X!tandem High Res K-score

[2kl...@gmail.com]

Hi All,
Is the high-resolution X!Tandem k-score the default K-score plugin (on TPP 4.6.2) or it require some specific command/setting in X!Tandem parameters file?
Thanks,
OK
 

[Joseph Slagel]

Its the default to use K-score.   If you are on Window's you'll find the defaults in the directory C:\Inetpub\wwwroot\ISB\data\parameters.

-Joe

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[Michael Hoopmann]

Hi OK,
In the tandem params, you need to change:

<note type="input" label="scoring, algorithm">k-score</note>

to

<note type="input" label="scoring, algorithm">hrk-score</note>

Then I would recommend lowering the "spectrum, fragment monoisotopic
mass error" values to something small and appropriate for hi-res data.

Cheers,
Mike

[2kl...@gmail.com]

Thanks to both of you.
Unfortunately after changing the parameters as Mike suggested (from k-score to hrk-score) all of X!tandem scores are not shown in pepXML viewer anymore.....in order to see them I had to manually change the resulting pepXML and to switch the
search_engine field in line 4 from "X! Tandem (hrk-score)" back to "X! Tandem (k-score)".
Cheers,
O

[szyf...@gmail.com]

I ran into the same problem, correcting hrk-score back to k-score in pepxml allows me to see the scores, but there are more problems came up:
my data was collected from a Oribtrap, I tried K-score with 2 Da and 0.4Da for parent and product mass error, which works fine (3000+hits with few decoys), K-score with 10 ppm and 20 ppm parent and product mass error works even better, however, hrk-score with 10 ppm and 20 ppm parent and product mass error gives me almost nothing, only 10 hits with exp<0.05 and lots of decoys.
I just don't know where I did it wrong......

sun

在 2013年5月14日星期二UTC+8下午12时44分04秒，2kl...@gmail.com写道：