How to show the entire data acquisition/retention time range

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How to show the entire data acquisition/retention time range mmr6q  2021-09-20
 

Nick,
Attached is the zipped file with Skyline files with two raw files, both of which are DDA LC-MS analyses of the Pierce PRTC mixture (plus two peptides). The first file has peptide RTs ~20-30 min., and the second has RTs ~10 min. longer. I cannot get Skyline to show the full RT range. Thank you.
Mark

 
 
Nick Shulman responded:  2021-09-20
I am not sure why your chromatograms look the way that they do.
Can you send me your raw files "20210729_AH_Leela_LQE_PRTC_00_TC20210729_KY.raw" and "20210911_MH_LQE_PRTC_MH_SN20138917_1.raw"?

I see that at:
Settings > Transition Settings > Full Scan
you have "Retention Time Filtering" set to "Use only scans within 30 minutes of MS/MS IDs".

That setting would certainly limit the length of chromatograms that were extracted to be about 60 minutes long, or longer if the MS/MS ids were far apart from each other (the extraction range extends 30 minutes from the first matching MS/MS ID to 30 minutes after the last MS/MS ID).

The chromatograms in your Skyline document are much shorter than 60 minutes. Was that Retention Time Filtering setting maybe different when you told Skyline to import results? If you make a change to a setting that affects chromatogram extraction, you should tell Skyline to extract the chromatograms again so that you can see the effect of that change. Typically you do that using:
Edit > Manage Results > Reimport

-- Nick
 
mmr6q responded:  2021-09-21
Nick,
Can you provide the settings required to view the entire chromatogram range?
In the files that I sent, when I import the first raw file, the entire range is shown. However, when I import the second file "MH...", a shorted range is shown. It makes me think that there is something different or wrong with the second raw file.
Mark
 
mmr6q responded:  2021-09-21
Nick,
The full RT display problem is resolved. I re-loaded the search and raw files with your suggested settings.
Thank you.
Mark