Lipidomic Analysis

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Lipidomic Analysis elizabeth waldron  2018-02-08 01:27
 
I analysed labelled lipid standards using a DDA experiment on the Q-Exactive machine. I imported my data into Skyline and found that Skyline was only extracting data around a specific time frame. The outcome is that my MS1 data is being extracted beautifully, but my MS2 data looks like a scheduling experiment gone wrong. I have attached a screenshot of my Skyline document. Can anyone advise why Skyline is extracting MS2 data in a limited time frame and not over the whole chromatogram?
 
 
Brian Pratt responded:  2018-02-08 08:04
This will be easier to diagnose if you can upload the Skyline document and the raw file.

For the Skyline document, please use Skyline's File > Share > Complete menu item to package up the document and supporting files. The raw file will need to be zipped up on its own. Upload those to http://skyline.ms/files.url and I'll take a look.

Thanks,

Brian Pratt