Supplementary Information Proteome-­‐wide selected reaction monitoring assays for the human pathogen Streptococcus pyogenes Christofer Karlsson1, #, Lars Malmström2, #, Ruedi Aebersold2, 3, Johan Malmström1,4 * 1) Department of Immunotechnology, Lund, Sweden 2) Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland 3) Faculty of Science, University of Zurich, Zurich, Switzerland 4) Biognosys AG, Zurich, Switzerland #) Equal author contribution Supplementary Figure S1 | Outline of the GAS proteome network topology and assay score. Prophage_encoded_Exotoxins Streptococcus_pyogenes_Virulome DNA_topoisomerases_Type_II_ATP_dependent pVir_Plasmid_of_Campylobacter DNA_repair_bacterial_MutL_MutS_system DNA_topoisomerases_Type_I_ATP_independent Resistance_to_fluoroquinolones Multidrug_Resistance_Efflux_Pumps Flavohaemoglobin Adhesion_of_Campylobacter Secreted Coenzyme_B12_biosynthesis CBSS_176280_1_peg_1561 Periplasmic_Stress_Response Streptococcal_Mga_Regulon Campylobacter_Iron_Metabolism Flagellum_in_Campylobacter Proteasome_bacterial Surface Listeria_surface_proteins_Internalin_like_proteins Two_component_regulatory_systems_in_Campylobacter Transport_of_Manganese ZZ_gjo_need_homes YbbK Polysaccharide_deacetylases At1g14345 DNA_Repair_Base_Excision Glutathione_regulated_potassium_efflux_system_and_associated_functions DNA_repair_bacterial_RecFOR_pathway Streptococcus_pyogenes_recombinatorial_zone DNA_structural_proteins_bacterial Teichoic_and_lipoteichoic_acids_biosynthesis DNA_replication DNA_repair_bacterial Lipid_A_Ara4N_pathway_Polymyxin_resistance_ D_Alanyl_Lipoteichoic_Acid_Biosynthesis DNA_repair_bacterial_DinG_and_relatives Central_meta_cleavage_pathway_of_aromatic_compound_degradation Proteolysis_in_bacteria_ATP_dependent Lipoprotein_Biosynthesis SpeB_SpeF_extended_regulon Potassium_homeostasis Iron_acquisition_in_Streptococcus Sortase rRNA_modification_Bacteria Beta_lactamase_cluster_in_Streptococcus RuvABC_plus_a_hypothetical De_Novo_Purine_Biosynthesis Transport_of_Iron Heme_hemin_uptake_and_utilization_systems_in_GramPositives dTDP_rhamnose_synthesis Lactose_and_Galactose_Uptake_and_Utilization Single_Rhodanese_domain_proteins Capsular_heptose_biosynthesis Fructose_utilization Asp_tRNA_Asn_transamidation Alginate_metabolism Protein_degradation D_ribose_utilization Streptolysin_S_Biosynthesis_and_Transport ABC_transporter_dipeptide_TC_3_A_1_5_2_ ATP_dependent_RNA_helicases_bacterial Rhamnose_containing_glycans YaaA Bacterial_Chemotaxis L_ascorbate_utilization_and_related_gene_clusters_ Mannitol_Utilization Pentose_phosphate_pathway Lactose_utilization Stringent_Response_p_ppGpp_metabolism At3g21300 D_tyrosyl_tRNA_Tyr_deacylase Sex_pheromones_in_Enterococcus_faecalis_and_other_Firmicutes D_Tagatose_and_Galactitol_Utilization Mannose_Metabolism COG3533 Teichuronic_acid_biosynthesis Nitric_oxide_synthase Sucrose_utilization Ribitol_Xylitol_Arabitol_Mannitol_and_Sorbitol_utilization Signal_peptidase tRNA_aminoacylation_Asp_and_Asn Glutathione_Redox_cycle Galactosylceramide_and_Sulfatide_metabolism cAMP_signaling_in_bacteria ABC_transporter_oligopeptide_TC_3_A_1_5_1_ Transcription_factors_bacterial Anaerobic_respiratory_reductases