Summary of Alignment Quality

Summary of Alignment Quality Protein Set Proteins in Set

WT 369

Set Proteins Aligned to WT

∆esxA, ∆esxB

139 124

Mutant Proteins Not Aligned to WT

15

% of Set Proteins Aligned

89.2%

% of Set Proteins Not Aligned

10.8%

WT Proteins Found in Set

369

WT Proteins Not Found in Mutant % of WT Proteins Found in Mutant

Number of Sets Aligned against WT

124 245

(100%)

1

33.6%

∆esxA. ∆esxB Mapped to WT MM

WT N Matched to Set N

(Primary mapping where multiple Master N are mapped)

Set N 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363

∆esxA. ∆esxB

WT MM

2 14 5 1 4 3 35 7 20 248 22 10 79 26 12 74 25 80 126 6 13 55 27 32 50 -1 97 71 23 8 155 30 81 66 37 29 123 130 115 51 192 159 31 153 42 67 242 64 93 9 69 15 106 52 111 117 40 16

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369

68 11 91 38 63 83 120 43 104 56 -1 135 77 199 60 21 17 139 -1 62 28 84 54 189 221 158 103 369 118 58 72 122 89 94 76 170 154 149 90 142 112 143 133 310 163 61 166 24 267 -1 204 129 202 151 303 -1 57 -1 131 342 145 48 -1 -1 39 312 307 105 -1 257 -1 229 156 -1 265 -1 -1 -1 136 -1 45

Representative Accession gi|183980783 cont|000134 gi|183982917 gi|183981941 gi|183981035 gi|183983934 gi|183981780 gi|183981146 gi|183982267 gi|183982214 gi|183982295 gi|183983328 gi|183981699 cont|000136 gi|183981273 gi|183982353 gi|183982252 gi|183984170 gi|183985420 gi|183984058 gi|183982825 gi|183981938 gi|183980391 gi|183982266 gi|183984612 gi|183981317 gi|183985365 gi|183984519 gi|183981833 gi|183981741 gi|183982454 gi|183983279 gi|183981011 gi|183981034 cont|000143 gi|183984364 gi|183982218 gi|183982299 gi|183980662 gi|183983783 gi|183982761 gi|183981698 gi|183981069 gi|183981054 gi|183982864 gi|183983268 gi|183983330 gi|183984644 gi|183981284 gi|183981145 gi|183983782 gi|183985056 gi|183984844 gi|183981109 gi|183985332 gi|183981015 gi|183981060 gi|183981010 gi|183984645 gi|183981832 gi|183983329 gi|183983777 gi|183984433 gi|183981356 gi|183985333 gi|183981110 gi|183984615 gi|183984520 gi|183985068 gi|183981056 gi|183981033 gi|183980518 gi|183981778 gi|183985108 gi|183980046 gi|183980107 gi|183983781 gi|183984345 gi|183982932 gi|183983327 gi|183984817 gi|183983251 gi|183982720 gi|183984060 gi|183980037 gi|183985421 gi|183982447 gi|183982290 gi|183985361 gi|183982464 gi|183980818 gi|183981785 gi|183985411 gi|183980824 gi|183983776 gi|183980558 gi|183980997 gi|183980208 gi|183980983 gi|183983791 gi|183981786 gi|183983399 gi|183984607 gi|183980192 gi|183981016 gi|183983504 gi|183983804 gi|183981728 gi|183980809 gi|183982683 gi|183981087 gi|183981126 gi|183980531 gi|183983718 gi|183984837 gi|183984836 gi|183981111 gi|183980516 gi|183981091 gi|183985448 gi|183982723 gi|183980110 gi|183983237 gi|183981774 gi|183982025 gi|183981074 gi|183985190 gi|183981053 gi|183981725 gi|183985201 gi|183985134 gi|183984439 gi|183982418 gi|183982303 gi|183981052 gi|183982281 gi|183984288 gi|183984046 gi|183982354 gi|183980539 gi|183980990 gi|183982344 gi|183982767 gi|183980694 gi|183980482 gi|183981813 gi|183981059 gi|183980188 gi|183984511 gi|183980203 gi|183984791 gi|183981372 gi|183980989 gi|183984843 gi|183981775 gi|183984421 gi|183981057 gi|183984910 gi|183985427 gi|183980532 gi|183983711 gi|183983789 gi|183980320 gi|183985414 gi|183985426 gi|183984824 gi|183984346 gi|183982253 gi|183985454 gi|183984309 gi|183980994 gi|183980941 gi|183985447 gi|183982429 gi|183981177 gi|183981076 gi|183980108 gi|183983713 gi|183982434 gi|183981278 gi|183981275 gi|183980355 gi|183985087 gi|183984442 gi|183983239 gi|183982347 gi|183981840 gi|183981099 gi|183981058 gi|183980574 gi|183980074 cont|000124 gi|183985136 gi|183985096 gi|183983749 gi|183982630 gi|183981303 gi|183981200 gi|183981068 gi|183982550 gi|183983822 gi|183982254 gi|183981732 gi|183983284 gi|183983712 gi|183981063 gi|183981788 gi|183980160 gi|183980086 gi|183985260 gi|183980496 gi|183980357 gi|183980556 gi|183981165 gi|183985336 gi|183980541 gi|183981237 gi|183981787 gi|183983747 gi|183981326 gi|183980804 gi|183981969 gi|183985383 gi|183982427 gi|183983270 gi|183984496 gi|183983775 gi|183984527 gi|183981661 gi|183984512 gi|183981757 gi|183983324 gi|183983073 gi|183982212 gi|183983566 gi|183983929 gi|183983820 gi|183981985 gi|183984866 gi|183981159 gi|183981743 gi|183982108 gi|183984166 gi|183983823 gi|183983246 gi|183983180 gi|183982620 cont|000126 gi|183983634 gi|183982482 gi|183980745 gi|183980817 gi|183983545 gi|183985051 gi|183980732 gi|183982112 gi|183981198 gi|183984927 gi|183982492 gi|183981327 gi|183981055 gi|183982995 gi|183981263 gi|183985243 gi|183983684 gi|183982715 gi|183981599 gi|183980936 gi|183980463 gi|183984277 gi|183983808 gi|183982322 gi|183981772 gi|183981715 gi|183980408 gi|183985410 gi|183984908 gi|183984877 gi|183984199 gi|183983787 gi|183983265 gi|183982732 gi|183982462 gi|183982443 gi|183981812 gi|183981684 gi|183981552 gi|183981415 gi|183980204 gi|183985413 gi|183985073 gi|183984359 gi|183983647 gi|183983200 gi|183982097 gi|183981916 gi|183981726 gi|183981591 gi|183981536 gi|183981525 gi|183981246 gi|183981164 gi|183981108 gi|183981073 gi|183981038 gi|183980992 gi|183980856 gi|183980834 gi|183980572 gi|183980375 gi|183980323 gi|183980205 gi|183984848 gi|183984576 gi|183984115 gi|183983834 gi|183982581 gi|183982082 gi|183982010 gi|183981245 gi|183981149 gi|183981105 gi|183980998 gi|183980829 gi|183980820 gi|183980801 gi|183980466 gi|183980325 gi|183980202 gi|183984014 gi|183983745 gi|183982587 gi|183983082 RRRRRgi|183980609 gi|183981182 gi|183982159 gi|183984861 gi|183981321 gi|183982407 gi|183981072 gi|183984539 gi|183982413 gi|183981134 gi|183982100 gi|183982724 gi|183985191 gi|183982736 gi|183983625 gi|183982319 gi|183982687 gi|183980418 gi|183984852 gi|183983271 gi|183981979 gi|183984491 gi|183983746 gi|183982595 gi|183983028 gi|183982483 gi|183982009 gi|183981138 gi|183982705 gi|183981817 gi|183981907 gi|183982216 gi|183985210 gi|183980194 gi|183981307 gi|183981127

