Identification and semi-quantification of protein allergens in complex mixtures using proteomic and AllerCatPro 2.0 bioinformatic analyses: a proof-of-concept investigation

Figures & data

Table 1. Source materials purchased from Stallergenes Greer Ltd. (Lenoir, NC), and used for proteomic and bioinformatic analyses.

Source material		Scientific Name	Product number by supplier	Lot #/Source Lot #	Protein mg/vial	Total protein content [%]	Proteome level (Taxonomic rank)	Proteome size*
Food nuts	Peanut	Arachis hypogaea	XPF171D3A25	352556/343466-2	410.13	77	Arachis hypogaea (species)	63536
	Hazelnut	Corylus americana	XPF120D3A25	346796/315123-4	68.48	59	Betulaceae (family)	27724
Grass pollen	Johnson	Sorghum halepense	XP15D3A25	265077/238478	76.85	31	Sorghum (genus)	35910
	Timothy	Phleum pratense	XP28D3A25	348714/346971	20.4	24	Poeae (tribe)	2216
Weed pollen	Lamb’s quarters	Chenopodium album	XP43D3A25	264918/261051	40.78	15	Chenopodioideae (subfamily)	22100
	Mugwort	Artemisia vulgaris	XP47D3A25	347799/320575-2	64.73	10	Artemisiinae (subtribe)	57069
	Ragweed	Ambrosia artemisiifolia	XP56D3A25	346227/199219-2	75.85	25	Heliantheae (tribe)	48610
Tree pollen	Birch	Betula pendula	XP527D3A25	357624/352640-1	17.3	21	Betulaceae (family)	27724
	Olive	Olea europaea	XP123D3A25	317197/296546-2	52.7	21	Oleaceae (family)	1476
Dander	Dog	Canis familiaris	XPE34D3A2S	366078/364719	27.48	18	Canis familiaris (species)	32019
	Cat	Felis catus	XPE6303A25	354823/283028-2	11.28	6	Felis catus (species)	30888
Mites	Dust mite	Dermatophagoides pteronyssinus	XPB82D3A25	371587/315636	29.35	25	Pyroglyphidae (family)	15379

*after deleting redundancy (90% homology).

Figure 1. Overview of proteomic and bioinformatic results for 12 source materials. Shown are the number (A) and sum of the relative abundances* (B) of all identified and semi-quantified protein sequences (n = 4,586) with AllerCatPro 2.0 predictions for strong, weak and no evidence for allergenicity. *total mass related to the total protein content of the material.

Figure 2. Relative abundance [%] of top 25 proteins identified and semi-quantified in 12 materials by proteomic analysis, their predicted ‘best hit protein name’ and prediction for strong, weak or no evidence for allergenicity using AllerCatPro 2.0.

Table 2. Identified species-specific allergens (n = 129) in 12 analyzed source materials, their relative abundance, and predicted evidence for allergenicity using AllerCatPro 2.0.

