Thank you for attaching that Skyline document.
I am not sure what we should be looking at, or what you were hoping it would look like instead.

The usual answer for "truncated chromatograms" is that you need to go to the "Full Scan" tab at "Settings > Transition Settings" and change "MS/MS filtering Acquisition Method" to "DDA".
When the acquisition method is PRM or DIA, Skyline will truncate the MS1 chromatograms so that the retention time range of the MS1 chromatograms is the same as the time range for the MS2 chromatograms. The reason that Skyline does this is that it is the correct thing to do for a scheduled PRM method where the mass spectrometer was told to only collect data for your analyte over a specific time range, and you would also want your MS1 chromatograms to match that range.

However, in your document, I see that you have already set the acquisition method to "DDA".

Can you give us an example of a molecule and a Replicate in your document that we should be looking at?

MS2 chromatograms extracted from DDA data are not very useful for quantification because the mass spectrometer does not sample any particular analyte at regular intervals so the chromatograms tends to have long straight lines connecting the times where a matching precursor happens to have been selected for fragmentation. Skyline does not use DDA MS2 chromatograms for quantification, and so always displays them as dotted lines in the chromatogram graph.

Could you post a screenshot of what you are looking at?
If you have a Skyline document where things look good, and a different document where they look bad, you could certainly send us both documents and we could tell you what is causing the difference.
-- Nick

Hi Nick,
many thanks for the timely response! I would propose the methionine trace in the sample 242063, 242064 and 242069, for instance. In sample 242063 the chromatogram reaches from "0-28 min" while in 242064 the is only data for the range "1-6 min". In case of sample 242069 again the range from "0-28 min" is present, but the peak is more than 25 min in width. While we can afterwards adjust peak width, we can not change the range in which the chromatograms are extracted.
Sometimes also peaks are truncated because the chromatograms are for individual runs not extracted as in other runs, e.g. phenylalanine in run 242068 is extracted from "min 1-12.5", but in run 242069 the peak is truncated because the chromatogram is only extracted for "min 1- 3.9". All runs are DDA-runs with exactly the same conditions, though.
Best regards,
Joerg

Can you send me the .raw files for those replicates?
Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
https://skyline.ms/files.url

It is indeed mysterious that the molecules in 242064 have MS1 chromatograms that cover different time ranges.

The usual cause of that is that the "Retention time filtering" setting on the Full Scan tab at "Settings > Transition Settings".
You have that set to "Use only scans within 5 minutes of MS/MS IDs". That setting could certainly cause you to have truncated chromatograms, but only if you had a spectral library with retention times in it, which you do not seem to have.
You could certainly try changing that to "Include all matching scans" and then telling Skyline to extract chromatograms again by going to "Edit > Manage Results" and pushing the "Reimport" button.

The other thing that could cause your MS1 chromatograms to be different lengths is that Skyline treats MS1 spectra with a m/z range less than 500 special to support SIM or boxcar data where MS1 spectra might be intended to be used for only the precursors that fall in the scan range. However, your dataset does not seem to have any spectra like that.

After I see you .raw files I will be able to watch Skyline extract chromatograms and I will probably be able to figure out what is going wrong.
-- Nick

Hi Nick,
many thanks, I uploaded the runs as "242069.zip", however, the restriction to 5 min in retention time seems to have caused the problem. After changing to "include all matching scans" and re-import it looks very different (much more like I would have expected)! Maybe the m/z-value has been triggered only once or two or more times per run.
Many thanks!
Joerg