Name 60 kDa chaperonin 2 GroEL2 [Mycobacterium marinum M] rf|NP_006112.2| keratin 1 [Homo sapiens (contaminant)] catalase-peroxidase-peroxynitritase T KatG [Mycobacterium marinum M] secreted L-alanine dehydrogenase Ald (40 kDa antigen) [Mycobacterium marinum M] iron-regulated elongation factor EF-Tu, Tuf [Mycobacterium marinum M] fatty acid synthase Fas [Mycobacterium marinum M] multifunctional mycocerosic acid synthase membrane-associated Mas [Mycobacterium marinum M] 60 kDa chaperone (GroEL1) [Mycobacterium marinum M] transketolase Tkt [Mycobacterium marinum M] integration host factor MihF [Mycobacterium marinum M] aconitate hydratase Acn [Mycobacterium marinum M] 3-oxoacyl-[acyl-carrier protein] synthase 1 KasA [Mycobacterium marinum M] electron transfer flavoprotein (alpha-subunit) FixB [Mycobacterium marinum M] cra|hCP1812051| keratin 10 (epidermolytic hyperkeratosis; keratosis palmaris et plantaris) [Homo bifunctional protein acetyl-/propionyl-coenzyme A carboxylase AC AccA3 [Mycobacterium marinum polyketide synthase Pks5 [Mycobacterium marinum M] glyceraldehyde 3-phosphate dehydrogenase Gap [Mycobacterium marinum M] malate dehydrogenase Mdh [Mycobacterium marinum M] Esat-6 like protein EsxB [Mycobacterium marinum M] ATP synthase beta chain AtpD [Mycobacterium marinum M] isocitrate lyase AceAb [Mycobacterium marinum M] bifunctional protein polyribonucleotide nucleotidyltransferase GpsI [Mycobacterium marinum M] short-chain type dehydrogenase/reductase [Mycobacterium marinum M] transaldolase Tal [Mycobacterium marinum M] hypothetical protein MMAR_4645 [Mycobacterium marinum M] adenosylhomocysteinase SahH [Mycobacterium marinum M] superoxide dismutase [Fe] SodA [Mycobacterium marinum M] succinyl-CoA synthetase (alpha chain) SucD [Mycobacterium marinum M] elongation factor Tsf [Mycobacterium marinum M] DNA-binding protein HU, HupB [Mycobacterium marinum M] iron-regulated protein [Mycobacterium marinum M] glutamine synthetase GlnA1 [Mycobacterium marinum M] 50S ribosomal protein L7/L12, RplL [Mycobacterium marinum M] elongation factor G, FusA1 [Mycobacterium marinum M] pdb|1FNI_A| A Chain A, Crystal Structure Of Porcine Beta Trypsin With 0.01% Polydocanol [Sus scro beta-ketoacyl CoA thiolase FadA3 [Mycobacterium marinum M] s-adenosylmethionine synthetase MetK [Mycobacterium marinum M] transcriptional regulatory protein, MoxR1 [Mycobacterium marinum M] chaperone protein DnaK [Mycobacterium marinum M] trigger factor (TF) protein TIG [Mycobacterium marinum M] alkyl hydroperoxide reductase C protein AhpC [Mycobacterium marinum M] electron transfer flavoprotein (beta-subunit) FixA [Mycobacterium marinum M] 50S ribosomal protein L5, RplE [Mycobacterium marinum M] 50S ribosomal protein L4, RplD [Mycobacterium marinum M] thiol peroxidase Tpx [Mycobacterium marinum M] multimeric flavodoxin WrbA [Mycobacterium marinum M] acetyl/propionyl-CoA carboxylase (beta subunit) AccD6 [Mycobacterium marinum M] fatty oxidation protein FadB [Mycobacterium marinum M] acyl-CoA dehydrogenase FadE25 [Mycobacterium marinum M] 10 kDa chaperone (GroES) [Mycobacterium marinum M] ATP-dependent Clp protease proteolytic subunit ClpP1 [Mycobacterium marinum M] carbonic anhydrase [Mycobacterium marinum M] metal cation transporter p-type ATPase, CtpV [Mycobacterium marinum M] 30S ribosomal protein S4, RpsD [Mycobacterium marinum M] polyketide synthase Pks13 [Mycobacterium marinum M] DNA-directed RNA polymerase, beta subunit, RpoB [Mycobacterium marinum M] 50S ribosomal protein L16, RplP [Mycobacterium marinum M] 50S ribosomal protein L10, RplJ [Mycobacterium marinum M] acyl-CoA thiolase FadA [Mycobacterium marinum M] 30S ribosomal protein S2 RpsB [Mycobacterium marinum M] 3-oxoacyl-[acyl-carrier protein] synthase 2 KasB [Mycobacterium marinum M] pyruvate:ferredoxin oxidoreductase, PorA, alpha subunit [Mycobacterium marinum M] enolase Eno [Mycobacterium marinum M] iron-regulated short-chain dehydrogenase/reductase [Mycobacterium marinum M] fatty acyl-AMP ligase FadD32 [Mycobacterium marinum M] DNA-directed RNA polymerase (alpha chain), RpoA [Mycobacterium marinum M] phosphoserine aminotransferase SerC [Mycobacterium marinum M] succinyl-CoA synthetase (beta chain) SucC [Mycobacterium marinum M] ATP-dependent protease ATP-binding subunit ClpC1 [Mycobacterium marinum M] 50S ribosomal protein L2, RplB [Mycobacterium marinum M] 30S ribosomal protein S7, RpsG [Mycobacterium marinum M] succinate-semialdehyde dehydrogenase [NADP+] dependent (SsdH) GabD1 [Mycobacterium marinu fatty acyl-AMP ligase FadD28 [Mycobacterium marinum M] cold shock protein A CspA_1 [Mycobacterium marinum M] peptidyl-prolyl cis-trans isomerase A, PpiA [Mycobacterium marinum M] 30S ribosomal protein S6 RpsF [Mycobacterium marinum M] ATP-dependent Clp protease proteolytic subunit ClpP2 [Mycobacterium marinum M] acyl-[acyl-carrier protein] desaturase DesA2 [Mycobacterium marinum M] hypothetical protein MMAR_2929 [Mycobacterium marinum M] meromycolate extension acyl carrier protein AcpM [Mycobacterium marinum M] hypothetical protein MMAR_4849 [Mycobacterium marinum M] pyruvate dehydrogenase (E2 component) SucB [Mycobacterium marinum M] malate synthase G GlcB [Mycobacterium marinum M] ATP synthase alpha chain AtpA [Mycobacterium marinum M] DNA polymerase III (beta chain) DnaN [Mycobacterium marinum M] 6 kDa early secretory antigenic target EsxA (EsaT-6) [Mycobacterium marinum M] ribosomal protein S1 RpsA [Mycobacterium marinum M] thioredoxin TrxB1 [Mycobacterium marinum M] bacterioferritin BfrB [Mycobacterium marinum M] 50S ribosomal protein L20 RplT [Mycobacterium marinum M] mycolic acid synthase UmaA [Mycobacterium marinum M] phenolpthiocerol synthesis type-I polyketide synthase PpsE [Mycobacterium marinum M] hypothetical protein MMAR_5440 [Mycobacterium marinum M] iron-regulated heparin binding hemagglutinin HbhA [Mycobacterium marinum M] pyruvate:ferredoxin oxidoreductase PorB, beta subunit [Mycobacterium marinum M] acyl-CoA dehydrogenase FadE6 [Mycobacterium marinum M] methoxy mycolic acid synthase 4, MmaA4 [Mycobacterium marinum M] polyketide synthase Pks16_1 [Mycobacterium marinum M] enoyl-CoA hydratase, EchA3 [Mycobacterium marinum M] aminopeptidase N PepN [Mycobacterium marinum M] phenolpthiocerol synthesis type-I polyketide synthase PpsD [Mycobacterium marinum M] pyruvate dikinase [Mycobacterium marinum M] citrate synthase I GltA2 [Mycobacterium marinum M] isocitrate dehydrogenase [NADP] Icd2 [Mycobacterium marinum M] DNA-directed RNA polymerase, beta chain, RpoC [Mycobacterium marinum M] chaperone protein HtpG [Mycobacterium marinum M] ATP-binding component of an ABC transporter [Mycobacterium marinum M] D-3-phosphoglycerate dehydrogenase SerA1 [Mycobacterium marinum M] dihydrolipoamide dehydrogenase Lpd [Mycobacterium marinum M] hypothetical protein MMAR_2676 [Mycobacterium marinum M] hypothetical protein MMAR_1067 [Mycobacterium marinum M] 50S ribosomal protein L13, RplM [Mycobacterium marinum M] 3-oxoacyl-[acyl-carrier protein] reductase FabG4 [Mycobacterium marinum M] acyl-CoA dehydrogenase FadE18_2 [Mycobacterium marinum M] sulphur metabolism protein, SseC2 [Mycobacterium marinum M] thiosulfate sulfurtransferase, CysA2 [Mycobacterium marinum M] 50S ribosomal protein L17, RplQ [Mycobacterium marinum M] acyl-CoA dehydrogenase FadE4 [Mycobacterium marinum M] adenylate kinase (ATP-AMP transphosphorylase), Adk [Mycobacterium marinum M] thioredoxin TrxC [Mycobacterium marinum M] inosine-5'-monophosphate dehydrogenase GuaB1 [Mycobacterium marinum M] 50S ribosomal protein L9 RplI [Mycobacterium marinum M] carbohydrate kinase CbhK [Mycobacterium marinum M] fatty-acid-CoA ligase FadD22 [Mycobacterium marinum M] RNA polymerase sigma factor SigA [Mycobacterium marinum M] 30S ribosomal protein S5, RpsE [Mycobacterium marinum M] aspartate-semialdehyde dehydrogenase Asd [Mycobacterium marinum M] 50S ribosomal protein L3 RplC [Mycobacterium marinum M] ketol-acid reductoisomerase IlvC [Mycobacterium marinum M] hypothetical protein MMAR_5232 [Mycobacterium marinum M] regulatory protein [Mycobacterium marinum M] ribose-phosphate pyrophosphokinase PrsA [Mycobacterium marinum M] hypothetical protein MMAR_2404 [Mycobacterium marinum M] enoyl-[acyl-carrier-protein] reductase, InhA [Mycobacterium marinum M] 30S ribosomal protein S10, RpsJ [Mycobacterium marinum M] ABC transporter ATP-binding protein [Mycobacterium marinum M] acetyl-CoA acetyltransferase FadA6_3 [Mycobacterium marinum M] acetyl-CoA acetyltransferase FadA4 [Mycobacterium marinum M] fatty acyl-AMP ligase FadD25 [Mycobacterium marinum M] succinate dehydrogenase (iron-sulfur subunit), SdhA_1 [Mycobacterium marinum M] hypothetical protein MMAR_0970 [Mycobacterium marinum M] hypothetical protein MMAR_2331 [Mycobacterium marinum M] bacterioferritin BfrA [Mycobacterium marinum M] fructose-bisphosphate aldolase, Fba [Mycobacterium marinum M] iron-regulated phosphoenolpyruvate carboxykinase [GTP] PckA [Mycobacterium