Spike variant predictions

Spike variant glycosylation predictions. (spike_mut_idx.v3.xlsx)

> Glycoimpact*: likelihood the glycosylation of a proximal site is perturbed 

> mannoseDist*: aggregate Fisher log-OR for any high-mannose (>5mannose) structure (taken from IMRs). LIkelihood high-mannose structures, in general, will increase or decrease

> IMR - Expected Change: a combination of proximity information with mannoseDist to estimate joint effect

> IMR/InSaNNE prediction: predictions of differential glycosylation from IMRs or InSaNNE respectively

*_seq refers to sequence-based predictions, _str refers to structure-based predictions

Generating R code is also provided without raw-data

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Update

v4: Mannose/Complex column updated to Mannose/ Complex+hybrid in v5

v5: Mannose+hybrid / Complex column added (one prediction changed). This column is more relevant to the validation MS observation.

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Added 8/4/2021

> Results_untilGamma...xlsx

Quantified using label-free analysis, which is semi-quantitative. We use precursor (peptide/MS1) peak area for quantitation, the spectral counts are also included. Peptide numbers, which give you the extent of sampling at each N-glycosylation site. We use Mean +/- SEM for the proportions of N-glycan variants (unoccupied, complex and high-mannose/hybrid).

Other column headings should be self-explanatory, but please let me know if in doubt.

The “Result” sheet is what you should look at. Other sheets are “raw” results. The first sheet “Sequences”, has all the sequence information. The color-coding is the regular one for N-glycans.