Skyline not compatible with Shimadzu LCMS-8060

Skyline not compatible with Shimadzu LCMS-8060 William  2021-04-19

I am porting the method to our new purchased Shimadzu LCMS-8060. I exported transition list from Skyline (choose Shimadzu QQQ) to txt file. However, when importing compound list to Shimadzu, it is completely chaos. I then check the title of each rows and find they don't match. Here I attach the compound export file from Shimadzu QQQ. Pls update Skyline so that exported file can be recognised by Shimadzu.

Brendan MacLean responded:  2021-04-20

Hi William,
We are looking into this with our contacts at Shimadzu. We need to understand better under what conditions the column change happened. e.g. Is it due to a software update that will impact all Shimadzu instruments on which the update is installed, or is it instrument-specific? Obiously, if we just jumped into changing the columns to be what you are currently seeing, we stand the risk of breaking someone else.

Once we work out these details, we will gladly integrate what we have learned into a Skyline-daily release, hopefully very soon.

Thanks for providing your method file format. We'll post more to this request as soon as we know more.


Kaipo responded:  2021-04-22

We will update the export to work for the new format. What version of LabSoultions are you using?


William responded:  2021-04-22

It's LabSolutions Version 5.99 SP2.

Kaipo responded:  2021-04-23

Hi William,

One more thing, Shimadzu has requested the following information:

  • A TSV file created by exporting the transition list from Skyline which results in a problem when they try to import it.
  • A screen capture showing the result when trying to import it into LabSolutions.


William responded:  2021-04-26

Here is the txt file (not csv) exported from Skyline. As you can see, I have set up step size of 2 and count of 5. But when importing to Shimadzu, all these step count is lost.

Kaipo responded:  2021-04-27

Hi William,

Shimadzu has looked into this and it actually turns out to be a bug in LabSolutions which will be fixed by upgrading to an upcoming release:

The phenomenon looks very similar to a problem that was reported by another customer in March; my investigation found that it was because of a bug in the LabSolutions Import Compound Table functionality. I reported this bug and it was fixed earlier this month.

I have just confirmed that if I try to import this customer’s transition list in an internal beta build of LabSolutions LCMS 5.109 that contains the bugfix, it appears to work fine – please see the attached LatestLabSolutionsResult.png file.

So the cause of this problem appears to be the same LabSolutions bug; no changes will be needed to Skyline.

LabSolutions LCMS 5.109 is scheduled for release in May; upgrading to this version should resolve the customer’s problem.


William responded:  2021-05-12

I cannot wait for the new patch and manually edit the method to fit in Shimadzu LabSolution software with step size of 2 and count of 5 (same as Skyine setting). However, after I have run the sample and got the data file, I found Skyline could not display the chrom of different CEs (file name CYREN_01) as before (file name CYREN2 and CYREN3). I wonder is there anything I did wrong or just the incompatibility between LabSolution and Skyline. Here I upload both data file and Skyline file FYI.

Nick Shulman responded:  2021-05-12

Skyline never looks at the actual CE value in raw (or .lcd) files.

When you export a collision energy optimization method, for each transition, Skyline specifies a group of chromatograms where the Q3 values differ by 0.01 m/z units. (For example, if the transition had an m/z of 405, and the step count was 3, the method would have Q3 values 404.97, 404.98, 404.99, 405.00, 405.01, 405.02, and 405.03).

When Skyline is reading the chromatograms in from a raw file, Skyline notices that there is a group of chromatograms whose Q3 values differ by 0.01, and then Skyline assumes that the collision optimizations of those chromatograms were what they would be based on your current settings.

The Q3 values for your chromatograms in your .lcd file are all the same. For this reason, Skyline does not know that these chromatograms came from a collision optimization experiment run, and Skyline does not know what to do with them.

If you really wanted Skyline to be able to understand this experiment, you could convert the .lcd file to .mzML, and then edit the text file and change the Q3 files so it would look to Skyline like a collision energy experiment.

-- Nick