marinum M] hypothetical protein MMAR_1800 [Mycobacterium marinum M] 30S ribosomal protein S3, RpsC [Mycobacterium marinum M] coenzyme F420-dependent oxidoreductase [Mycobacterium marinum M] magnesium chelatase [Mycobacterium marinum M] hypothetical protein MMAR_0169 [Mycobacterium marinum M] cold shock protein a, CspA [Mycobacterium marinum M] hypothetical protein MMAR_1349 [Mycobacterium marinum M] hypothetical protein MMAR_0969 [Mycobacterium marinum M] hypothetical protein MMAR_4875 [Mycobacterium marinum M] polyketide synthase Pks15/1 [Mycobacterium marinum M] hypothetical protein MMAR_4450 [Mycobacterium marinum M] 50S ribosomal protein S19, RpsS [Mycobacterium marinum M] two-component system response phosphate regulon transcriptional regulator, PhoP [Mycobacteriu hypothetical protein MMAR_5456 [Mycobacterium marinum M] acetyl-CoA acyltransferase FadA2 [Mycobacterium marinum M] hypothetical protein MMAR_3731 [Mycobacterium marinum M] hypothetical protein MMAR_3815 [Mycobacterium marinum M] ribosomal protein S18 RpsR2 [Mycobacterium marinum M] hypothetical protein MMAR_5443 [Mycobacterium marinum M] hypothetical protein MMAR_5455 [Mycobacterium marinum M] acyl-[acyl-carrier protein] desaturase DesA1 [Mycobacterium marinum M] serine hydroxymethyltransferase 1 GlyA1 [Mycobacterium marinum M] phosphoglycerate kinase Pgk [Mycobacterium marinum M] hypothetical protein MMAR_5484 [Mycobacterium marinum M] 6-phosphogluconate dehydrogenase, decarboxylating Gnd2 [Mycobacterium marinum M] 50S ribosomal protein L1, RplA [Mycobacterium marinum M] hypothetical protein MMAR_0920 [Mycobacterium marinum M] thioredoxin reductase TrxB2 [Mycobacterium marinum M] tryptophan synthase, alpha subunit TrpA [Mycobacterium marinum M] hypothetical protein MMAR_1155 [Mycobacterium marinum M] 50S ribosomal protein L15, RplO [Mycobacterium marinum M] single-strand binding protein Ssb [Mycobacterium marinum M] 30S ribosomal protein S20 RpsT [Mycobacterium marinum M] pyruvate kinase PykA [Mycobacterium marinum M] propionyl-CoA carboxylase beta chain 5 AccD5 [Mycobacterium marinum M] thiosulfate sulfurtransferase SseA [Mycobacterium marinum M] serine protease PepA [Mycobacterium marinum M] EsaT-6 like protein EsxN_2 [Mycobacterium marinum M] 50S ribosomal protein L25 RplY [Mycobacterium marinum M] hypothetical protein MMAR_3248 [Mycobacterium marinum M] nucleotidyltransferase [Mycobacterium marinum M] ribosome recycling factor Frr [Mycobacterium marinum M] methylmalonate semialdehyde dehydrogenase, MmsA [Mycobacterium marinum M] 50S ribosomal protein L22, RplV [Mycobacterium marinum M] EsaT-6 like protein EsxG [Mycobacterium marinum M] hypothetical protein MMAR_0039 [Mycobacterium marinum M] spt|P81605| Dermcidin precursor (Preproteolysin) (Contains: Survival-promoting peptide; DCD-1) [ hypothetical protein MMAR_5166 [Mycobacterium marinum M] inorganic pyrophosphatase Ppa [Mycobacterium marinum M] nucleoside diphosphate kinase NdkA [Mycobacterium marinum M] hypothetical protein MMAR_2620 [Mycobacterium marinum M] F420 biosynthesis protein FbiA [Mycobacterium marinum M] hypothetical protein MMAR_1178 [Mycobacterium marinum M] 50S ribosomal protein L24, RplX [Mycobacterium marinum M] hypothetical protein MMAR_2537 [Mycobacterium marinum M] acyl-CoA dehydrogenase FadE19 [Mycobacterium marinum M] triosephosphate isomerase Tpi [Mycobacterium marinum M] glutamyl-tRNA synthetase GltS [Mycobacterium marinum M] glutamine synthetase GlnA2 [Mycobacterium marinum M] hypothetical protein MMAR_3732 [Mycobacterium marinum M] arylsulfatase AtsA [Mycobacterium marinum M] phenolpthiocerol synthesis type-I polyketide synthase PpsB [Mycobacterium marinum M] hypothetical protein MMAR_0126 [Mycobacterium marinum M] hypothetical protein MMAR_0051 [Mycobacterium marinum M] hypothetical protein MMAR_5292 [Mycobacterium marinum M] hypothetical protein MMAR_0467 [Mycobacterium marinum M] hypothetical protein MMAR_0326 [Mycobacterium marinum M] fatty-acid-CoA ligase FadD2 [Mycobacterium marinum M] hydrolase [Mycobacterium marinum M] secreted antigen 85-A FbpA [Mycobacterium marinum M] hypothetical protein MMAR_0513 [Mycobacterium marinum M] hypothetical protein MMAR_1215 [Mycobacterium marinum M] phenolpthiocerol synthesis type-I polyketide synthase PpsC [Mycobacterium marinum M] 50S ribosomal protein L21 RplU [Mycobacterium marinum M] hypothetical protein MMAR_1304 [Mycobacterium marinum M] aldehyde dehydrogenase, PutA_1 [Mycobacterium marinum M] alanine rich