S1R1 S1R2 S2R1 S2R2 S1R4 S2R3 S2R4S1R3

S1R1 S1R2 S2R1 S2R2S1R1 S1R2 S2R1 S2R2 S1R3 S1R4 S2R3 S2R4S1R3 S1R4 S2R3 S2R4

PT SET PT SET PT SET PT SET PT SET PT SET PT SET PT SET

PT- porcine trypsin SET – Streptomyces erythraeus trypsin

S1R1 S1R2 S2R1 S2R2S1R1 S1R2 S2R1 S2R2 S1R3 S1R4 S2R3 S2R4S1R3 S1R4 S2R3 S2R4

Protein extraction with B-PERGel electrophoresis

Protein digestion in gel

LC-MS/MS analysis – Qstar Elite

Database search – Mascot and Xtandem!

Protein identification validation and quantitation - Scaffold

Optimal biocathodes Suboptimal biocathodes

Proteins:90% protein probability95% peptide probabilityAt least 1 peptide

579 proteins

Peptides:90% protein probability95% peptide probabilityAt least 1 peptide

Spectra:90% protein probability95% peptide probabilityAt least 1 peptide

Proteins:90% protein probability70% peptide probabilityAt least 2 peptides

286 proteins

Peptides:90% protein probability70% peptide probabilityAt least 2 peptides

Spectra:90% protein probability70% peptide probabilityAt least 2 peptides

Proteins:90% protein probability70% peptide probabilityAt least 2 peptides

286 proteins

peptides:90% protein probability70% peptide probabilityAt least 2 peptides

spectra:90% protein probability70% peptide probabilityAt least 2 peptides

Category Bio Sample MS/MS Sample #Prot #IDs #Spec %IDsPT S1R1 PT mascot_daemon_merge (S1R1_gel2_opt_F003330) 43 200 2989 0.06691201PT S1R2 PT mascot_daemon_merge (S1R2_gel2_opt_F003339) 110 676 4815 0.1403946PT S2R1 PT mascot_daemon_merge (S2R1_gel2_opt_F003342) 64 262 4891 0.05356778PT S1R3 PT mascot_daemon_merge (S1R3_gel2_subopt_F003341) 52 353 4616 0.07647314PT S1R4 PT mascot_daemon_merge (S1R4_gel2_subopt_F003340) 150 760 6230 0.12199037PT S2R3 PT mascot_daemon_merge (S2R3_gel2_subopt_F003343) 85 412 5109 0.08064201PT S2R4 PT mascot_daemon_merge (S2R4_gel2_subopt_F003344) 47 182 4857 0.03747169PT S2R2 PT mascot_daemon_merge (S2R2_gel2_opt_F003345) 64 222 3933 0.05644546SET S1R1 SET mascot_daemon_merge (F003578_S1R1_Oct_9bands) 233 1033 3418 0.30222353SET S1R3 SET mascot_daemon_merge (F003577_S1R3_Oct_9bands) 106 373 3642 0.102416255SET S1R2 SET mascot_daemon_merge (F003582_S1R2_Oct_9bands) 190 725 4313 0.16809645SET S1R4 SET mascot_daemon_merge (F003581_S1R4_Oct_9bands) 243 1250 7084 0.17645398SET S2R1 SET mascot_daemon_merge (F003583_S2R1_Oct_9bands) 190 546 6708 0.08139535SET S2R3 SET mascot_daemon_merge (F003584_S2R3_Oct9bands) 225 757 6912 0.109519675SET S2R2 SET mascot_daemon_merge (F003586_S2R2_Oct_9bands) 201 668 4812 0.13881962SET S2R4 SET mascot_daemon_merge (F003587_S2R4_Oct_9bands) 184 559 4797 0.11653116

Proteins:90% protein probability95% peptide probabilityAt least 1 peptide

579 proteins

peptides:90% protein probability95% peptide probabilityAt least 1 peptide

spectra:90% protein probability95% peptide probabilityAt least 1 peptide

Category Bio Sample MS/MS Sample #Prot #IDs #Spec %IDsPT S1R1 PT mascot_daemon_merge (S1R1_gel2_opt_F003330) 63 243 2989 0.08129809PT S1R2 PT mascot_daemon_merge (S1R2_gel2_opt_F003339) 148 602 4815 0.12502596PT S2R1 PT mascot_daemon_merge (S2R1_gel2_optF003342) 87 273 4891 0.055816807PT S1R3 PT mascot_daemon_merge (S1R3_gel2_subopt_F003341) 75 362 4616 0.078422874PT S1R4 PT mascot_daemon_merge (S1R4_gel2_subopt_F003340) 217 738 6230 0.11845907PT S2R3 PT mascot_daemon_merge (S2R3_gel2_subopt_F003343) 111 429 5109 0.08396947PT S2R4 PT mascot_daemon_merge (S2R4_gel2_subopt_F003344) 71 218 4857 0.044883672PT S2R2 PT mascot_daemon_merge (S2R2_gel2_opt_F003345) 88 241 3933 0.06127638SET S1R1 SET mascot_daemon_merge (F003578_S1R1_Oct_9bands) 347 1028 3418 0.3007607SET S1R3 SET mascot_daemon_merge (F003577_S1R3_Oct_9bands) 121 376 3642 0.103239976SET S1R2 SET mascot_daemon_merge (F003582_S1R2_Oct_9bands) 246 694 4313 0.16090888SET S1R4 SET mascot_daemon_merge (F003581_S1R4_Oct_9bands) 337 1180 7084 0.16657256SET S2R1 SET mascot_daemon_merge (F003583_S2R1_Oct_9bands) 226 485 6708 0.07230173SET S2R3 SET mascot_daemon_merge (F003584_S2R3_Oct9bands) 308 724 6912 0.10474537SET S2R2 SET mascot_daemon_merge (F003586_S2R2_Oct_9bands) 279 669 4812 0.13902743SET S2R4 SET mascot_daemon_merge (F003587_S2R4_Oct_9bands) 220 493 4797 0.10277256