ascore for phospho site localization

[LW]

Hi,

I am wondering if anyone has use the ascore for
phospho site localization on XTandem/TPP processed data.
The software in Gygi lab seems to be based on sequest dta/out output.

Thanks,
LW

[David Shteynberg]

Hi LW,

Yes I have used ascore with some success, although it is not
integrated with TPP and crashes sometimes on longer peptides. We have
a TPP integrated tool that is faster and as good or better than Ascore
from some initial testing. The tool is available on commandline only
at the moment and is not distributed with the installer yet. It is
called PTMProphet and you can get an initial Windows only version of
the test executable from this link:
http://dl.dropbox.com/u/21286225/PTMProphetParser.exe

Hope that helps,
-David

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[钟传奇]

Hi,David,
The link you provided for downloading PTMProphet not valid,could you
offer any other way I can download PTMProphet?

[LW]

Hi David,

Thanks for the tip. I am interested in knowing how does PTMProphet
algorithm differs from Ascore.
Are they exactly same except implementation.
Also, I can locate the PTMProphetParser in my linux build of TPP4.5.0.
Can this be used instead of the window binary?
It says the usage is PTMProphetParser <OPTIONS> <file1.pep.xml>
May I know the options available? I am assuming it takes in
PeptideProphet
processed pep.xml.

Thanks,
LW

On Oct 17, 4:29 pm, David Shteynberg

[LW]

Hi David,

I got a segmentation fault when I tried to run the command-line linux
build.
Is there a working linux version?

Thanks,
LW

[David Shteynberg]

Hi LW,

The version distributed in the release is perhaps a bit older than the
one in SVN trunk. Have you tried building it from trunk? I know my
version is working on Linux, if you build from trunk and it still
doesn't work please let me know and I will commit my absolute latest
code (that I've been testing without seg faults).

Thanks,
-David

[LW]

Hi David,

Thanks. I tried the version from trunk and still got the segmentation
fault.
I ran it using: PTMProphetParser STY,80 interact.pep.xml
Is this the correct?

I also ran gdb on it:
Program received signal SIGSEGV, Segmentation fault.
0x00000000004d906e in
SpectraSTLibImporter::SpectraSTLibImporter(std::vector<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> > > >&, SpectraSTLib*, SpectraSTCreateParams&) ()

Could you commit your latest code

Thanks,
LW

On Oct 20, 10:41 am, David Shteynberg
<David.Shteynb...@systemsbiology.org> wrote:
> Hi LW,
>

[David Shteynberg]

I checked in some code that yesterday that might address the issue.
Perhaps you can send me your file and I can try to run my tool on it
here? The FTP site is listed here:
http://tools.proteomecenter.org/wiki/index.php?title=TPP:Frequently_Asked_Questions#How_do_I_upload_files_to_the_SPC_tools_team.3F

Thanks,
-David