And you must make sure that the format of spectrum title is 
'name.id.id.charge'. No modification you can make.

在 2014年10月21日星期二UTC+8上午11时15分33秒,李桂林写道:
>
> I think I have resolved the problem. The spectrum title in pepXML must 
> contains no space while running PeptideProphet.
> Thank you very much!
>
> 在 2014年10月17日星期五UTC+8下午11时09分41秒,David Shteynberg写道:
>>
>> In this case you will need to delve into the details of the pepXML 
>> format output by your method and correct the problems therein.  If you 
>> post an example pepXML file you have generated I can see if it is an 
>> easy fix. 
>> -David 
>>
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