How to analyze Shimadzu .lcd files?

How to analyze Shimadzu .lcd files? AWY  2024-01-19 21:37

I outsourced LCMS running and received .lcd files for targeted metabolites.

Files contain (samples with replicates, blanks , standard curv / dilution series ).

I don’t have access to shimadzu software to process targeted LCQQQ .lcd files. This was not possible with MSDIAL, I heaerd the best open source software for processing targeted LCQQQ data.

How can I analyze .lcd files from targeted metabolics?

I would be grateful if you could share any tutorial please.

Nick Shulman responded:  2024-01-19 21:50
Skyline is a great tool for analyzing liquid chromatography data from triple quadrupole instruments from many manufacturers including Shimadzu.

With Skyline, the first step that you would need to do would be to tell Skyline which targets you are interested in. If you are doing a proteomics experiment, you could give Skyline the list of peptides using the menu item "Edit > Insert > Peptides". You can find more information about other ways of adding targets to a Skyline document in the first part of the Targeted Method Editing tutorial:

If you are interested in small molecules which are not peptides then you should look at the small molecule tutorial:

After you have told Skyline about your targets you can use the "File > Import > Results" menu item to read the chromatograms from your .lcd files.

Alternatively, if you want to have a look at your data without Skyline getting in the way, you could install ProteoWizard:

After you have installed ProteoWizard there will be two new items on your Windows Start Menu:
1. "MSConvert" can be used to convert your .lcd files to .mzML. I believe MSDIAL can read .mzML files.
2. "SeeMS" will allow you to view the list of chromatograms that are in your .lcd file and plot the chromatograms on the screen.

-- Nick
AWY responded:  2024-01-20 00:30
Thank you very much Nick. This is helpful.

Btw, How can I know what is the Transition list to insert?

From the lab I only received .lcd files for each samples (treatments, controls, blanks, standards).

Does Transition list information (Molecule List Name, Precursor Name etc) embedded into these .lcd files or
Do I have to get the Transition list information separately from the analytical lab for?
Nick Shulman responded:  2024-01-20 01:07
You should probably ask the lab for the transition list.

It's possible that you already know what the transition list is. If a lab was told to collect data, they must have also been told what transition list to use.

You can use ProteoWizard SeeMS to see the list of Precursor m/z (Q1) and Product m/z (Q3) values of the chromatograms in the .lcd file.
But, someone must have a list which says which molecules those values were intended to be targeting.
-- Nick
AWY responded:  2024-01-28 15:13
Hi Nick,
If you could please help me with this.
I get an error message "Adduct [M-H] charge -1 does not agree with declared charge 1" while trying to import transition list for small molecules.

Attached herewith my simplified transition list "CCM_TransitionList.csv" that I am trying to import.

Also attached original file I received from the lab "processing method.xlsx"

Could you please help me to figure out from is the reason.
Nick Shulman responded:  2024-01-28 15:27
You should change the numbers in your "Precursor Charge" and "Product Charge" columns to be "-1" instead of "1".
If your adduct is "M-H" then that means your precursor has a charge of "-1".

You can find more information about adducts in Skyline here:
-- Nick
AWY responded:  2024-01-29 16:11
Thanks a heap Nick. This works.

Another question, during small molecular transition list importing, how to add qualifier data? Which category I should choose from the menu (see attached)

If you could refer to my previous file "CCM_TransitionList.csv "
Nick Shulman responded:  2024-01-29 16:52
Skyline considers that the qualifier and quantifier product ions are two separate transitions so there should be two separate rows in your transition list.
So, for that first row in your screenshot, you should make two rows where one of the rows has "117.05" in the "Product m/z" column, and the next row has everything the same except it has "94.05" in the "Product m/z" column.
-- Nick