Chromatogram information unavailable

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Chromatogram information unavailable joaopcnunes  2020-02-05
 

Hello,

I analysed some data files in Mascot and then import the .dat files into Skyline (v.20.1.0.31) but i can´t see the chromatogram (Chromatogram information unavailable). I already changed the name of the .dat file for the same of the raw file, but it didn´t solve the problem.

Could you please help me on this problem?

Thank you very much

João

 
 
Brendan MacLean responded:  2020-02-05

There are not chromatograms in a .dat file. You should be using File > Import > Peptide Search or the "Import DDA Peptide Search" icon on the Start page, which will guide you through building a library from your .dat file and then directing Skyline to the DDA raw data files for chromatogram extraction.

You should also be following the MS1 Full-Scan Filtering tutorial:

https://skyline.ms/tutorial_ms1_filtering.url

Or one of the associated webinars.

Hope this helps to get you started with Skyline for analyzing DDA data.

--Brendan

 
joaopcnunes responded:  2020-02-05

Hello Brendan,

Thanks for the answer, but I used the "Import DDA Peptide Search" for building the library from my .dat file and my raw file was found.

Thanks,

João

 
Brendan MacLean responded:  2020-02-05

Please post a screenshot of your Transition Settings - Full-Scan settings. In general, the more you capture with screenshots, the more likely we are to be able to give you a useful answer on your next request. Not much information provided in your first request.

 
joaopcnunes responded:  2020-02-05

Sorry for the lack of information. I have already tried to put DDA in the acquisition method.

Thanks in advance

 
Brendan MacLean responded:  2020-02-05

Can you also post a screenshot where you have expanded one of the peptides to allow us to see the precursor and transitions targeted and also the Transition Settings - Filter Tab?

We may end up needing to get you Skyline document and a raw data file, which you can post to:

https://skyline.ms/files.url

You resolving power (10,000) looks unusually low for a modern instrument. Why type of instrument are you using? Do you really expect 10,000 resolving power? Also what kind of sample matrix? If it is not a purified sample, you probably want "High selectivity extraction".

The points are not relevant to why you are not seeing any chromatograms extracted from your data files, but they will become relevant as soon as chromatogram extraction is working.

Thanks for the extra information.

--Brendan

 
joaopcnunes responded:  2020-02-05

Hello again Brendan,

I attached the screenshot of what you asked.

I was changing some settings and i can see the BPC and the TIC of the sample (also attatched). However when I chose a peptide, nothing appears.

Right now, i am uploading the files, but it will take a while (CSE_JoaoNunes.sky).

I am using a Q-TOF. I can put 30.000 of resolving power.

We are working one with one protein.

Thank you a lot for all your help!

João Nunes