Trouble finding spectrum files - can they be input through a command line interface

Trouble finding spectrum files - can they be input through a command line interface jharrison  2020-11-23

Hi Skyline team,

Thank you for making such a useful software. I want to do some ms1 filtering in some data and I have been having some issues when I try to open the .pep.xml file. I keep getting the error message below and I do have the .mzML file in the appropriate folder. I think the issue is that I am using VMware fusion on a mac to run windows and I think it is somehow frustrating your auto search tools. I am wondering if there is a way I can pass the spectrum file into skyline through a command line interface like skyline runner. Or maybe I am doing something else silly that is giving me an issue. I am grateful for any help you can offer.

System.IO.IOException: ERROR: Could not find spectrum file 'NA[.mz5|.mzML|.mzXML|.ms2|.cms2|.bms2|.pms2]' for search results file 'WT_Roos_1.pep.xml' in current directory, ../,../../.


Nick Shulman responded:  2020-11-23
This does not sound like something that would be caused by VMWare fusion.

The error message says that it is looking for a file that might be called "NA.mzML".
My guess is that you do not actually have a file called "NA.mzML" (or with some other file extension: NA.mz5, NA.mzXML etc....?).
It sounds like the problem might be that the filename is being misread from inside of the pepXML file.

The place that BiblioSpec looks in the pepXML file for the name of the mass spec data file depends on the type of peptide search engine that was used. Often the filename is specified in the "baseName" attribute near the beginning of the pepXML file.

Which type of peptide search engine did you use? This is the page which lists all of the search engines that BiblioSpec knows how to handle:

If you would like, you can send us your .pep.xml file. If that file is less than 50MB, you can attach it to this support request. Otherwise, you can upload it here:

-- Nick
jharrison responded:  2020-11-23
Thank you Nick you are a legend!

I used the crux pipeline to do the peptide search and I guess my poor use of crux, I didn't put the name of the data into the pep.xml file properly. Just replacing the NA in the file name with the spectrum data did the trick and everything is loaded now!

Thank you again,