starplast.palmitome

S-palmitoylation, from the palmitome ToxoDB serves for Foe et al. 2015.

The paper's supplementary tables are behind PMC's download interstitial and the article is not open access, so the numbers come from ToxoDB's own query service for the same dataset -- which returns the authors' fold differences per gene rather than a re-analysis.

The two comparisons, and why only one of them is palmitoylation

Both label proteins with 17-ODYA, an alkyne palmitate analogue that click chemistry then pulls down.

• against hydroxylamine -- hydroxylamine cleaves thioester bonds, which is the bond an S-palmitoyl group makes. A protein enriched here lost its label to hydroxylamine, so the label was on a cysteine thioester. This is the S-palmitoylation-specific comparison.
• against palmitic acid -- competition with unlabelled palmitate. It shows the label is fatty-acid-dependent, but it does not distinguish a thioester from an amide, so it includes N-myristoylated and otherwise lipidated proteins.

Both are shipped because they answer different questions and the difference between them is informative. The slot is filled by the hydroxylamine column.

What the sign means

ToxoDB reports a signed fold DIFFERENCE, not a ratio: -3.12 means three-fold down, not a negative quantity. Reading it as a ratio and taking its logarithm would produce NaN for every depleted protein and quietly drop half the table, so it is converted explicitly.