Skyline understands .msp files, which is the NIST spectral library format.

The way to use a .msp file in Skyline is to go to:
Settings > Molecule Settings > Library
and push the "Edit List" button and then push the "Add" button and then point Skyline at your .msp file.

After you have added the .msp library to your document you can use the menu item "View > Spectral Libraries" to see what is in the .msp library and you can use the "Add" button on the Spectral Library Explorer to add molecules to your document.
-- Nick

Tryed, it does not work, on attempt to add library got a message attached in errormessage.png, apparently word null is in place of formula. Opened Msp file in excel. It looks like in file attached in MSP_base in excel.png. How to go around it? Is there other ways to prepare library or transition list? Thank you for the prompt answer,
regards
Stjepan

Yes, that's a not very useful MSP file. Perhaps we could have a look at the .txt representation you mentioned?

Two files are attached, first unedited .txt as exported from MS-DIAL, it does not work, many collumns, does not look as a suitable format. Second is .csv file, manualy edited, much shorter version of original .txt stored in .csv format, it works as a transition list. Problem is that editing can not be done for entire original file. May be MS-Dial has some other means of exporting list I am not aware of? Should ask them.
regards
Stjepan

No need for a lot of work in Excel. This should get you started:

Open the .tsv file in any text editor
Remove all occurrences of "null" to blank (change "null" to be an empty field - Skyline doesn't know how to read that, but I'll make a note to treat that as an empty field)
Select All, Copy
Paste into Skyline's Targets window
Set the column headers identifications as needed using the controls at the top of each column
Use "Check for Errors" button to see how you're coming along

There are a number of interesting issues remaining, though.
Skyline is confused by an adduct description [M+H-2H2O] where there is no chemical formula given to use with the water loss.
Claimed negative charge on an adduct [M+H-H2O]
Skyline doesn't know what the * in "[M+Li]+*" is supposed to mean
and others.

I'd be curious to know how you think these should be resolved.

Best,

Brian

Thank you Brian,
I will try to edit file as suggested, most likely on monday, I will let you know what is going on with it.
regards
Stjepan

Dear Brian,
Did as suggested, opened in notepad, removed nulls, pasted in Import transition list identify Columns, there are 1008 errors out of 21852 lines. Errors are of three kind (three columns) Most often in column 7 like two following copied from error list.

Precursor m/z 86,9918 does not agree with value 87,09167 as calculated from ion formula and charge state (delta = 0,09987435, Transition Settings | Instrument | Method match tolerance m/z = 0,055). Correct the m/z value in the table, or leave it blank and Skyline will calculate it for you.
Delta is relatively small, probably MS-DIAL missidentified compound, end up with wrong formula for detected mass
Precursor m/z 243,0184 does not agree with value 220,0342 as calculated from ion formula and charge state (delta = -22,98414, Transition Settings | Instrument | Method match tolerance m/z = 0,055). Correct the m/z value in the table, or leave it blank and Skyline will calculate it for you.
Delta corresponds to the mass of the sodium, Skyline does not recognize suggested adduct with Na.

Error number two is found in the column 10
Failed parsing adduct description "[M+H-H2O]-": declared charge -1 does not agree with calculated charge 1,
Failed parsing adduct description "[M+2H]+": declared charge 1 does not agree with calculated charge 2
Adduct "[M-2H2O+H]" calls for removing more O atoms than are found in the molecule C21ClH30NO
Unknown symbol "*" in adduct description "[M]+*"
as you suggested Skyline does not recognise adduct description
 
Error number three is for column 0 like this one:
Inconsistent molecule description ("InChiKey:GFFGJBXGBJISGV-UHFFFAOYSA-N SMILES:N=1C=NC2=C(N=CNC12)N" / "InChiKey:GFFGJBXGBJISGV-UHFFFAOYSA-N SMILES:C1=NC2=C(N1)C(=NC=N2)N")

If I include column named MSMS spectrum from .txt file containing data in the following format: 50.60177 10;50.98618 24;50.98819 12;50.99020 12;51.19501 10;53.99615 36 (presumably product ion m/z intensity;) and declare it (obviously wrong) as a Product m/z I got a lot of errors of the kind:
Invalid m/z value 50.60177 10;50.98618 24;50.98819 12;50.99020 12;51.19501 10;53.99615 36
How should I use date from this column to describe product ions m/z and their intensity?

Where to go from here, goal is to deconvolute/describe compounds detected in the Swath file (small molecules) using data recorded in the DDA file of the similar samples.
Thank you in advance,
Stjepan

It does appear that the .txt file contains the most useful information. It's frustrating and weird that the fragment data was left out of that .msp file.

We'll have to do some work to pick apart the pairs in that "MSMS spectrum" column. And I'll have to look into that "Inconsistent molecule description" issue.

But from my previous message:

There are a number of interesting issues remaining, though.
Skyline is confused by an adduct description [M+H-2H2O] where there is no chemical formula given to use with the water loss.
Claimed negative charge on an adduct [M+H-H2O]
Skyline doesn't know what the * in "[M+Li]+*" is supposed to mean

Again, what are your thoughts there?

Dear Brian,
My plan was to follow workflow from an article mentioned in first message, as ilustrated in the document attached. It should be straightforward but it is not, now I do not know how they prepared transition list, obviusely it involves some manual editing. I will post a question to MS-DIAL support and will let you know their response.
regards
Stjepan