hydrolase [Mycobacterium marinum M] NADH-dependent glutamate synthase (small subunit) GltD [Mycobacterium marinum M] indole-3-glycerol phosphate synthase TrpC [Mycobacterium marinum M] hypothetical protein MMAR_3280 [Mycobacterium marinum M] pterin-4-alpha-carbinolamine dehydratase MoaB2 [Mycobacterium marinum M] molybdopterin-guanine dinucleotide biosynthesis protein a MobA [Mycobacterium marinum M] glucose-6-phosphate isomerase Pgi [Mycobacterium marinum M] ribonucleoside-diphosphate reductase (beta chain) NrdF2 [Mycobacterium marinum M] bifunctional purine biosynthesis protein PurH [Mycobacterium marinum M] oxidoreductase [Mycobacterium marinum M] pyruvate dehydrogenase E1 component AceE [Mycobacterium marinum M] hypothetical protein MMAR_3074 [Mycobacterium marinum M] carbamoyl-phosphate synthase large chain CarB [Mycobacterium marinum M] hypothetical protein MMAR_3586 [Mycobacterium marinum M] acetylornithine deacetylase ArgE [Mycobacterium marinum M] citrate (pro-3s)-lyase (beta subunit) CitE [Mycobacterium marinum M] 35 kDa alanine rich protein [Mycobacterium marinum M] hypothetical protein MMAR_4898 [Mycobacterium marinum M] inosine-5'-monophosphate (imp) dehydrogenase, GuaB3 [Mycobacterium marinum M] polyphosphate kinase Ppk [Mycobacterium marinum M] pyridoxine biosynthesis protein, SnzP [Mycobacterium marinum M] alpha-ketoglutarate decarboxylase Kgd [Mycobacterium marinum M] acetyl-/propionyl-coenzyme A carboxylase alpha chain AccA1 [Mycobacterium marinum M] branched-chain amino acid transaminase IlvE [Mycobacterium marinum M] cell division protein FtsZ [Mycobacterium marinum M] aldehyde dehydrogenase [Mycobacterium marinum M] spt|P48666| Keratin, type II cytoskeletal 6C (Cytokeratin 6C) (CK 6C) (K6c keratin) [Homo sapiens (c EsaT-6 like protein EsxP_2 [Mycobacterium marinum M] argininosuccinate synthase ArgG [Mycobacterium marinum M] hypothetical protein MMAR_0722 [Mycobacterium marinum M] 3-hydroxybutyryl-CoA dehydrogenase FadB2 [Mycobacterium marinum M] quinone reductase, Qor_1 [Mycobacterium marinum M] transcriptional regulatory protein [Mycobacterium marinum M] F420-dependent glucose-6-phosphate dehydrogenase Fgd1 [Mycobacterium marinum M] hypothetical protein MMAR_2098 [Mycobacterium marinum M] bifunctional protein: methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cycloh hypothetical protein MMAR_4959 [Mycobacterium marinum M] long-chain acyl-CoA synthase [Mycobacterium marinum M] preprotein translocase SecA1 1 subunit [Mycobacterium marinum M] 50S ribosomal protein L23, RplW [Mycobacterium marinum M] hypothetical protein MMAR_2993 [Mycobacterium marinum M] hypothetical protein MMAR_1241 [Mycobacterium marinum M] long-chain-fatty-acid-CoA ligase FadD15_1 [Mycobacterium marinum M] acyl-[acyl-carrier protein] desaturase DesA1_1 [Mycobacterium marinum M] glycine dehydrogenase GcvB [Mycobacterium marinum M] citrate lyase beta subunit, CitE_2 [Mycobacterium marinum M] glycerol-3-phosphate dehydrogenase, GpdA1 [Mycobacterium marinum M] dihydroxy-acid dehydratase IlvD [Mycobacterium marinum M] short-chain type dehydrogenase/reductase [Mycobacterium marinum M] bifunctional transmembrane phospholipid biosynthesis enzyme PlsC [Mycobacterium marinum M] UDP-glucose 6-dehydrogenase, UdgL [Mycobacterium marinum M] fatty acyl-AMP ligase FadD29 [Mycobacterium marinum M] glutamyl-tRNA (Gln) amidotransferase (subunit A), GatA [Mycobacterium marinum M] NAD(P) transhydrogenase (subunit alpha) PntAa [Mycobacterium marinum M] hypothetical protein MMAR_5439 [Mycobacterium marinum M] hypothetical protein MMAR_4940 [Mycobacterium marinum M] phosphoribosylaminoimidazole- succinocarboxamide synthase, PurC [Mycobacterium marinum M] hypothetical protein MMAR_4227 [Mycobacterium marinum M] ribose/galactose isomerase RpiB [Mycobacterium marinum M] hypothetical protein MMAR_3275 [Mycobacterium marinum M] urease accessory protein UreG [Mycobacterium marinum M] initiation factor IF-3 InfC [Mycobacterium marinum M] two-component system transcriptional regulator [Mycobacterium marinum M] 30S ribosomal protein S16 RpsP [Mycobacterium marinum M] hypothetical protein MMAR_1670 [Mycobacterium marinum M] hypothetical protein MMAR_1537 [Mycobacterium marinum M] hypothetical protein MMAR_1392 [Mycobacterium marinum M] hypothetical protein MMAR_0170 [Mycobacterium marinum M] hypothetical protein MMAR_5442 [Mycobacterium marinum M] pantoate--beta-alanine ligase PanC [Mycobacterium marinum M] cystathionine gamma-synthase