Shimadzu Triple Q data in Skyline

Shimadzu Triple Q data in Skyline t j f m voermans  2019-04-29


In the article: "The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics" it is stated that skyline supports SRM files from Shimadzu (.gpd). However, the only files I have are .lcd files (see attachment). This file is of a scan+ measurement done on a Shimadzu LCMS-8045.

Any way to import these in Skyline as well? (When I use the normal way of importing data via File - Import - Results, I get a message that there is no usable data found.

Thank you.


Brian Pratt responded:  2019-04-29

Hi Tim,

Skyline should be able to read Shimadzu .lcd without problem. But when I tried to have a look at your example file (thanks for sending that) in SeeMS, it throws an error message. We'll have to look into that and get back to you.

Thanks for using the Skyline support board!

Brian Pratt

matt.chambers42 responded:  2019-04-30

Hi Tim,

Should this file have any SRM or MS/MS data in it? All I'm seeing are MS1s.

t j f m voermans responded:  2019-05-01


Yes it is indeed MS1. But seeing the comment, I think that Skyline only works with Shimadzu SRM/MRM measurements. I thought I checked that as well, but today I was able to import an MRM file. However, if it is possible to import an MS1 file as well, that would be great.

Brendan MacLean responded:  2019-05-01

Hi Tim,
It seems we have two separate DLLs for reading .lcd files from Shimadzu and Skyline used to expect the QQQ reader to fail entirely on seeing QTOF data, but your file showed us that it might return a success code, but then provide no spectra and no chromatograms. Hence the error about "no usable data".

Matt Chambers, today, made a fix to consider the QQQ reader to have failed in this case and move on to trying the QTOF reader, and my latest build of Skyline can no ready your file and extract chromatograms from it.

So, you should be able to use the next Skyline-daily release (click the green "Skyline-daily (beta)" button on the installation page) with your .lcd file.

Thanks for reporting the issue and providing the example file.


t j f m voermans responded:  2019-05-02

A big thank you. Looking forward to the update.