Protein allergen	Number of individuals tested for IgE	Relative abundance (%)
		Strong evidence	Weak evidence	Sum
Cat dander - Felis catus				32
Fel d 1	19096	27.0		27.0
Fel d 4	1275	1.2		1.2
Fel d 7	86	1.2		1.2
Fel d 2	1849	0.9		0.9
Fel d 3	86	0.8	0.1	0.8
Fel d S100	86	0.1	0.6	0.7
Fel d Hp	86	0.26		0.26
Dog dander - Canis familiaris				36
Can f 4	162	11.9		11.9
Can f 1	18061	6.3		6.3
Can f 8	–	5.7	0.4	6.0
Can f 2	1488	5.3		5.3
Can f 6	279	3.4		3.4
Can f 3	18200	2.2		2.2
Can f 5	250	0.01	0.42	0.44
Can f Feld1	–	0.14		0.14
Can f 7	–	0.02		0.02
Dust Mite - Dermatophagoides pteronyssinus				52
Der p 30	–	16.8		16.8
Der p 5	2678	7.4		7.4
Der p 7	1594	5.0		5.0
Der p 14	751	4.0		4.0
Der p 2	21941	3.7		3.7
Der f 27	–	2.6	0.1	2.7
Der p 1	22064	2.0	0.1	2.0
Der p 25		1.3		1.3
Der p 8	1089	0.8	0.0	0.8
Der f 34	–	0.8		0.8
Der p 13	225	0.8		0.8
Der p 21	–	0.8		0.8
Der f 35	–	0.6		0.6
Der f 11	198	0.6		0.6
Der p 4	814	0.5		0.54
Der f HSP	–	0.5		0.51
Der f 15	–	0.5		0.46
Der p 3	464	0.5		0.45
Der p 38	–	0.3		0.33
Der p 32	–	0.2		0.25
Der f 29	51	0.2		0.23
Der f 22	–	0.2		0.20
Der f 16	17	0.2		0.18
Der p 18	211	0.2		0.16
Der p 36	–	0.2		0.15
Der p 9	35	0.1		0.12
Der f 14	–	0.1	0.1	0.12
Der f 13	–		0.1	0.12
Der p 28	–	0.1		0.11
Der f 8	–	0.1		0.10
Der f 31	–	0.1		0.07
Der f 28	51	0.1		0.05
Der f 20	–	0.0		0.04
Der f 26	–	0.0		0.04
Der f 6	88	0.0		0.03
Der p 24	–	0.0		0.01
Hazelnut - Corylus americana				33
Cor a 9	1628	22.9		22.9
Cor a 11	303	5.1		5.1
Cor a 14	322	1.4		1.4
Cor a 1	21295	1.4		1.4
Cor a 6	–	0.8		0.8
Cor a 8	–	0.8		0.8
Cor a 10	–	0.5		0.54
Cor a 13	–	0.2		0.18
Peanut - Arachis hypogaea				49
Ara h 3	2989	20.3		20.3
Ara h 1	3405	14.8		14.8
Ara h 6	618	5.2		5.2
Ara h 2	3161	4.1		4.1
Ara h Aggl	–	1.3		1.3
Ara h 18	–	1.2		1.2
Ara h 8	2648	1.4		1.4
Ara h 12	–	0.5		0.52
Ara h 7	267	0.3		0.30
Ara h 10	–	0.1		0.12
Ara h 17	–	0.1		0.11
Ara h 13	–	0.1		0.09
Ara h 9	1293	0.1		0.07
Ara h 11	–	0.0		0.04
Ara h 14	–	0.0		0.01
Olive pollen - Olea europaea				63
Ole e 1	21481	35.1		35.1
Ole e 5	66	8.4		8.4
Ole e 2	18546	6.4		6.4
Ole e 9	2464	4.9		4.9
Ole e 11	277	3.7		3.7
Ole e 12	–	3.7		3.7
Ole e 3	872	0.4		0.37
Ole e 10	442	0.2		0.24
Ole e 8	324	0.1		0.09
Birch pollen - Betula pendula				57
Bet v 1	26925	17.9		17.9
Bet v 6	415	13.1		13.1
Bet v 7	265	11.9		11.9
Bet v 8	–	8.7	0.1	8.8
Bet v 2	23377	5.0		5.0
Bet v 4	3980	0.3		0.28
Mugwort pollen - Artemisia vulgaris				37
Amb a CPI	–		7.2	7.2
Art an 7	–	5.2		5.2
Art v 4	516	4.9		4.9
Art v 6	63	1.3	3.5	4.8
Art v 2	38	3.9		3.9
GOxidase	–	3.3		3.3
Amb a 12	–	2.1		2.1
Art v 5	397	0.8	0.6	1.5
Amb a 11	–		1.0	1.0
Amb a 3	–		0.7	0.7
Art v 3	4457	0.6		0.6
Amb t 13	–	0.0		0.05
Amb a 10	423		0.0	0.04
Art v 1	21516	0.0		0.02
Ragweed pollen - Ambrosia artemisiifolia				44
Amb a 1	2988	31.7	0.1	31.9
Amb a 12	–	2.9		2.9
Amb a 8	423	2.4		2.4
Amb a CPI	–	1.3	0.2	1.5
Art v 5	397	0.4	0.9	1.3
GOxidase	–	1.0		1.0
Art v 6	63	0.0	1.0	1.0
Amb a 11	–	0.9		0.9
Amb a 3	–	0.8		0.8
Amb a 10	423	0.3	0.1	0.04
Amb t 13	–	0.3		0.03
Lamb’s quarters pollen - Chenopodium album				0.8
Che a 2	151	0.7		0.7
Che a 3	1206	0.1		0.06
Johnson grass pollen - Sorghum halepense				35
Sor h 2	–	19.8	5.3	25.1
Sor h 1	–	6.6		6.6
Sor h 13	–	2.7	0.2	2.9
Timothy grass pollen - Phleum pratense				40
Phl p 6	20126	14.1		14.1
Phl p 5	22812	12.8		12.8
Phl p 12	20847	5.1		5.1
Phl p 1	24116	4.4		4.4
Phl p 2	21315	2.0		2.0
Phl p 13	570	1.1		1.1
Phl p 4	4121	0.4		0.45
Phl p 7	–	0.2		0.24
Phl p SOD	–	0.2		0.23