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，[email protected]写道： > > 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 > > > > On Tuesday, May 14, 2013 2:52:54 AM UTC+10, Michael Hoopmann wrote: >> >> 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 >> >> On 5/12/2013 11:45 PM, [email protected] wrote: >> > 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 >> > >> > >> > -- >> > You received this message because you are subscribed to the Google >> > Groups "spctools-discuss" group. >> > To unsubscribe from this group and stop receiving emails from it, send >> > an email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at >> http://groups.google.com/group/spctools-discuss?hl=en. >> > For more options, visit https://groups.google.com/groups/opt_out. >> > >> > >> >> -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
