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Table S2. Mass Spectrometry Based Quantitation (LFQ Scores) of Proteins Co-Purifying from Yeast with Exoy-TAP

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Table S2. Mass Spectrometry Based Quantitation (LFQ Scores) of Proteins Co-Purifying from Yeast with Exoy-TAP Table S2. Mass spectrometry based quantitation (LFQ scores) of proteins co-purifying from yeast with ExoY-TAP. PEP - posterior error probability - the probability of a false hit given the peptide identification score and length of peptides (defined in Cox, J. & Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide quantitation. Nat Biotechnol. 2008 Dec;26(12):1367-72. doi: 10.1038/nbt.1511.) LFQ - Label Free Quantitation score - proportional to the average peptide signal intensity for all the peptides used to identify a given protein. Approximates the relative amounts of protein and can be used to compare protein levels between two conditions. Uniprot Description Gene Number Number PEP log2(LFQ) log2(LFQ) identifier names of of control TAP-ExoY similar unique identi- peptides fied for proteins protein identify- cation P07342 Acetolactate synthase catalytic subunit, ILV2 1 27 8.77E-214 29.174 26.40759 mitochondrial Q87022 Probable RNA-directed RNA polymerase;Major gag- 4 26 1.42E-267 28.34672 28.81559 ;P32503;Q capsid protein pol;gag 87024 P25605 Acetolactate synthase small subunit, ILV6 1 14 7.28E-99 28.14865 25.68654 mitochondrial P23172; Probable RNA-directed RNA polymerase;Major gag- 216 1.63E-75 25.06163 20.40561 Q87026 capsid protein pol;gag P02994 Elongation factor 1-alpha TEF1 1 14 1.47E-75 24.22957 25.30567 P10591 Heat shock protein SSA1 SSA1 2 8 2.54E-173 23.31451 25.41361 P04147 Polyadenylate-binding protein, cytoplasmic and PAB1 126 1.06E-95 23.29782 23.92488 nuclear Q00955 Acetyl-CoA carboxylase;Biotin carboxylase ACC1 2 44 1.54E-164 23.02989 20.97337 P0C2I6;P0 Transposon Ty1-LR3 Gag-Pol polyprotein;Capsid TY1B- 57 3 1.88E-88 22.48395 23.64713 C2I9;P0C2 protein;Ty1 protease;Integrase; Reverse LR3;TY1B- J1;P47098 transcriptase/ribonuclease H (Rev. t./r. PR1;TY1B- ;Q03434; H);Transposon Ty1-PR1 Gag-Pol polyprotein;Capsid PR3;TY1B- Q03612;P protein;Ty1 protease;Integrase;Rev. t./r. JR1;TY1B- 0C2I3;P0C H;Transposon Ty1-PR3 Gag-Pol polyprotein;Capsid ML2;TY1B 2I5;P0C2I7 protein;Ty1 protease;Integrase;Rev. t./r. - ;Q12414;P H;Transposon Ty1-JR1 Gag-Pol polyprotein;Capsid ER1;TY1B- 0C2J0;P47 protein;Ty1 protease;Integrase;Rev. t./r. DR6;TY1B- 100;Q121 H;Transposon Ty1-ML2 Gag-Pol polyprotein;Capsid LR2;TY1B- 41;P0C2I2; protein;Ty1 protease;Integrase;Rev. t./r. LR4;TY1B- Q12269;Q H;Transposon Ty1-ER1 Gag-Pol polyprotein;Capsid PL;TY1B- 12273;Q0 protein;Ty1 protease;Integrase;Rev. t./r. PR2;TY1B- 4711;Q07 H;Transposon Ty1-DR6 Gag-Pol polyprotein;Capsid JR2;TY1B- 793;O135 protein;Ty1 protease;Integrase;Rev. t./r. GR1;TY1B- 35;Q0467 H;Transposon Ty1-LR2 Gag-Pol