Table I

Examples of true-positive, false-negative, and false-positive identifications by MS BLAST

MS BLAST queries were assembled from M. musculus proteins and searched against the T. rubripes protein database. The precomputed significance threshold scores were: for 1 HSP, 59; for 2 HSPs, 99; 3 HSPs, 131; 4 HSPs, 167 and are reported in bold in the “MS BLAST scoring” column. A full list of threshold scores is provided in the supplemental materials.

Queried protein/MS BLAST queryMS BLAST hitHSPsMS BLAST scoring/resultaFull-length BLAST hit (% identity)Hit
AK002456.1ID 15391Score = 6464 > 59ID 15391 (61%)TRUE POSITIVE
Query: 67 CEHXVNGXRP 76POSITIVE
VNVXVSAEDL-CEH VNG RP
GAFTXXSDFL-Sbjct: 184 CEHHVNGSRP 193
XEGDTPRXNK-
GVYNXHVXCL-Score = 51
QIRDQXSXGS-Query: 45 QIRDQXSXGS 54
VXFGEDIDLP-+IRDQ S GS
CEHXVNGXRP-Sbjt: 96 EIRDQGSCGS 105
YKXEAGDXMG
Score = 42
Query: 1 VNVXVSAEDL 10
+ VSAEDL
Sbjct: 127 ISVELSAEDL 136
Score = 41
Query: 12 GAFTXXSDF 20
GAFT DF
Sbjct: 249 GAFTVYEDF 257
Score = 39
Query: 34 GVYNXHVXC 42
G Y+ H+ C
Sbjct: 168 GLYDSHIGC 176
Score = 30
Query: 78 YKXEAG 83
Y EAG
Sbjct: 207 YRCEAG 212
AK002456.1ID 15391Score = 5050 < 59ID 15391 (61%)FALSE NEGATIVE
Query: 56 VNVEXSAEDL 65
CNKSCXAXYS-+ VE SAEDL
AGRNFYXXDI-Sbjct: 127 ISVELSAEDL 136
XSYSVSXSVK-
XLGGPKLPGR-Score = 3750 + 37 < 99
EDIDLPXTFD-Query: 12 AGRNF 16
VNVEXSAEDL-AGRNF
YKHXAGXMMG-Sbjct: 41 AGRNF 45
LPGXVAFXED
Score = 3550 + 37 + 35 < 131
Query: 24 SYSVS 28
SYSVS
Sbjct: 227 SYSVS 231
Score = 3450 + 37 + 35 + 34 < 167
Query: 37 GPKLP 41NEGATIVE
GPKLP
Sbjct: 63 GPKLP 67
BAB31737.1ID 13094Score = 6060 > 59No hitFALSE POSITIVE
Query: 56 LFVSFLXRAL 65POSITIVE
WXTFGLTDTN-LFVSF+ RA+
XPLSCSLLLV-Sbjct: 137 LFVSFILRAI146
XTGXLGLNLA-
XQLITQAKQT-
GPMXKLVXKL-
LFVSFLXRAL-
SFLNRAXRTD-
XQLTLALXSA