• Sign In
  1. Requests

OpenMS converted pepXML

support

View Request

view list print
OpenMS converted pepXML leon bichmann  2018-07-20 02:18
 

Hi,

I would like to import a pepXML database search result using the Comet + Percolator combination into Skyline to generate a spectral library.

As I used OpenMS for the database search pipeline I had to convert the resulting idXML to pepXML.

Unfortunately, loading the pepXML seems to cause an error that I dont get rid of:

System.IO.IOException: ERROR: ...pepXML(line 11): The .pep.xml file is not from one of the recognized sources

I hope you have an idea how I could fix this problem to pipe my pipeline results into skyline.

The files are deposited in the file sharing folder for skyline support:
170407_AM_BD-ZH12_Spleen_W_10%DDA#1_400-650mz_msms38.pepXML
170407_AM_BD-ZH12_Spleen_W_10%DDA#1_400-650mz_msms38.mzML
170407_AM_BD-ZH12_Spleen_W_10%DDA#1_400-650mz_msms38.idXML_merged_perc_fdr_filtered.pepXML (merged replicate IDs)

Thanks and best regards,
Leon
 
 
Nick Shulman responded:  2018-07-20 14:31
This is the list of peptide search result formats that BiblioSpec currently knows how to handle:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

I can see that one person asked us to support idXML a few years ago, but we never got around to doing the work.
https://skyline.ms/announcements/home/support/thread.view?entityId=3f464255-75a2-1031-bb23-da2025828190&_anchor=8572#row:8572
https://skyline.ms/issues/home/issues/details.view?issueId=325

Each of the variants of pepXML that BiblioSpec knows how to handle have different ways of specifying the Q-values, and other things that is pretty complicated and I am not the expert on.

If you have your own search results, we normally recommend that you produce our own ".ssl" format which just a tab-delimited list of peptides and scan numbers.

Here is the page that talks about the .ssl format:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec%20input%20and%20output%20file%20formats

Hope this helps!
-- Nick
 
leon bichmann responded:  2018-07-25 14:49
Thanks Nick, converting to .ssl worked out very well.