Ribonucleotide_reduction Glutaredoxins Glu_tRNA_Gln_transamidation Restriction_Modification_System Oxidative_stress ABC_transporter_glutamine_TC_3_A_1_3_2_ Calvin_Benson_cycle tRNA_modification_Bacteria L_Arabinose_utilization IbrA_and_IbrB_co_activators_of_prophage_gene_expression Copper_homeostasis tRNA_aminoacylation_Glu_and_Gln Glycogen_metabolism Fructooligosaccharides_FOS_and_Raffinose_Utilization Sucrose_Metabolism Glycolysis_and_Gluconeogenesis tRNA_aminoacylation Cobalt_zinc_cadmium_resistance Entner_Doudoroff_Pathway Maltose_and_Maltodextrin_Utilization YcfH CBSS_342610_3_peg_1536 Pyridoxin_Vitamin_B6_Biosynthesis Conserved_gene_cluster_possibly_involved_in_RNA_metabolism Beta_Glucoside_Metabolism RNA_polymerase_bacterial NAD_and_NADP_cofactor_biosynthesis_global Riboflavin_FMN_and_FAD_metabolism Heme_and_Siroheme_Biosynthesis Pyruvate_metabolism_I_anaplerotic_reactions_PEP N_Acetyl_Galactosamine_and_Galactosamine_Utilization COG2509 Threonine_and_Homoserine_Biosynthesis Nudix_proteins_nucleoside_triphosphate_hydrolases_ PnuC_like_transporters GroEL_GroES Hexitol_degradation Methionine_Degradation Cysteine_Biosynthesis Methionine_Salvage Methylglyoxal_Metabolism Niacin_Choline_transport_and_metabolism NAD_regulation D_gluconate_and_ketogluconates_metabolism Glycolysis_and_Gluconeogenesis_including_Archaeal_enzymes Chitin_and_N_acetylglucosamine_utilization Glutathione_Non_redox_reactions Staphylococcal_pathogenicity_islands_SaPI Biogenesis_of_c_type_cytochromes Programmed_frameshift Phenylalanine_and_Tyrosine_Branches_from_Chorismate Thiamin_biosynthesis Deoxyribose_and_Deoxynucleoside_Catabolism Sialic_Acid_Metabolism Phenylalanine_synthesis Adenosyl_nucleosidases Polyamine_Metabolism Autoinducer_2_AI_2_transport_and_processing_lsrACDBFGE_operon_ Glutamine_Glutamate_Aspartate_and_Asparagine_Biosynthesis Coenzyme_A_Biosynthesis ECF_class_transporters Redox_dependent_regulation_of_nucleus_processes Aminotransferases_Aromatic_Pathway_and_More_A_work_in_progress Fermentations_Mixed_acid Periplasmic_disulfide_interchange Type_IV_pilus Chorismate_Synthesis Purine_conversions UDP_N_acetylmuramate_from_Fructose_6_phosphate_Biosynthesis At5g11840_At5g67370 Methionine_Biosynthesis D_Galacturonate_and_D_Glucuronate_Utilization Peptide_methionine_sulfoxide_reductase At5g04520_AT1G06240 Purine_Utilization Arginine_Deiminase_Pathway Proline_Synthesis Na_translocating_decarboxylases_and_related Conserved_gene_cluster_associated_with_Met_tRNA_formyltransferase Putative_sugar_ABC_transporter_ytf_cluster_ Ammonia_assimilation Xanthine_Metabolism_in_Bacteria _biotin_dependent_enzymes Arginine_and_Ornithine_Degradation Soluble_cytochromes_and_functionally_related_electron_carriers At4g10620_At3g57180_At3g47450 Ribosome_LSU_bacterial Poly_gamma_glutamate_biosynthesis Protein_chaperones Quinate_degradation Glycerol_and_Glycerol_3_phosphate_Uptake_and_Utilization Arginine_Biosynthesis_extended Bacteriocin_like_peptides_Blp Unknown_carbohydrate_utilization_cluster_Ydj_ CBSS_262719_3_peg_410 Trehalose_Uptake_and_Utilization Heat_shock_dnaK_gene_cluster_extended Respiratory_dehydrogenases_1 Glycerol_fermenation_to_1_3_propanediol Glutamine_synthetases