MetB (cgs) [Mycobacterium marinum M] glycyl-tRNA synthetase GlyS [Mycobacterium marinum M] regulatory protein [Mycobacterium marinum M] hypothetical protein MMAR_2083 [Mycobacterium marinum M] enoyl-CoA hydratase, EchA16_2 [Mycobacterium marinum M] hypothetical protein MMAR_1713 [Mycobacterium marinum M] oxidoreductase [Mycobacterium marinum M] hypothetical protein MMAR_1521 [Mycobacterium marinum M] acyl-CoA dehydrogenase FadE24 [Mycobacterium marinum M] dihydrolipoamide dehydrogenase LpdA [Mycobacterium marinum M] glycosyl hydrolase [Mycobacterium marinum M] 30S ribosomal protein S11, RpsK [Mycobacterium marinum M] 50S ribosomal protein L18, RplR [Mycobacterium marinum M] ferredoxin reductase [Mycobacterium marinum M] transcription antitermination protein, NusG [Mycobacterium marinum M] hypothetical protein MMAR_0832 [Mycobacterium marinum M] short-chain type oxidoreductase [Mycobacterium marinum M] PE family protein, PE5 [Mycobacterium marinum M] hypothetical protein MMAR_0344 [Mycobacterium marinum M] 50S ribosomal protein L28 RpmB2 [Mycobacterium marinum M] ATP-binding protein ABC transporter [Mycobacterium marinum M] 5'-phosphoribosyl-5-aminoimidazole synthetase, PurM [Mycobacterium marinum M] hypothetical protein MMAR_4609 [Mycobacterium marinum M] phosphohistidine phosphatase SixA [Mycobacterium marinum M] oligoribonuclease Orn [Mycobacterium marinum M] succinate-semialdehyde dehydrogenase [NADP+] dependent (SsdH) GabD2 [Mycobacterium marinu hypothetical protein MMAR_2068 [Mycobacterium marinum M] hypothetical protein MMAR_1996 [Mycobacterium marinum M] hypothetical protein MMAR_1223 [Mycobacterium marinum M] PPE family protein [Mycobacterium marinum M] translation initiation factor IF-1, InfA [Mycobacterium marinum M] methoxy mycolic acid synthase 3, MmaA3 [Mycobacterium marinum M] amidohydrolase [Mycobacterium marinum M] mycolic acid synthase PcaA [Mycobacterium marinum M] hypothetical protein MMAR_0777 [Mycobacterium marinum M] secretory protein [Mycobacterium marinum M] 50S ribosomal protein L31 RpmE_1 [Mycobacterium marinum M] hypothetical protein MMAR_0168 [Mycobacterium marinum M] metal-dependent hydrolase [Mycobacterium marinum M] GTP1/OBGfamily GTP-binding protein Obg [Mycobacterium marinum M] hypothetical protein MMAR_2577 [Mycobacterium marinum M] hypothetical protein MMAR_3083 [Mycobacterium marinum M] REVERSED glucose kinase [Mycobacterium marinum M] nitroreductase [Mycobacterium marinum M] hypothetical protein MMAR_2146 [Mycobacterium marinum M] 29 kDa antigen Cfp29 [Mycobacterium marinum M] two-component sensory transduction transcriptional regulatory protein MtrA [Mycobacterium mar nicotinate-nucleotide pyrophosphatase NadC [Mycobacterium marinum M] 50S ribosomal protein L6, RplF [Mycobacterium marinum M] hypothetical protein MMAR_4570 [Mycobacterium marinum M] phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase HisA [Mycobacterium glucosamine-fructose-6-phosphate aminotransferase, GlmS [Mycobacterium marinum M] oxidoreductase [Mycobacterium marinum M] 6-phosphogluconate dehydrogenase Gnd1 [Mycobacterium marinum M] aspartate kinase Ask [Mycobacterium marinum M] oxidoreductase [Mycobacterium marinum M] cysteine synthase a CysK1 [Mycobacterium marinum M] hypothetical protein MMAR_2306 [Mycobacterium marinum M] hypothetical protein MMAR_2680 [Mycobacterium marinum M] 20-beta-hydroxysteroid dehydrogenase FabG3 [Mycobacterium marinum M] lipoprotein [Mycobacterium marinum M] acetolactate synthase (large subunit) IlvB1_2 [Mycobacterium marinum M] short chain dehydrogenase [Mycobacterium marinum M] UTP--glucose-1-phosphate uridylyltransferase GalU [Mycobacterium marinum M] 50S ribosomal protein L27 RpmA [Mycobacterium marinum M] transcriptional accessory protein Tex [Mycobacterium marinum M] hypothetical protein MMAR_3027 [Mycobacterium marinum M] argininosuccinate lyase ArgH [Mycobacterium marinum M] hypothetical protein MMAR_1995 [Mycobacterium marinum M] glutamate decarboxylase, GadB [Mycobacterium marinum M] preprotein translocase ATPase SecA2 [Mycobacterium marinum M] 50S ribosomal protein L19 RplS [Mycobacterium marinum M] translation initiation factor IF-2 InfB [Mycobacterium marinum M] DNA-directed RNA polymerase (omega chain) RpoZ [Mycobacterium marinum M] transcriptional regulator [Mycobacterium marinum M] hypothetical protein MMAR_0160 [Mycobacterium marinum M] phosphomannomutase PmmA [Mycobacterium marinum M] ribosomal protein S9, RpsI [Mycobacterium marinum M]

