Table 1.

Common residues differentially phosphorylated upon activation of RPS2 and flg22 treatment.

	ETI (AvrRpt2 expression by Dex treatment)					PTI (flg22 treatment)	CPKs or MAPKs phosphorylation motif
	Ratio Dex 3 h / 0 h in Dex:avrRpt2			Ratio Dex 3 h / 0 h in rpm1rps2/Dex:avrRpt2		Ratio flg22/mock
	Phosphorylation		Protein level	Phosphorylation	Protein level	Phosphorylation
RBOHD (AT5G47910)	S163	10.97	3.32	1.39	1.28	3.72*1
	S343	13.08		0.83		4.7*1, 20.69*2, 4
	S347	13.83		0.94		3.5*1, 20.69*2, 4	φ-X-X-X-X-S/T-X-B*7
PEN3 (AT1G59870)	S40	6.87	1.44	0.86	0.98	8.21*2	φ-X-X-X-X-S/T-X-B*7
	S45	27.23*5, 12.85*6		0.18*5, 1.34*6		4.66*2
ACA8 (AT5G57110)	S22	20.80	1.50	2.48	0.68	3.74*2	φ-X-X-X-X-S/T-X-B*7
XLG2 (AT4G34390)	S23	13.23	nd	0.32	nd	Not quantified*3
	S169	3.02		0.20		Not quantified*3
CBS domain-containing protein (AT4G33700)	S331	5.65	1.11	1.07	0.66	1.8*1
	T336	5.96		0.70		2.9*1	S/T-P*8
PEARLI 4 (AT2G16900)	S63	9.95	nd	1.33	nd	4.2*1	S/T-P*8
AHA1 (AT2G18960)	T948	0.10	1.06	0.78	0.90	0.33*2
AHA2 (AT4G30190)	T947	0.22	1.07	0.97	0.92	0.42*2
AHA3 (AT5G57350)	T882	0.22	nd	0.60	nd	0.38*2

ETI, effector-triggered immunity; PTI, PAMP-triggered immunity.

Phosphorylation data after flg22 treatment is extracted from the papers indicated. The data are shown as fold change. For the data of RPS2, the fold change of the phosphorylated sites are calculated based on raw intensities. The fold change of the protein levels is calculated based on the Maxquant label-free quantitation intensities transformed to raw intensities (see Methods S1). Significantly differentially phosphorylated sites with a ratio higher than 1.5 or lower than 0.5 were kept, see also Tables S1–S3.

^*1The phosphorylation ratio at 10 min after flg22 treatment (Benschop et al., 2007)

^*2The best phosphorylation ratio at 7 min after flg22 treatment out of 5 reps is shown (Nühse et al., 2007).

^*3Phosphorylated but not quantified (Liang et al., 2016)

^*4Double phosphorylated peptide

^*5Calculated based on singly phosphorylated phosphopeptide intensities (Table S1 Multiplicity = __1)

^*6Calculated based on doubly phosphorylated phosphopeptide intensities (Table S1 Multiplicity = __2)

nd, not detected

^*7CPK phosphorylation motif: φ-X-X-X-X-S/T-X-B (S/T is the phosphorylated residue, B is a basic residue, φ is a hydrophobic residue, X is any residue) (Huang et al., 2001; Huang & Huber, 2001; Hernandez Sebastia et al., 2004)

^*8MAPK phosphorylation motif S/T-P (S/T is the phosphorylated residue)