1. In current versions of Skyline, the "Integrate All" setting really only affects the colors of the dots next to the Transitions in the Targets tree. If "Integrate All" is turned on, the dots next to the transitions will nearly always be green, unless the chromatogram peak really is completely flat. If "Integrate All" is turned off, the dots will be red if the apex of the peak for a particular transition is not close to the apexes of the other peptide transition peaks.
"Integrate All" should be turned on if you are doing quantification, and you care about the values of the peak areas.
"Integrate All" should be turned off if you are developing an SRM method and want to know which transitions have misshapen peaks.
Nowadays, it is very unlikely that "Integrate All" will have any impact on the numbers in your exported report, so it does not matter whether you have it on or off, but you should have it on in your case. (It used to be that when "Integrate All" was off, many of your transition peak areas would be NULL instead of their measured value, and that caused a big problem for people who forgot to turn it on when doing quantification, so, we fixed it so that it only affects the colored dots in the Targets tree).
2. I don't know the answer to this one.
3. Can you send us your Skyline document? In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
https://skyline.ms/files.url
I am not sure which columns in your report might be causing the report export to be slow. If I had to guess, I would say maybe if you remove the "Protein Abundance" column the report might go faster. It is not supposed to be slow for Skyline to calculate any of the columns in your report. If you send me your Skyline document I will try to improve the performance of Skyline on exporting that report.
4. I am not sure I understand your question. The way that peptides are grouped into proteins do not affect the peptide chromatograms or peak areas.
5. That's a good question. I do not know the answer.
I was going to say, if you have a .tsv file, you get it into the document with "File > Import > Assay Library".
You would use "Settings > Peptide Settings > Library > Build" if you have peptide search results. Here is a page which lists the types of peptide search results that you can build a library from:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild
However, now that I look at that page, I see that it says you can build a spectral library from OpenSwath tsv, so now I don't know whether you should build a spectral library versus import an assay library.
6. I do not know the answer to this, but maybe someone else does.
7. The "Protein Abundance" column that you have in the report is the best way to sum the peak areas across all of the transitions under the protein. Those peak areas are normalized according to the Normalization Method that you have specified at "Settings > Peptide Settings > Quantification". If that Normalization Method is "None", then the Protein Abundance will usually be the same as the sum of all of the precursor's Total Area values. Sometimes the Protein Abundance value will be null if any of the transitions have missing or truncated peaks, because Skyline decides that that replicate's Protein Abundance value cannot be compared to the other replicates.
Please do send us your Skyline document. It is important that we figure out why your report export is slow, since that sounds like something that will be easy for us to fix.
-- Nick