Unused ProtScore of Matched Proteins ∆esxA, ∆esxB 4 1 6 5 3 20 8 30 50 12 60 15 21 2 52 58 75

9 74 11 29 106 17 14 23 79 36 32 43 24

7 35 62 123 57 45 66 139

120 25 40 54 81 22 68 115 88 73 104 78 63 48 34 46 59 51 28 89 16 93 71 13 18 33 64 80

91 97 61 49 92

27

85 67 126 53

55 99

39 56 87 65 90 37

19

110 38 117 101 70 137

76

98 100 119

96 112 44 95 31 131 84 42

103

105

94

82

41

72

111 109

83

130

47

10

128

133 107

113

125

102 124

118

86

WT 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369

∆esxA, ∆esxB 27.01 53.36 21.67 24.25 29.62 5.69 9.22 4 3.35 7.6 2.25 6.88 5.47 30.42 2.95 2.28 2

8.22 2 7.73 4.06 1.68 6.11 7.29 4.7 2 4 4 4 4.53

19.92 4 2.21 0.27 2.49 3.85 2.09 0.07

0.39 4.38 4 2.72 2 4.97 2.04 0.81 2 2.01 1.74 2 2.17 3.49 4 3.62 2.26 3.32 4.13 2 6.13 2 2.01 7.52 6.1 4 2.14 2

