Skyline analysis of LTQ XL Targetted Metabolomics

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Skyline analysis of LTQ XL Targetted Metabolomics sawhelan  2019-01-24
 

Hi,
Are files from Thermo LTQ XL compatible with Skyline analysis? Trying to upload targeted analyses of small molecules and it appears the data is loading but I am unable to see any peaks, RT, etc. All uploaded raw files are blank.
Thank you for any insight or directions provided.

 
 
Nick Shulman responded:  2019-01-24
Can you send us your files?

In Skyline, you can use the menu item:
File > Share > (complete)
to create a .zip file containing your Skyline document and supporting files.

You should also send us at least one of your .raw files.

If those files are less than 50MB you can attach them to this support request.
Otherwise, you can upload them here:
https://skyline.ms/files.url

I imagine the problem has something to do with your settings on:
Settings > Transition Settings > Full Scan
but we will be able to figure out what you should do once we see your files.
-- Nick
 
Brian Pratt responded:  2019-01-24
It's probably just some problem with your Skyline settings. If you can provide your Skyline .sky.zip file (using File > Share > Complete) and the raw data I'd be happy to have a look. You can upload to http://skyline.ms/files.url or send by other means as you prefer.

Thanks for using the Skyline support board!


Brian Pratt
 
sawhelan responded:  2019-01-25
Hi,
Thank you for your support! I uploaded the file (Description: LTQ XL Small molecule Skyline analysis). I probably do have the wrong parameters set. I am signing up for the skyline classes at Northeastern this may, but will hopefully be able to learn as much as possible before then.
Thank you!
Steve
 
Brian Pratt responded:  2019-01-25
Hi Steve,

In Settings > Transition Settings > Filter > Small Molecules make sure Ion Types has precursors enabled (set to "f,p").

Not your fault, this is way too easy to miss. We need to improve here.

Cheers

Brian Pratt
 
sawhelan responded:  2019-01-25
Hi Brian,
Thank you, I had no idea about "p"? Can we also view only the fragment ions of the targeted parent ion? I also had an error trying to create precursor adduct for M-H for negative ions in the transition list upload, it kept failing. How do I create transition lists for negative mode precursor ions?
Thank you,
Stephen
 
Brian Pratt responded:  2019-01-25
>> Can we also view only the fragment ions of the targeted parent ion?

I'm not sure what you're asking, sorry.

>> How do I create transition lists for negative mode precursor ions?

It sounds like you have the right idea, may I see what you've tried?

Brian
 
sawhelan responded:  2019-01-25
 
Brian Pratt responded:  2019-01-25
It's just that you have some charge declarations that disagree with the charge of the adduct. [M-H] precursor and product charges should be negative. When I try to load your transition list I see an error message to that effect.

Change, for example, your line 2 from
Metabolite    Indoxyl Sulfate    C8H7NO4S    [M-H]    1    3.6    50    80.9    1
to
Metabolite    Indoxyl Sulfate    C8H7NO4S    [M-H]    -1    3.6    50    80.9    -1

and it should be fine.

Cheers

Brian
 
sawhelan responded:  2019-01-28
Hi Brian,
Thank you for you help. I still think I have some of the settings incorrect. I have attached a power point slide with peaks and areas calculated in Xcaliber software from different standard concentrations of three molecules. When I load these files into skyline I do not see similar peaks? The amino acid tutorial works well and I have seen similar results using data from Q Exactive to analyze amino acids. Are the peaks the attached slides to broad?

Thank you,
Stephen
 
Brian Pratt responded:  2019-01-28
Can you provide your current Skyline document?

Thanks

Brian
 
sawhelan responded:  2019-01-28
Hi Brian,
I see the Peaks from the standards. I now need to figure out how to calculate peak area and plot to concentrations. I was calculating Standard Curves manually using Xcaliber and excel. Is there a tutorial going through this process to determine unknowns?

Thank you,

Stephen
 
Brian Pratt responded:  2019-01-28