Importing MRM method *from* MassLynx

Importing MRM method *from* MassLynx Koen  2020-01-30
First post here!

I'm unable to find any info how to import an existing MassLynx method with MRMs *into* SkyLine. Most tutorials, etc are the other way around. We're using MassLynx 4.2.

Is this possible?


- Koen.
Nick Shulman responded:  2020-01-30
Can you get a list of peptide sequences, precursor m/z and product m/z values out of your MassLynx method?

If so, you could probably make use of the menu item in Skyline:
Edit > Insert > Transition List
File > Import > Transition List

Not sure if this suggestion is helpful.
-- Nick
Koen responded:  2020-01-31
Thanks Nick.

As far as I know there is no simple way to get the the transitions out of the MassLynx method. Basically it is a plain text file, but it would require some tedious combing through each line or a funky script to get the info in a format suitable for SkyLine. I also looked at extracting the info from the TargetLynx processing method. But again, there is no way that I found to just copy paste that table.

Probably it'll be easier just to type it in an Excel sheet.

EDIT: I indeed ended up creating the Excel sheet manually. In the MS method in MassLynx, if you double click the MRM line for each component (the green bar), you can actually select the lines and copy those into Excel. But still one at a time. After that the import into SkyLine is easy.

One thing I noted: don't label your internal standard as "compound-d3" in SkyLine, just call it "compound" and add a light/heavy label column.
Will Thompson responded:  2020-01-31
Thanks Koen

I am going to be working with Waters on easier translation into/out of Masslynx and your note is an important aspect to consider for legacy methods. Thank you for bringing it up. Also, a note on your last comment about the compound name. Either approach would work; if you label your internal standard with a different name you would need to use the use the "surrogate standard" quantification workflow as outlined in our small molecule quant tutorial. Sometimes this has an advantage for deuterated internal standards, because with the heavy/light workflow Skyline requires the same retention time boundaries between the native and SIL compound. Since deuterated compounds have slightly earlier retention in RPLC, sometimes it is useful to have them named separately, thus integrated independently, and use the surrogate standard workflow.


Will Thompson
Duke Univ.
Koen responded:  2020-01-31
Hi Will,

Glad to help, and I'm happy to test anything regarding the MassLynx import/export procedure if needed.

And thanks for the pointer to the surrogate standard workflow - that was very helpful.

- Koen.