Issues importing Small molecule transition list

Issues importing Small molecule transition list m3g4n  2023-12-04 14:07

Hello! I'm having an issue where I'm trying to copy-paste a list of 30 compounds into skyline and it's breaking apart some of the entries (quant and qual are separate). I don't know how to add them together, or insert one into the other, etc. If anyone knows what I should be looking in depth into in terms of excel syntax that would be super helpful.

Thank you!

Nick Shulman responded:  2023-12-04 14:09
Can you send us the transition list that you are trying to paste into Skyline? We will probably be able to figure out how to get Skyline to do what you want it to do.
-- Nick
m3g4n responded:  2023-12-08 11:52
Hello! Here is the version that I currently have. The amount of errors generated when I try to upload something like this that I've exported from SciexOS or from literature is staggering.
Nick Shulman responded:  2023-12-08 12:25
It might be easier for us to answer your questions if we focus on getting one molecule at a time to work correctly.

Attached is the transition list that I used for adding the first molecule "Lactate" to the document.
I added columns "Precursor Charge" and "Product Charge" which both have "-1" in them.
I removed the column that you had called "Q1" because you already had a column with the molecular formula, and it seemed that Skyline disagreed with the transition list as to what the actual precursor m/z should be.

One thing that I noticed is that when I insert this transition list into the Skyline document, Skyline asks whether I want to enable "Auto-select".
There seems to be a bug in Skyline which requires that you choose "Disable" in that dialog. If you choose "Enable" then Skyline will delete one of the transitions that you are trying to insert.
I will ask around and try to find someone to fix this.

I hope this helps.

Let me know which other molecules in the transition list we should try to get working.
-- Nick
Nick Shulman responded:  2023-12-08 14:05
I have figured out why one of the transitions disappeared when I chose to enable "Auto Select".
One of the transitions had a product m/z of 43, which was lower than the "Min m/z" that I had chosen at "Settings > Transition Settings > Instrument".

The default value for "Min m/z" in Skyline is 50, so, if you do want to have transitions with lower m/z's than that, you should go to "Settings > Transition Settings > Instrument" and set "Min m/z" to a lower number.
-- Nick
Brian Pratt responded:  2023-12-11 09:35
I would definitely take a step back and carefully consider the problems reported by Skyline - for example, how is it that the molecule "Indole-3-acetic acid" has more than one chemical formula? And how is it possible that all three all result in the same m/z value? Something is amiss here.

Best regards,

Brian Pratt
m3g4n responded:  2023-12-12 09:56
Whoops, yeah that's just the drag down doing the number addition, that's an oversight on my part, fixed.

The big thing is we have a lot of these methods on the Xevo and on a 7500, and we want to now get them uploaded into skyline, so I'm dealing with someone else's stock transition lists in a lot of formats to then get them through. This one I had half the transitions and had to build out the other half to fulfill the researchers full analysis.

And because small molecules have spaces or different punctuation or in the case of the 7500, numbers, it's creating a very messy import.

But these are helpful suggestions!
Brian Pratt responded:  2023-12-12 10:16
I'd be happy to look at the originals and see if I can offer any useful observations.
m3g4n responded:  2024-02-15 09:16
Here's the bee in my bonnet this week - we are setting up the System Suit, we've optimized transitions (we need to pare down but that's next steps) - I'll include our Agilent DB export, and the skyline version of transitions, but I can't get skyline to import them properly. It either imports improperly and doesn't complain (I have to leave out charges and molecular formula) or I include everything and it fails to import at all. Right now charge state in the Skyline sys suit says positive or negative but on the instrument computer it says [M+H]+, etc, in the same way as the agilent file but with skyline formatting.
Brian Pratt responded:  2024-02-20 14:35
This is actually pretty close to working, though there is something fishy in "SysSuit Agilent DB import file.csv" on line 5 - it claims negative polarity with an M+H adduct. Also it's a little strange that "(M+2H)+" isn't written as "(M+2H)+2" or "(M+2H)++" (and that it uses parens instead of brackets), but again there aren't really any standards for this so we try to stay flexible.

There really aren't any standards at all for describing transitions lists, so we're always extending Skyline to deal with new varieties as users provide them. Thanks for the file, we'll use it to make future version of Skyline a little smarter when reading files like these.

Anyway, see attached for some light edits that allow import into Skyline.

m3g4n responded:  2024-02-20 15:13
Thanks Brian - could you look at the other file (skyline system suit csv) - that's the one that I made from the Agilent database import file and I curated it for Skyline but something is still not right. I included the agilent file because that's what we've optimized on the instrument and I'm attempted to take that and make a skyline compatable transition import for our QC auto upload. so the "Skyline System Suit csv" is me trying to minimize info so it hates it less and to provide a good guideline to our other uses as to how to format going forward. Skyline fully hates the ( instead of [ I've found as well. For the doubly charged ions should it have two charges on the outside for skyline to like it more?

Thank you so much for your help.

Brian Pratt responded:  2024-02-20 16:22
Really just a few changes needed -

Let Skyline calculate the precursor m/z from the formula, and drop the "Precursor m/z" column

What you have in the "Polarity" column is really the "Precursor Adduct"

For Product Charge, an integer is fine but understand that it's a signed value that has to agree with the precursor charge. So a bunch of those should be -1, not 1.

Also note that you don't have to indicate charge in the molecule name, or sort them into lists by charge if you don't want to - Skyline understands the idea of a molecule having more than one kind of ionizing adduct, even when they are different polarities.

m3g4n responded:  2024-02-27 11:15
When I drop the precursor m/z, it has a lot of errors importing the values. Is there a window I should broaden to allow it to parse the import properly?
Brian Pratt responded:  2024-02-27 13:45
Can you be more specific? A screenshot would be helpful.