import peptide search from Mascot

support
import peptide search from Mascot io  2019-07-11
 
Hi,
I am trying to import peptide search from MASCOT (.dat file and .mzid). I am able to see the library match but I cannot see the chromatograms.
With dat file I have an error of Missing results file.
With mzid file I have this error
---------------------------
Skyline
---------------------------
ERROR: [References::resolve()] Failed to resolve reference.
ERROR: object type: struct pwiz::identdata::Contact
ERROR: reference id: PERSON_DOC_OWNER
ERROR: referent list: 4
ERROR:
ERROR:
ERROR: ORG_MSL
ERROR: ORG_DOC_OWNER
ERROR:
ERROR: reading file ESE10D2.mzid

---------------------------
OK More Info
---------------------------
System.IO.IOException: ERROR: [References::resolve()] Failed to resolve reference.
ERROR: object type: struct pwiz::identdata::Contact
ERROR: reference id: PERSON_DOC_OWNER
ERROR: referent list: 4
ERROR:
ERROR:
ERROR: ORG_MSL
ERROR: ORG_DOC_OWNER
ERROR:
ERROR: reading file ESE10D2.mzid

   en pwiz.Common.SystemUtil.ProcessRunner.Run(ProcessStartInfo psi, String stdin, IProgressMonitor progress, IProgressStatus& status, TextWriter writer) en C:\proj\skyline_4_2_x64\pwiz_tools\Shared\Common\SystemUtil\ProcessRunner.cs:línea 59
   en pwiz.BiblioSpec.BlibBuild.BuildLibrary(LibraryBuildAction libraryBuildAction, IProgressMonitor progressMonitor, IProgressStatus& status, String[]& ambiguous) en C:\proj\skyline_4_2_x64\pwiz_tools\Shared\BiblioSpec\BlibBuild.cs:línea 171
   en pwiz.Skyline.Model.Lib.BiblioSpecLiteBuilder.BuildLibrary(IProgressMonitor progress) en C:\proj\skyline_4_2_x64\pwiz_tools\Skyline\Model\Lib\BiblioSpecLiteBuilder.cs:línea 137
---------------------------

Could you help me?
Thanks in advance
Best
Irene
 
 
Brendan MacLean responded:  2019-07-11

Hi Irene,
This request seems so similar to another request we just received from another user:

https://skyline.ms/announcements/home/support/thread.view?rowId=40773

Could you possibly be working together? As I said in the other request:

  1. We would be very interested in seeing the .mzid file, which seems like it may be poorly formed in some way. Does it come directly from Mascot?
  2. The missing result file is really for you to solve by clicking the "Add" or "Add from Folder" button and pointing Skyline to where it can find the original mass spectrometer files you performed your search on. Without the mass spec data files, Skyline cannot extract chromatograms. The search result files alone do not contain the necessary MS1 spectra.

Hope this helps. Thanks for using Skyline in your research.

--Brendan

 
io responded:  2019-07-12

Hi Brendan,
I work in a different laboratory but I have read the other response and probably the problem is the same. My Mascot server is very old, 2.3
I have solved the .dat issue
Thank you!