Skyline cannot import iProphet pepXML files to build a spectral library - if X!Tandem was used as a search engine marc isaksson  2019-10-07
 

Hi,

I have noticed that Skyline (v.19.1) cannot import a iProphet pepXML file, if X!Tandem was one of the search engines, or the only search engine. I have tried to combine Comet searches and X!Tandem searches into an iProphet pepXML. When importing into Skyline, I get a error message saying(see attached for full error message):

ERROR: comet_tandem.ipro.pep.xml(line 555966): Missing required attribute 'spectrumNativeID'.
ERROR:

Command-line: C:\Users\marc\AppData\Local\Apps\2.0\W8H7VL7Y.7R9\HMJZHTQA.5XR\skyl..tion_e4141a2a22107248_0013.0001_f6e2bff174ff9e23\BlibBuild -s -A -H -o -c 0.999677 -i H9D_6F_190913_lib1 -S "C:\Users\marc\AppData\Local\Temp\tmp17BF.tmp" "D:\Data_Skyline\H9D_6F_190913\H9D_6F_190913_lib1.redundant.blib"
Working directory: D:\Data_TPP\RAW_files

Apparently, Skyline/Blibbuild is looking for the term SpectrumNativeID. Problem is that only Comet results have such a reference. X!Tandem does not produce any column or reference saying SpectrumNativeID. I was using X!Tandem version Jackhammer 2013.06.15.1, as part of the TPP 5.0.2 distribution.

When I created an iProphet pepXML file from Comet searches only (v.2018.01 rev.4), it was no problem to import the pepXML file into Skyline.

I would be really happy if search results from Comet and X!Tandem could be combined into iProphet and then imported into Skyline! As I understand, BlibBuild is supposed to import X!Tandem results, given that the file format is xtan.xml.

Best,

Marc

 
 
matt.chambers42 responded:  2019-10-08