S1R1S1R2S2R1S2R2S1R4 S2R3 S2R4 S1R3 S1R1S1R2S2R1S2R2S1R1S1R2S2R1S2R2 S1R3S1R4S2R3S2R4S1R3S1R4S2R3S2R4 PT SET PT SET PT SET PT SET PT SET PT SET PT SETPT.

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S1R1S1R2S2R1S2R2S1R4 S2R3 S2R4 S1R3 S1R1S1R2S2R1S2R2S1R1S1R2S2R1S2R2 S1R3S1R4S2R3S2R4S1R3S1R4S2R3S2R4 PT SET PT SET PT SET PT SET PT SET PT SET PT SETPT SET PT- porcine trypsin SET – Streptomyces erythraeus trypsin S1R1S1R2S2R1S2R2S1R1S1R2S2R1S2R2 S1R3S1R4S2R3S2R4S1R3S1R4S2R3S2R4 Protein extraction with B-PER Gel 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 probability 95% peptide probability At least 1 peptide 579 proteins

Peptides: 90% protein probability 95% peptide probability At least 1 peptide

Spectra: 90% protein probability 95% peptide probability At least 1 peptide

Proteins: 90% protein probability 70% peptide probability At least 2 peptides 286 proteins

Peptides: 90% protein probability 70% peptide probability At least 2 peptides

Spectra: 90% protein probability 70% peptide probability At least 2 peptides

Proteins: 90% protein probability 70% peptide probability At least 2 peptides 286 proteins

peptides: 90% protein probability 70% peptide probability At least 2 peptides

spectra: 90% protein probability 70% peptide probability At least 2 peptides

CategoryBio SampleMS/MS Sample#Prot#IDs#Spec%IDs PTS1R1 PTmascot_daemon_merge (S1R1_gel2_opt_F003330) PTS1R2 PTmascot_daemon_merge (S1R2_gel2_opt_F003339) PTS2R1 PTmascot_daemon_merge (S2R1_gel2_opt_F003342) PTS1R3 PTmascot_daemon_merge (S1R3_gel2_subopt_F003341) PTS1R4 PTmascot_daemon_merge (S1R4_gel2_subopt_F003340) PTS2R3 PTmascot_daemon_merge (S2R3_gel2_subopt_F003343) PTS2R4 PTmascot_daemon_merge (S2R4_gel2_subopt_F003344) PTS2R2 PTmascot_daemon_merge (S2R2_gel2_opt_F003345) SETS1R1 SETmascot_daemon_merge (F003578_S1R1_Oct_9bands) SETS1R3 SETmascot_daemon_merge (F003577_S1R3_Oct_9bands) SETS1R2 SETmascot_daemon_merge (F003582_S1R2_Oct_9bands) SETS1R4 SETmascot_daemon_merge (F003581_S1R4_Oct_9bands) SETS2R1 SETmascot_daemon_merge (F003583_S2R1_Oct_9bands) SETS2R3 SETmascot_daemon_merge (F003584_S2R3_Oct9bands) SETS2R2 SETmascot_daemon_merge (F003586_S2R2_Oct_9bands) SETS2R4 SETmascot_daemon_merge (F003587_S2R4_Oct_9bands)

Proteins: 90% protein probability 95% peptide probability At least 1 peptide 579 proteins

peptides: 90% protein probability 95% peptide probability At least 1 peptide

spectra: 90% protein probability 95% peptide probability At least 1 peptide

CategoryBio SampleMS/MS Sample#Prot#IDs#Spec%IDs PTS1R1 PTmascot_daemon_merge (S1R1_gel2_opt_F003330) PTS1R2 PTmascot_daemon_merge (S1R2_gel2_opt_F003339) PTS2R1 PTmascot_daemon_merge (S2R1_gel2_optF003342) PTS1R3 PTmascot_daemon_merge (S1R3_gel2_subopt_F003341) PTS1R4 PTmascot_daemon_merge (S1R4_gel2_subopt_F003340) PTS2R3 PTmascot_daemon_merge (S2R3_gel2_subopt_F003343) PTS2R4 PTmascot_daemon_merge (S2R4_gel2_subopt_F003344) PTS2R2 PTmascot_daemon_merge (S2R2_gel2_opt_F003345) SETS1R1 SETmascot_daemon_merge (F003578_S1R1_Oct_9bands) SETS1R3 SETmascot_daemon_merge (F003577_S1R3_Oct_9bands) SETS1R2 SETmascot_daemon_merge (F003582_S1R2_Oct_9bands) SETS1R4 SETmascot_daemon_merge (F003581_S1R4_Oct_9bands) SETS2R1 SETmascot_daemon_merge (F003583_S2R1_Oct_9bands) SETS2R3 SETmascot_daemon_merge (F003584_S2R3_Oct9bands) SETS2R2 SETmascot_daemon_merge (F003586_S2R2_Oct_9bands) SETS2R4 SETmascot_daemon_merge (F003587_S2R4_Oct_9bands)