Peptidoglycan_Biosynthesis Ioja p Arginine_Biosynthesis Inorganic_Sulfur_Assimilation Intracellular Benzoate_transport_and_degradation_cluster Fatty_Acid_Biosynthesis_FASII High_affinity_phosphate_transporter_and_control_of_PHO_regulon F0F1_type_ATP_synthase Ribosomal_protein_S12p_Asp_methylthiotransferase Biotin_biosynthesis Yfa_cluster V_Type_ATP_synthase 16S_rRNA_modification_within_P_site_of_ribosome Glycerolipid_and_Glycerophospholipid_Metabolism_in_Bacteria Ribosome_biogenesis_bacterial Cell_envelope_associated_LytR_CpsA_Psr_transcriptional_attenuators Cinnamic_Acid_Degradation LMPTP_YfkJ_cluster Ribosomal_protein_S5p_acylation MLST Acetyl_CoA_fermentation_to_Butyrate Translation_factors_bacterial Ribosome_SSU_bacterial Control_of_cell_elongation_division_cycle_in_Bacilli ATP_dependent_Nuclease At4g38090 Biphenyl_Degradation Threonine_anaerobic_catabolism_gene_cluster tRNA_processing tRNAmodification_position_34 Flavodoxin Phosphate_metabolism Cyanate_hydrolysis Pyruvate_metabolism_II_acetyl_CoA_acetogenesis_from_pyruvate Trans_translation_by_stalled_ribosomes Transport_of_Zinc Acetoin_butanediol_metabolism COG2302 Bacterial_Cell_Division Universal_GTPases Translation_elongation_factor_G_family Allantoin_degradation Propanediol_utilization At1g26220_At1g32070 At1g69340_At2g40600 Node Color Ethanolamine_utilization Di_Inositol_Phosphate_biosynthesis Inositol_catabolism Murein_hydrolase_regulation_and_cell_death COG0523 Lipoic_acid_metabolism D_galactarate_D_glucarate_and_D_glycerate_catabolism Fermentations_Lactate General_secretory_pathway_Sec_SRP_complex_TC_3_A_5_1_1_ Glycine_and_Serine_Utilization COG1399 19.5 1 Allantoin_Utilization Bacterial_Cytoskeleton Bacterial_signal_recognition_particle_SRP_ YjeE Hfl_operon Polyhydroxybutyrate_metabolism Two_cell_division_clusters_relating YgjD_and_YeaZ Folate_Biosynthesis Photorespiration_oxidative_C2_cycle_ _to_chromosome_partitioning Chorismate_Intermediate_for_synthesis_of_PAPA_antibiotics_ score PABA_anthranilate_3_hydroxyanthranilate_and_more_ Cold_shock_CspA_family_of_proteins Ribonuclease_H Alkylphosphonate_utilization Ribosome_activity_modulation n_Phenylalkanoic_acid_degradation EcsAB_transporter_affecting_expression_and_secretion_of_secretory_preproteins Chorismate_Intermediate_for_synthesis_of_Tryptophan_PAPA_antibiotics_PABA_3_hydroxyanthranilate_and_more_ Unspecified_monosaccharide_transport_cluster Queuosine_Archaeosine_Biosynthesis Serine_Biosynthesis RNA_processing_and_degradation_bacterial Glycine_Biosynthesis Assay Macromolecular_synthesis_operon CRISPRs Butanol_Biosynthesis At5g48545_and_At3g56490_At1g31160 Copper_homeostasis_copper_tolerance Molybdenum_cofactor_biosynthesis vg. Flagellum Tryptophan_synthesis Leucine_Biosynthesis Isoprenoid_Biosynthesis Coenzyme_F420_synthesis A Phage_capsid_proteins Experimental_Histidine_Degradation Serine_glyoxylate_cycle Experimental_Ubiquinone_BiosynthesisVDC Pyruvate_Alanine_Serine_Interconversions One_carbon_metabolism_by_tetrahydropterines Plasmid_replication Iron_sulfur_cluster_assembly Transcription_initiation_bacterial_sigma_factors Histidine_Degradation Ketoisovalerate_oxidoreductase Glycine_cleavage_system Polyprenyl_Diphosphate_Biosynthesis