Coherent pipeline for biomarker discovery using mass spectrometry and bioinformatics

BMC Bioinformatics

Table 2 Sequence and functions of C. botulinum candidate biomarkers

Rank	Biomarker Sequence	Algorithm(s)	Protein Annotation
1	EAEYIFGNFGK	X ∩ M ∩ S	Unknown
	EDLTNVFDLSER	X ∩ M ∩ S	Unknown
	ENLITAPENTTIGEAK	X ∩ M ∩ S	Metabolism Multiple pathways
	GMDTLLESFIK	X ∩ M ∩ S	Metabolism Multiple pathways
	INEFPEILEYK	X ∩ M ∩ S	Enzyme Families
	MNEIMQDDTLER	X ∩ M ∩ S	Carbohydrate Metabolism
	TIVSLDEIEIK	X ∩ M ∩ S	Translation
	YANIADYLSLGGK	X ∩ M ∩ S	Unknown
2	AAGLEIGETGAIK	X ∩ M	Unknown
	AFIESVEEALEGGEK	X ∩ M	Replication and Repair
	GAYVLNKEEIEK	X ∩ M	Metabolism Multiple pathways
	GEPIVLDNGAVAGQAFR	X ∩ M	Replication and Repair/Cell motility
	IMNDFSMLASK	X ∩ M	Unknown
	NDIVVVSPDLGSVTR	X ∩ M	Metabolism Multiple pathways
	QAATAIDEYLSK	X ∩ M	Metabolism Multiple pathways
	TSAEGIEIVAK	X ∩ M	Amino Acid Metabolism
	DLSTNSWTMIR	X ∩ S	Replication and Repair
	IIDMNNAAIDEGVNAIVK	X ∩ S	Unknown
	TTTIPSMVEALSR	X ∩ S	Translation
3	AMESILVVIPAEK	X	Unknown
	CLVAEEETGLTTR	X	Metabolism Multiple pathways
	EALTEYLLNMSTR	X	Metabolism Multiple pathways
	EGSFIYVIGPK	X	Energy Metabolism
	GIENVNVFTVR	X	Unknown
	GLEVQEEVLNK	X	Nucleotide Metabolism
	GTNIVNIIPIENNEK	X	Replication and Repair
	GTNIVNLIPIENNEK	X	Replication and Repair
	IGNIVEHEETPQISGMIK	X	Translation
	ISTVGDVVDYIK	X	Unknown
	KWDEDKFEEVMK	X	Unknown
	TFGVELEDEPSGK	X	Amino Acid Metabolism
	VGIAHNVTPETVEK	X	Amino Acid Metabolism
	WYIVDAADKPLGR	X	Translation
	LGLAEDEAIESK	M	Membrane Transport
	MIGYDIFENEEAK	M	Carbohydrate Metabolism
	MIGYDLFENEEAK	M	Carbohydrate Metabolism
	QVLSFVTEETVVQR	M	Unknown
	SMPALITAISELNQPR	M	Unknown
	TRFETNLAVANHLVDK	M	Translation

X = X!Tandem, M = Mascot, S = Sequest and ∩ = intersection. The first column indicates the rank of the biomarkers. Rank 1 markers have higher confidence than the other markers due to the concordance of the search algorithms in their identification. The second column shows the amino acid sequence of the candidate biomarker. Column 3 shows the algorithm(s) used to identify the candidate biomarker. Where there is no algorithm intersection, the candidate biomarker was exclusively identified by the single algorithm. The final column indicates the functional classification of the proteins (of the listed peptides) obtained from KEGG [21]. The biomarkers fall into 4 different categories: Metabolism, Genetic Information Processing (Replication and Repair, Cell motility and Translation), Enviromental Information Processing (Membrane Transport) and Unknown.

ISSN: 1471-2105