polyprotein;Capsid DR5;TY1B- 0;Q92393; protein;Ty1 protease;Integrase;Rev. t./r. GR2;TY1B- Q03855;Q H;Transposon Ty1-LR4 Gag-Pol polyprotein;Capsid OL;TY1B- 12193;Q0 protein;Ty1 protease;Integrase;Rev. t./r. ML1;TY1B 3619;Q12 H;Transposon Ty1-PL Gag-Pol polyprotein;Capsid - 088;Q123 protein;Ty1 protease;Integrase;Rev. t./r. DR4;TY1B- 16;Q9923 H;Transposon Ty1-PR2 Gag-Pol polyprotein;Capsid H;TY1B- 1;Q99337; protein;Ty1 protease;Integrase;Rev. t./r. MR2;TY1B O13527 H;Transposon Ty1-JR2 Gag-Pol polyprotein;Capsid -OR;TY1B- protein;Ty1 protease;Integrase;Rev. t./r. DR1;TY1B- H;Transposon Ty1-GR1 Gag-Pol polyprotein;Capsid BR;TY1B- protein;Ty1 protease;Integrase;Rev. t./r. ER2;TY1B- H;Transposon Ty1-DR5 Gag-Pol polyprotein;Capsid LR1;TY1B- protein;Ty1 protease;Integrase;Rev. t./r. GR3;TY1B- H;Transposon Ty1-GR2 Gag-Pol polyprotein;Capsid DR3;TY1B- protein;Ty1 protease;Integrase;Rev. t./r. NL2;TY1B- H;Transposon Ty1-OL Gag-Pol polyprotein;Capsid A protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-ML1 Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-DR4 Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-H Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-MR2 Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-OR Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-DR1 Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-BR Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-ER2 Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-LR1 Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-GR3 Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-DR3 Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Transposon Ty1-NL2 Gag-Pol polyprotein;Capsid protein;Ty1 protease;Integrase;Rev. t./r. H;Truncated transposon Ty1-A Gag-Pol polyprotein;Integrase;Rev. t./r. H P32324 Elongation factor 2 EFT1 1 22 2.20E-91 22.08787 22.89421 P00925 Enolase 2 ENO2 1 8 1.53E-72 21.85441 21.80104 P00359; Glyceraldehyde-3-phosphate dehydrogenase TDH3;T 27 7.95E-37 21.84782 22.01522 P00358 3;Glyceraldehyde-3-phosphate dehydrogenase 2 DH2 P04385 Galactokinase GAL1 2 18 5.97E-76 21.82209 22.63668 P00560 Phosphoglycerate kinase PGK1 1 16 1.19E-66 21.61827 21.80589 P06634 ATP-dependent RNA helicase DED1 DED1 2 21 2.06E-100 21.53521 23.9657 P00549 Pyruvate kinase 1 CDC19 213 1.88E-48 21.5243 22.82557 P04911; Histone H2A.1;Histone H2A.2 HTA1;H 2 2 2.44E-13 21.33527 23.03391 P04912 TA2 P53865 Chaotic nuclear migration protein 67 CNM67 1 14 1.26E-58 21.33473 18.91132 Q06010 A-factor-processing enzyme STE23 116 9.44E-48 21.10815 17.92515 P38011 Guanine nucleotide-binding protein subunit beta- ASC1 1 9 1.99E-40 21.10764 22.89462 like protein P04397 Bifunctional protein GAL10;UDP-glucose 4- GAL10 119 2.75E-89 21.02168 22.0254 epimerase;Aldose 1-epimerase P02309 Histone H4 HHF1 1 5 1.95E-57 20.83399 22.83389 P09624 Dihydrolipoyl dehydrogenase, mitochondrial LPD1 1 9 8.46E-43 20.80971 17.60161 P15646 rRNA 