How did skyline read the OpenSWATH results? andyzcq  2020-09-19
 

I followed the tutorial, and found there is no merged.osw file in OpenSWATH results.

I have used OpenSWATH (V. 2.5) to analyze my DIA data.

So how did Skyline read OpenSWATH (V. 2.5) results?

 
 
Nick Shulman responded:  2020-09-19
I am not sure I understand your question.

Are you saying that you followed the steps of a tutorial and some file that you expected to be there was not there? Which tutorial are you asking about?

The way to get Skyline to read open swath results is with the menu item:
File > Input > Peptide Search
which walks you through several steps, the first of which is building a BiblioSpec spectral library.
".osw" is one of the file types that can be used to build a BiblioSpec spectral library.

Are you saying that there is something different about the file types in OpenSwath version 2.5 and there is no ".osw" file?
-- Nick
 
andyzcq responded:  2020-09-19
Nick, I followed the tutorial at https://skyline.ms/wiki/home/software/Skyline/page.view?name=import_openswath.

The file that is loaded into the skyline in the video is named "merged.osw”, which is a combined osw file contained all run identifications.

But in the current version of OpenSWATH (2.5), there is no merged.osw file in the outputs of OpenSWATH. There are two files "model.oswm" and "model_global.oswm" in the outputs of OpenSWATH, which should be combined osw files containing all run identifications (47 runs in my case).

There are osw files for each run in the outputs of OpenSWATH, but these files contained identifications for separate run, not all of them.
 
Nick Shulman responded:  2020-09-20
I am not sure whether anyone on this support board is an expert on OpenSwath search results.

You can build a spectral library from multiple search result files. What happens if you use the .osw files from each of your 47 runs to build a spectral library? Is there some sort of false discovery rate stuff that you are missing out on by not having a merged.osw file?

BiblioSpec looks at the filename extension in order to decide what to do with peptide search result files. If you think these .oswm files might be similar enough to a .osw file that BiblioSpec might be expecting, you could try renaming them to .osw and see whether it works. (although "model" does not sound like the name of a file that would contain a list of results).

The first version of BiblioSpec that could read .osw files was in 2018. Has OpenSwath changed the format of their output files in a way that we need to support? You can certainly send us your files and we can take a look.
You can upload large files here:
https://skyline.ms/files.url

-- Nick
 
andyzcq responded:  2020-09-20
I have renamed "model.oswm" file into "model.osw", and Skyline can not read "model.osw".

I have uploaded "model.oswm", "model_global.oswm" and separate .osw file to https://skyline.ms/files.url.
 
andyzcq responded:  2020-09-20
The uploaded zipped file is named as "output of OpenSWATH".
 
matt.chambers42 responded:  2020-09-25
Hi Andy,

When I rename model.oswm to model.osw, BlibBuild and Skyline are able to read it. What issue did you run into when you renamed the file? What version of Skyline? The schema is very similar between the two files. The .oswm file seems to only drop the FEATURE_PRECURSOR and SCORE_PROTEIN tables, and BlibBuild doesn't use either of those.

-Matt