Supplemental Table 4: Summary of TagRecon Results	
						
	VNDL Leaf Replicate 1	VNDL Leaf Replicate 2	VNDL Leaf Replicate 3		DENA Leaf Replicate 1	DENA Leaf Replicate 2	DENA Leaf Replicate 3
Spectra	143205	136774	138469	Spectra	150600	144022	145535
Distinct Peptide Matches	34976	27283	32969	Distinct Peptide Matches	31543	39729	36090
Distinct Peptides	23559	18704	22228	Distinct Peptides	20879	25970	24109
Proteins	13290	10919	12474	Proteins	11168	13418	12792
Protein Groups	7283	5922	6814	Protein Groups	6099	7349	6993
Modifications	44432	42000	42629	Modifications	43565	44674	42356
Protein FDR %	1.13	1.12	1.20	Protein FDR %	1.43	1.58	1.25
							
	VNDL Stem Replicate 1	VNDL Stem Replicate 2	VNDL Stem Replicate 3		DENA Stem Replicate 1	DENA Stem Replicate 2	DENA Stem Replicate 3
Spectra	131679	152409	143157	Spectra	170676	164692	167969
Distinct Peptide Matches	32533	35810	33765	Distinct Peptide Matches	39337	35981	43259
Distinct Peptides	23210	25433	24787	Distinct Peptides	27120	24878	29521
Proteins	13749	14313	14253	Proteins	14177	13505	15343
Protein Groups	7349	7739	7753	Protein Groups	7902	4738	8507
Modifications	37141	43671	42201	Modifications	47022	43762	46903
Protein FDR %	1.08	1.22	1.16	Protein FDR %	1.75	1.47	1.59
							
	VNDL Root Replicate 1	VNDL Root Replicate 2	VNDL Root Replicate 3		DENA Root Replicate 1	DENA Root Replicate 2	DENA Root Replicate 3
Spectra	177849	164947	173479	Spectra	185879	169761	173503
Distinct Peptide Matches	39845	40813	42266	Distinct Peptide Matches	46054	47636	45437
Distinct Peptides	28139	28701	29500	Distinct Peptides	31773	33120	30106
Proteins	13903	14123	14393	Proteins	15133	15780	14125
Protein Groups	7854	7975	8177	Protein Groups	8636	9000	8071
Modifications	52902	48578	50750	Modifications	53601	48189	52602
Protein FDR %	1.93	1.66	1.89	Protein FDR %	1.93	1.83	1.81