Table 1.

Types of ubiquitomics experiment.

Aim	Sample Requirement	Enrichment Method	MS Factors and Analysis	Example
Deep ubiquitome	Up to 50 mg cell culture	UbiSite	Prefractionation to increase depth	[21]
Multiple PTMs	1–20 mg cell culture	UbiSite or K-GG with additional PTM pulldowns	Multi-Omic data analysis	[31]
Multiple conditions	0.5–20 mg cell culture	K-GG or TUBE	Use of SILAC or TMT— in-solution or on-bead	[19,29]
Chain type specific	1–200 mg cell culture/yeast	TUBE, possible to combine with K-GG	-	[38]
Low abundance modifications	<1 mg lysate	K-GG	Use of DIA to increase MS sensitivity	[22,23]