2 2 2.23 3.38 2

4.14

2 2.04 0.22 2.82

2.58 2

4 2.53 2 2.11 2 4

5.85

1.29 4 0.57 2 2.02 0.08

2

2 2 0.4

2 1.24 4 2 4 0.13 2 4

2

1.7

2

2

4

2.01

1.26 1.36

2

0.14

3.55

8.07

0.18

0.11 1.44

1.19

0.25

2 0.27

0.5

2

# Set Proteins Mapped to Each Master ∆ esxA, ∆ esxB WT Interpreting the Alignment Multiplicity Worksheet Mul tipli city maps - Simla r to the alignment maps on the previous worksheet, the fi rs t two tables on this worksheet provide detail about the alignment from two perspecti ves - how the set proteins account for master proteins and vi ce versa. However here we a re focused on the mul tiplici ty of alignment. Tha t is, a single set protein can map to more than one master/WT protein . The converse is also possible.. A value of one means onl y a single protein is ma tched, 2 means two a re ma tched to tha t one row, 3 mea ns 3 to 1 ma tching, etc. Condi tional forma tting is used here to highlight a reas of concern. Green means a single protein is aligned and all is well. Grey means no proteins a re aligned, and red means more than one protein is aligned. Alignment Multipli ci ty Frequency Anal ysis - The his togra m tables a t the fa r ri ghtt of this worksheet measure the degree of a l ignment multiplicity from each direction. Unders tanding alignment mul tipl city - The observa tion of alignment mul tipli city is not necessaril y a bad thing. There are two ma in causes of i t: - di fferential s pecificity of protein ID - a l i gnment process problems This fi rs t a na tural effect and the second is a problem we want to mi minize. The fi rst point of anal yzing alignment multipli ci ty here is for quality control to hopefully demons trate tha t the degree of mul tiplici ty in aligning sets of interes t is appropriatel y low, so there is l ittle a mbiguity about what i s being measured. From a quality control perspective, we expect: (1) The degree of alignment multipli city should be in the low ha ndful of percents at most i n either direction. (2) If the mas ter/WT set has been made well, i t should ha ve a hi gher degree of specifi ci ty, meaning i t will ha ve less a ccession ambi gui ty, so a s maller number of proteins in ea ch group on a vera ge. This means tha t mos t of the multipli ci ty we detect should be in the di rection of mul tiple master proteins mapping to a single set protein. For exa mple, in a gi ven set protein, we ma y not be able to resol ve isoforms A and B, so they appear in one ambi guous group AB. If the mas ter search has additi onal peptide IDs that allow us to report both A and B a re present, then when the mas ter is aligned agains t our set of interes t two master proteins, A a nd B, will be aligned a gainst one s et protein, AB.

1 2 3 4 5 6 7

1

8 9 10

1

11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369

1 1

1 1 1 1 1 1

1 1

1 1 1 1 1 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1 0 1 1 1 1 0 1 1 0 1 0 0 1 0 1 1 1 0 1 1 1 1 1 0 1 1 1 1 1 0 1 1 1 1 0 1 1 0 1 0 1 1 0 1 1 1 0 1 1 0 0 0 0 1 1 1 0 1 1 0 0 1 0 0 0 0 0 1 1 1 1 0 0 0 0 1 1 0 0 1 0 1 1 0 1 0 1 1 0 0 1 0 0 1 1 1 0 1 0 1 1 0 0 1 0 0 1 1 0 1 0 0 0 1 0 1 0 1 1 1 1 0 1 1 0 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1

# WT Proteins Mapped to Each Set N ∆ esxA, ∆ esxB Set N 1 2 3 4 5 6 7

1

8 9 10

1

11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363

1 1

1 1 1 1 1 1

1 1

1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 0 1 0 1 1 1 1 0 0 1 1 1 1 0 1 0 1 1 0 1 0 0 0 1 0 1

Protein Level FDR Analysis

Estimated False Discovery Rates

12%

Global FDR

False Discovery Rate

Proteins Identified at Critical False Discovery Rates Number of Proteins Detected Critical FDR 1.0% 5.0% 10.0%

Global FDR 401 433

Local FDR 338 369 382

Global FDR from Fit 395 439

* It is recommended you use numbers in bold and avoid using numbers in italics.

Correspondence between FDR Levels and ProteinPilot Reported Confidences

Local FDR

10%

Critical Values (Global) Critical Values (Local)

8%

Corresponding ProteinPilot Confidence

Global FDR (Fit)

Critical FDR 1.0% 5.0% 10.0%

6% 4%

0

Critical FDR 1.0% 5.0% 10.0%

100

200

300

400

500

Ranked Proteins

Nonlinear Fitting

15 10 5 0 0

100

200

300

Ranked Proteins

400

500

100%

400

90%

350

80%


Fit

True Positives

Cumulative Reverse

20

Numeric ROC plot

450

Data

Global FDR 61.1% 24.1%

Global FDR from Fit 66.1% 18.7%

Corresponding Unused ProtScore

2% 0%

25

Local FDR 97.8% 92.6% 84.5%

300 250 200 150

0%

False Positives

50

Local FDR Global FDR (Fit)

30%

0 40

Global FDR

40%

10% 30

ProteinPilot Reported vs. Estimated FDR

50%

50 20

Global FDR from Fit 0.470 0.090

60%

20%

10

Global FDR 0.410 0.120

70%

100

0

Local FDR 1.660 1.130 0.810

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Reported Protein Confidence

Distinct Peptide Level FDR Analysis

Number of Peptides Identified Local FDR 1397 1528 1586

Global FDR 1637 1841 2000

Global FDR from Fit 1643 1836 2005


Peptides Identified at Critical False Discovery Rates Critical FDR 1.0% 5.0% 10.0%

Estimated False Discovery Rates

12%

Global FDR Local FDR Critical Values (Global) Critical Values (Local) Global FDR (Fit)

10% 8%

Correspondence between FDR Levels and ProteinPilot Reported Confidences Corresponding ProteinPilot Confidence

6%

Critical FDR 1.0% 5.0% 10.0%

4%

Local FDR 99.2% 95.9% 90.7%

Global FDR 82.9% 39.9% 22.4%

Global FDR from Fit 82.0% 40.3% 22.2%

2% * It is recommended you use numbers in bold and avoid using numbers in italics.

* It is recommended you use numbers in bold and avoid using numbers in italics.

0% 0

500

1000

1500

2000

2500

Ranked Peptides

Nonlinear Fitting Data

120

Fit

True Positives

Cumulative Reverse

140

Numeric ROC plot

2000

100 80 60

100%

1800

90%

1600

80%


160

1400 1200 1000 800 600

40 20 0 0

500

1000

1500

Ranked Distinct Peptides

2000

2500

40% 30% 10%

0

0% 150

False Positives

200

250

300

Global FDR (Fit)

50%

200 100

Local FDR

60%

20%

50

Global FDR

70%

400

0

ProteinPilot Reported vs. Estimated FDR

0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%

Reported Peptide Confidence