. 2012 Dec 13;3:279. doi: 10.3389/fpls.2012.00279

Table 1.

Abundant proteins identified in the EGTA and LiCl extracts of cell walls prepared from basal and apical alfalfa stems.

CWP#^a	MGI#^b	MGI-IDs short annotation	TargetP^c	LFQ values (×10⁹)^d
				Basal stem	Apical stem	Total
Proteins acting on carbohydrates (PAC)
#313	Medtr2g034440	GH family 17 (glucan endo-1,3-β-glucosidase)	S	2.36	0.65	3.02
#334	Medtr2g034470	GH family 17 (glucan endo-1,3-β-glucosidase)	S	1.33	0.31	1.63
#324	Medtr8g074330	GH family 19 (endochitinase)	S	1.53	0.41	1.95
#318	Medtr2g094060	GH family 35 (β-galactosidase)	S	0.69	0.99	1.68
#045	Medtr3g118390	GH family 19 (endochitinase)	S	0.86	0.21	1.06
Oxidoreductases (OR)
#322	Medtr8g089110	Blue copper protein, cupredoxin	S	0.68	0.38	1.06
#312	Medtr5g074970	Peroxidase MtPrx29	S	5.37	1.70	7.07
#023	Medtr7g111240	Germin, manganese binding site	S	1.34	0.49	1.83
#333	Medtr3g094650	Peroxidase MtPrx54	S	0.96	0.18	1.15
#315	Medtr3g072190	Peroxidase MtPrx34	S	2.45	1.30	3.74
#007	Medtr2g029820	Peroxidase MtPrx11	Other	2.41	2.10	4.51
#323	Medtr2g084020	Peroxidase MtPrx28	S	0.48	0.96	1.44
#317	Medtr4g095450	Peroxidase MtPrx38	S	0.80	1.01	1.81
#015	Medtr2g029750	Peroxidase MtPrx16	S	0.61	0.13	0.74
#332	Medtr1g085140	Germin-like protein 19	S	1.16	0.58	1.74
Proteins with interacting domains (ID)
#086	Medtr7g023690	Polygalacturonase inhibitor protein, LRR	S	1.42	0.76	2.18
#319	Medtr7g023590	Polygalacturonase inhibitor protein, LRR	S	0.73	2.14	2.87
#083	Medtr7g092740	Polygalacturonase inhibitor protein, LRR	S	0.79	2.00	2.79
#011	Medtr2g098250	Polygalacturonase inhibitor protein, LRR	S	0.07	2.12	2.19
#341	Medtr6g078070	Kunitz-type trypsin inhibitor alpha chain	S	0.38	0.36	0.74
Proteases (P)
#314	Medtr7g081750	Peptidase S8, subtilisin-related	S	3.31	1.18	4.49
Signaling (S)
#140	Medtr4g085480	Receptor protein kinase (LRR)	S	0.53	0.93	1.46
#325	Medtr7g075270	Fasciclin-like arabinogalactan protein 13	S	0.13	0.59	0.73
Proteins related to lipid metabolism (LM)
#321	Medtr4g029350	Lipid-transfer protein and hydrophobic protein	S	1.69	0.93	2.61
#338	Medtr4g050400	Unknown Protein, MD-2-related lipid-recognition	S	0.81	1.10	1.92
Miscellaneous functions (M)
#316	Medtr5g033960	Ubiquitin	Other	0.36	0.41	0.77
#320	Medtr8g014650	Stem 28 kDa glycoprotein, acid phosphatase, plant	S	0.17	1.93	2.10
Unknown function (UF)
#052	Medtr4g094240	Os08g0485000, phosphate-induced protein 1	S	0.61	0.37	0.98

^aCWP numbers were assigned arbitrarily and do not represent any ranking.

^bMedicago MGI# http://gbrowse.jcvi.org/cgi-bin/gbrowse/medicago/

^cPrediction of subcellular localization by TargetP (Emanuelsson et al., 2007). S: secreted; other: any other location (i.e., no chloroplast, mitochondria, or secretory pathway signal present).

^dLabel-free Quantitation Intensity (LFQ) as determined by MaxQuant (Cox et al., 2011).

Accession numbers of proteins that were identified for the first time in a cell wall proteome analysis are underlined. Numbers in the “total” column are the Label-free Quantitation Intensity (LFQ) as determined by MaxQuant from the combined EGTA and LiCl fractions for both the apical and basal stems. An LFQ threshold value of 0.73 × 10⁹ was used to select the top 10% most abundant proteins. The complete list of 272 proteins including additional information for each protein is available in Table S2 in Supplementary Material, provided as an Excel file.