi all,
I would be interested in this as well.
Checking the source code of xinteract I couldn't find anything that
would indicate that it can handle ms-gf+.
Would be great if any of the developers could comment on that or point
out the appropriate script for ms-gf+ to pepxml conversion.
Thanks a lot
Philipp
On Thursday, March 14, 2013 5:59:43 PM UTC-7, Jesse wrote:
Hi all,
I am told that the most recent version of Peptide/ProteinProphet is
compatible with MS-GF+ search output. Is this true? If so, where
can I
obtain it? I've already tried using TPP version 4.6.2 and xinteract
fails upon calling PeptideProphet with the message that MS-GF+ is not
recognized.
Thanks in advance for any help.
Best,
Jesse
--
Jesse G. Meyer
Graduate Student
Department of Chemistry and Biochemistry
University of California, San Diego
[email protected] <javascript:>
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University of California, San Diego
[email protected]
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