Spectral library

Spectral library andreas kalagasidis  2024-02-24 03:38

I am trying to create Spectral library for use with OpenMS analysis. I created Spectral library using DDA files. When I export this as a Report, it contains no fragment charge in the Skyline transition list due to the use of MS1 filtering flow.

Could this have a major impact on subsequent steps in the Open Swath workflow (I haven't been able to complete the workflow)?

Any suggestions?

Nick Shulman responded:  2024-02-24 11:18
It sounds like you have successfully created a spectral library (.blib file), but, because you said it was DDA instead of DIA, Skyline did not add MS2 transitions to the document.
If you don't want to start over, you could get those MS2 transitions added to the document by doing the following:
1. Go to "Settings > Transition Settings > Filter" and change "Ion Types" to something that includes the ion types that you care about (I recommend setting it to "p, y, b" so that you get the precursor isotopes as well as the y and b ions.
2. Go to "Settings > Transition Settings > Full Scan" and change the "Acquisition Method" to "DIA" and change the isolation scheme to something appropriate. The easiest isolation scheme to choose is "Results Only" which means that Skyline will use whatever isolation windows are in the mass spec data file.
3. After you make these two changes, the Targets tree should now contain MS2 transitions, but these MS2 transitions will not have any extracted chromatograms. You should tell Skyline to extract chromatograms again by using the "Reimport" button at "Edit > Manage Results". Alternatively, if you do not have any replicates in your document you can tell Skyline to extract chromatograms using the "File > Import > Results" menu item.

It sounds like you had trouble at some point in the Import Peptide Search wizard.
The Import Peptide Search wizard is roughly equivalent to the following steps:
1. Go to "Settings > Peptide Settings > Library" and use the "Build" button to build a spectral library.
2. Use "File > Import > FASTA" to add peptides to your document
3. Use "File > Import > Results" to tell Skyline to extract chromatograms.
Sometimes if things go wrong in the Import Peptide Search wizard you might want to cancel out of the wizard and complete the rest of the steps using the Skyline menu items.

If you are having trouble you can always let us know what sort of error message you are seeing. You can also zip up all of your files and upload them here and we can take a look:
If you want to send us your Skyline document you can use the "File > Share" menu item to create a .zip file containing your Skyline document and supporting files including spectral library and extracted chromatograms.

Also, if you have not already looked at it, you might find some useful information in the SWATH tutorial:
-- Nick
andreas kalagasidis responded:  2024-02-28 09:40
Thanks for the reply

So if I want to have MS2 transitions in the document I need to specify that the Acquisition method is DIA, even if the data is comes from DDA measurements?

Apart from the spectral library, Skyline found CiRTs in the DDA input data which I used to create iRT assay library (as an input for OpenSwath workflow). I created retention time calculator from purified CiRT measurements, which I then also applied to the Spectral library measurements.
Is this approach correct?

Nick Shulman responded:  2024-02-28 10:57
I think I misunderstood your original question.
If the data that you collected is DDA then you should choose "DDA" as the MS/MS Acquisition Method at "Settings > Transition Settings > Full Scan".

Note that Skyline is not a very good tool for looking at DDA data. Skyline's user interface mainly revolves around extracting chromatograms, and, when you extract chromatograms from DDA data the chromatograms tend to have long straight lines connecting the places where a matching precursor happened to be selected for fragmentation. Skyline draws those DDA MS2 chromatograms in dotted lines to indicate that they are not being used for quantification. You can click on points along those lines to bring up a spectrum viewer which will show you the MS2 spectrum that that point along the chromatogram was extracted from.

I think you will have a hard time getting iRT to work with DDA data. Skyline wants to be able to find the iRT standard peptides in the extracted chromatograms, and it is difficult to reliably choose the correct peak when the only information that you have is MS1 chromatograms.
-- Nick
Nick Shulman responded:  2024-02-28 11:00
By the way, for looking at DDA data like you have, the best tutorials are:

MS1 Full Scan filtering: This tutorial will show you how to use peptide search results from another peptide search engine

DDA Search for MS1 Filtering: This tutorial will show you how to use Skyline's built-in peptide search engine called "MS Amanda"
-- Nick
andreas kalagasidis responded:  2024-02-29 09:18
Thanks again for your response

My interest in using skyline for DDA analysis was related to building spectral libraries for Open SWATH. Open MS state that Open MS flow is able to accept spectral libraries exported directly from Skyline. They don't mention the issue that you don't get fragment intensities from DDA analysis flow in Skyline.

I could easily finish the analysis using SWATH workflow with Skyline according to the tutorial you mentioned in your post with both DDA and DIA measurements, but I would like to be able to use other Proteomics tools as well (e.g. the ones provided in the Galaxy). That is why I engaged with Skyline.

Is there any way I can use CiRTs that Skyline found in the DDA measurements for creation of Open Swath library? Reading a lot of different articles tells me that it should be possible.

One more issue
You mentioned in your posts that for DDA data, one should follow DDA workflow (DDA with MS1 filtering). If I apply DIA workflow on DDA data, I get also MS2 chromatograms, but what kind of meaning do the obtained results have?

Nick Shulman responded:  2024-02-29 10:03
If all that you want is a spectral library, then you will have one pretty early in the Import Peptide Search wizard. The file will have the file extension ".blib" and as soon as you see that appear in the same folder as your .sky file, you could cancel out of the Import Peptide Search wizard and then use that spectral library somewhere else.

-- Nick