RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration

BMC Genomics

Table 1 Summary of Enhanced Organismal Databases Searchable by RAId_DbS

Organism	DB_name	Protein	NP	NM	SP	SAPs	PTMs	DB_size (byte)
Homo sapiens	hsa	29284	35059	35031	15030	116073	84406	16,265,018
Anopheles gambiae	angam	12388	12719	12706	112	350	50	6,042,277
Arabidopsis thaliana	artha	29651	31740	31711	5527	5207	11977	12,318,213
Bos taurus	botau	23796	26504	26491	3979	3295	15810	11,188,490
Caenorhabditis elegans	caele	22563	23097	23097	2890	1045	7756	10,050,609
Canis familiaris	cafam	31705	33834	33821	528	2766	4196	18,458,474
Danio rerio	darer	31192	36150	36137	1552	7358	3841	14,477,794
Drosophila melanogaster	drmel	17232	20207	20207	2568	5611	9290	9,796,785
Equus caballus	eqcab	17300	17637	17624	171	485	1045	9,404,150
Gallus gallus	gagal	18154	18724	18681	1455	1109	6522	8,728,501
Macaca mulatta	mamul	32547	38141	38128	207	1370	1262	14,498,187
Mus musculus	mumus	28506	35503	35451	12170	27614	61684	14,363,491
Oryza sativa	orsat	26636	26784	26777	1205	1291	2182	10,679,924
Pan troglodytes	patro	41464	52130	52117	482	3721	3734	20,217,986
Plasmodium falciparum	plfal	5240	5267	5267	88	56	184	3,995,386
Rattus norvegicus	ranor	28914	39425	39389	5569	9297	33240	15,879,569
Saccharomyces cerevisiae	sacer	5699	5880	0	5807	5507	13220	2,927,330

The header abbreviations in this table are explained as follows. The second column, headed by DB_name, documents the abbreviated database name for searches using standalone version of RAId_DbS. The column headed by "Protein" indicates the final number of protein clusters in the processed organismal databases. The columns headed by NP, NM, and SP summarize the breakdown of the total number of accession numbers included respectively from protein products, transcript products, and SwissProt protein entries. The columns headed by SAPs and PTMs indicate respectively the total number of annotated SAPs and PTMs included. The last column shows the database size in bytes.

ISSN: 1471-2164