Skyline not compatible with Shimadzu LCMS-8060

Skyline not compatible with Shimadzu LCMS-8060 William  2021-04-19 21:10

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 13:16

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 Tamura responded:  2021-04-22 15:33

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


William responded:  2021-04-22 16:05

It's LabSolutions Version 5.99 SP2.

Kaipo Tamura responded:  2021-04-23 12:23

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 17:06

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 Tamura responded:  2021-04-27 08:22

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 14:15

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 14:44

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
aaron reyes responded:  2024-01-03 06:43
Hi Skyline Team,

I exported my transition list to Shimadzu LC-MS 8060. However, the transitions do not seem to be carried over properly. Almost all the heavy peptides are missing on the list (.txt file) and the m/zs looks a bit jumbled. I attach here my .txt file and also the .sky file where I exported my list for your reference. The Skyline version I used is Skyline (64-bit) For the parameters, I selected Instrument Type: Shimadzu, Collision Energy: Shimadzu QQQ, Delustering Potential: ABI.

 I would like to hear your thoughts on this. Thank you.
Nick Shulman responded:  2024-01-03 07:25

No .txt file has been attached to this support request. Could you try attaching it again?
Also, it would be helpful if you could give us a file instead of the .sky file that you attached.
In Skyline you can use the menu item:
File > Share
to create a file containing your Skyline document and supporting files including spectral libraries.

Files which are less than 50MB can be attached to this support request. If you have larger files than that, you can upload them here:
-- Nick
aaron reyes responded:  2024-01-03 07:50
Hi Nick,

Thanks. I have attached here the .txt file and the in this message. Please have a look.


Nick Shulman responded:  2024-01-03 12:51

I am not the expert on Shimadzu transition list export, but I believe, even though the text file you attached only has 55 rows in it, the precursor and product m/z's of all of the transitions from your Skyline document are in that text file.
For some reason, up to six transitions might be written in a single line in the text file.
The first transition's precursor and product m/z's get written to the "m/z(1)" and "m/z(2)" columns. Additional transitions may be written in the "Ref.(###) m/z(1)" and "Ref.(###) m/z(2)" columns where "###" is a number.

If this information is not helpful I could try to find someone who is an expert on Shimadzu method export who might be able to give a better explanation of what is going on.
-- Nick
aaron reyes responded:  2024-01-04 10:28
Hi Nick,

Thanks. I got your point. When Skyline exports the Shimadzu Transition List, it lists down 6 transitions per single line.

I will test if changing the Peptide Name in the txt file will allow Lab Solutions to recognize the list more accurately.

I'll keep you posted if it works or not.

Nick Shulman responded:  2024-01-04 10:52
By the way, the usual way to export lists of stuff from Skyline is to create a custom report.
You can learn about creating custom reports and the Document Grid in the Custom Reports tutorial:

When you install Skyline, there is a custom report already defined "Peptide Transition List" which might have all of the data that you need in it.
If not, you could create your own custom report.
-- Nick
andre deoliveira responded:  2024-03-08 09:06
Dear Skyline team,

We are recently using skyline to analyse data from a LCMS-8060 (Shimadzu). Everything is working fine, however skyline is not importing the Sample Name nor the Sample ID from the results. When I try to include a column for the Sample Name, it says that it is blank. Do you guys have experienced it before? Is there a way to fix it?


Nick Shulman responded:  2024-03-08 09:42

The "Sample Name" column in the Document Grid is only ever used for Sciex WIFF files.
There can be multiple runs in the same .wiff file, and the "Sample Name" column in can be used to distinguish them.

The "Sample ID" column in the Document Grid would be the appropriate place to find the sample name from the mass spec data file, but, I believe, the only type of files that this actually works for is Thermo .raw files.

If you send us your Shimadzu .lcd file we might be able to get something working in the future. I am not the expert on reading metadata from raw files, so I can't predict whether or when this work would actually happen.
If your .lcd file is less than 50MB you can attach it to this support request.
You can upload larger files here:

-- Nick