The usual reason that a Protein would be missing from the fold change results is that some of the transitions had missing values or the peaks were truncated.
If any particular replicate is missing a value for any transition, then that replicate is excluded from the group comparison. If there are zero valid replicates for either group in the group comparison, then that protein will be missing from the results.
If you change the Group Comparison settings and check the checkbox "Use zero for missing peaks" then you will probably get results for a few more Proteins.
One reason that the Tukey's media polish might have results for more Proteins is that Tukey's media polish ignores a particular Transition if there not at least two replicates that have a peak area greater than 1. For this reason, the complete set of transitions that a Replicate needs is less, so there might be a few more Proteins included in the results.

If you still have questions about why a particular Protein has been excluded you can 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.

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
-- Nick

Thank you so much Nick for your quick response. I uploaded the Skyline file as "Skyline_volcano plot question.sky". Some peptide peaks were not truncated but were still missed. Such as peptides IEDLSQQAQLAAAEK from protein NACA, Skyline looked like captured the whole peak but that peptide was missed in both volcano plots. Also peptide QLQQAQAAGAEQEVEK from FEN1 protein was missed, is it because the peptide peak is not good enough (looked like the 3 transitions were all detected)?

Thanks again Nick!
Qingling

Hi Nick, another example is- Some peptides such as LLPCLHSFCLR or LEQDQLWIGTK peaks shape/abundance were not good but were kept in volcano plot, peptides like DGMDNQGGYGSVGR looked good but was missed in both volcano plots

Thank you!
Qingling

When the boundary of the peak integration coincides with the edge of the acquired chromatogram, Skyline declares that the peak is "truncated" and decides that its area cannot be trusted.
In the attached screenshot "TruncatedPeaks.png" the integration boundary is at the edge of the chromatogram.
If the chromatogram intensity at the edge is less than 1% the height of the peak apex then Skyline would not consider the peak to be truncated, but, in the attached screenshot, it is truncated.

When a peak is truncated, Skyline excludes the replicate from the group comparison calculation.

You can salvage the data by manually adjusting the peak boundary so that it is no longer at the edge of the chromatogram data.

If you want to see all of the replicates which are being excluded because of peak truncation, you can use the Document Grid to create a Report with the "Protein Abundance" column.
In the attached screenshot "ProteinAbundanceReportEditor.png", I have created a report with the Protein Abundance column. I have also checked the "Pivot Replicate Name" checkbox so that all of the results for a protein will appear in the same row.
The attached screenshot "ProteinAbundancesReportWithTooltip.png" shows the report. There are red exclamation marks next to all of the values which will not be used by the Group Comparison feature because some of the peaks are truncated.

Unfortunately, manually adjusting the peak boundaries is the only way to get Skyline to accept the values and use them in the Group Comparison feature.

We have been considering making some sort of improvement to this to give you more control over when Skyline considers a peak area to be truncated.
Specifically, the requirement that the intensity at the edge be less than 1% of the apex height is overly strict, and it could be that we should add a way for your to change that.

-- Nick

This is very helpful! Thank you so much Nick! Will try your suggestions.

Best,
Qingling