Table 1. Results of the MS homology search for the peptide m/z 1466.

Protein Score	Peptide Score	Peptide Sequence	Matching Sequence	MS-Digest Index Nr.	Protein MW (Da)/pI	Accession Nr.	Species	Protein Name
48	48	FSYIADYPYTAR	(K)FMLTADYPYTAR(D)	2595889	34641/8.4	Q27107	T. vaginalis	Clan CA, family C1, cathepsin L-like cysteine peptidase
	48	FSYLADYPYTAR	(K)FMLTADYPYTAR(D)
45	45	FSYIADYPYTAR	(K)FMTEADYPYTAR(D)	1626529	33768/7.5	A2E0N7	T. vaginalis	Clan CA, family C1, cathepsin L-like cysteine peptidase
	45	FSYLADYPYTAR	(K)FMTEADYPYTAR(D)
45	45	FSYIADYPYTAR	(K)FMTEADYPYTAR(D)	1641664	33796/6.9	A2FD35	T. vaginalis	Clan CA, family C1, cathepsin L-like cysteine peptidase
	45	FSYLADYPYTAR	(K)FMTEADYPYTAR(D)
45	45	FSYIADYPYTAR	(K)FMTEADYPYTAR(D)	2595891	32281/7.6	Q27109	T. vaginalis	Cysteine proteinase, putative (Fragment)
	45	FSYLADYPYTAR	(K)FMTEADYPYTAR(D)
45	45	FSYIADYPYTAR	(K)FMTEADYPYTAR(D)	2632915	33798/7.5	Q49P75	T. vaginalis	Cathepsin L-like cysteine proteinase
	45	FSYLADYPYTAR	(K)FMTEADYPYTAR(D)

All matches selected by MS homology search are displayed. Following parameters were used for search: Taxonomy search in Trichomonas vaginalis; Database searched: UniProtKB.2011.01.11; Mass Tolerance: 0.5 Da; Digest Used: No enzyme; Max. # Missed Cleavages: 1; Min matches: 1; Score matrix: BLOSUM62; Peptide Sequence: 1 FSY [I|L]ADYPYTAR 3 (number left to the peptide sequence is used as the name of the peptide, whereas the number right to the peptide sequence refers to the maximal number of allowed mismatches). Mismatched amino acids are shown in bold.