2-O-methyltransferase fibrillarin NOP1 1 9 2.04E-37 20.74435 22.4207 P0C0V8 40S ribosomal protein S21-A;40S ribosomal RPS21A 26 2.32E-25 20.70016 21.91138 ;Q3E754 protein S21-B ;RPS21B P32473 Pyruvate dehydrogenase E1 component subunit PDB1 1 5 9.33E-22 20.61495 17.82488 beta, mitochondrial P0CX53; 60S ribosomal protein L12-A;60S ribosomal RPL12A; 27 1.25E-55 20.59696 23.06067 P0CX54 protein L12-B RPL12B P38631 1,3-beta-glucan synthase component FKS1 FKS1 1 12 7.93E-95 20.54576 21.86302 P10080 Single-stranded nucleic acid-binding protein SBP1 1 9 1.73E-26 20.53241 22.00898 P00330 Alcohol dehydrogenase 1 ADH1 38 2.40E-34 20.49921 20.72783 P32905; 40S ribosomal protein S0-A;40S ribosomal protein RPS0A; 2 7 3.89E-26 20.47833 22.33535 P46654 S0-B RPS0B P39990 13 kDa ribonucleoprotein-associated protein SNU13 1 5 5.61E-16 20.44374 21.45443 P46784; 40S ribosomal protein S10-B;40S ribosomal RPS10B 23 5.05E-15 20.42008 22.01591 Q08745 protein S10-A ;RPS10A P05030; Plasma membrane ATPase 1;Plasma membrane PMA1;P 2 15 2.06E-64 20.41183 20.51326 P19657 ATPase 2 MA2 O14467 Multiprotein-bridging factor 1 MBF1 17 2.28E-25 20.31307 20.78429 P38701 40S ribosomal protein S20 RPS20 1 4 1.96E-28 20.23608 21.08083 P12695 Dihydrolipoyllysine-residue acetyltransferase LAT1 1 5 1.07E-19 20.194 17.39632 component of pyruvate dehydrogenase complex, mitochondrial P04840 Mitochondrial outer membrane protein porin 1 POR1 1 10 1.42E-39 20.03604 21.43959 P16387 Pyruvate dehydrogenase E1 component subunit PDA1 15 9.63E-30 20.0084 17.99899 alpha, mitochondrial P24276 Protein SSD1 SSD1 130 3.39E-103 19.99673 22.49865 P37292 Serine hydroxymethyltransferase, mitochondrial SHM1 1 8 2.68E-62 19.83686 19.71453 P00950 Phosphoglycerate mutase 1 GPM1 1 8 2.32E-29 19.79983 19.73945 P32380 Spindle pole body component 110 SPC110 1 9 8.93E-33 19.79425 17.33769 Q01560 Nucleolar protein 3 NPL3 17 4.66E-25 19.78982 21.26774 P02400 60S acidic ribosomal protein P2-beta RPP2B 1 3 4.51E-48 19.58632 21.95642 P41940 Mannose-1-phosphate guanyltransferase PSA1 1 7 1.27E-23 19.57917 19.40279 P0CX49; 60S ribosomal protein L18-A;60S ribosomal RPL18A; 2 5 1.69E-71 19.57723 22.5724 P0CX50 protein L18-B RPL18B P10592 Heat shock protein SSA2 SSA2 2 7 2.63E-167 19.51324 21.71695 P08431 Galactose-1-phosphate uridylyltransferase GAL7 1 11 2.36E-45 19.47799 20.72692 P14832 Peptidyl-prolyl cis-trans isomerase CPR1 1 5 1.06E-19 19.44996 18.86912 P0CX23; 60S ribosomal protein L20-A;60S ribosomal RPL20A; 26 9.24E-28 19.42597 22.3531 P0CX24 protein L20-B RPL20B P0CX55; 40S ribosomal protein S18-A;40S ribosomal RPS18A 2 8 7.74E-40 19.33604 21.74891 P0CX56 protein S18-B ;RPS18B P04456 60S ribosomal protein L25 RPL25 15 1.49E-21 19.30354 21.98329 P15992 Heat shock protein 26 HSP26 1 6 2.20E-23 19.23121 19.40949 P21373 NAD(+) kinase UTR1 1 9 4.43E-51 19.04695 20.59377 P0CX82; 60S ribosomal protein L19-A;60S ribosomal RPL19A; 2 5 6.33E-53 19.04033 21.96877 P0CX83 protein L19-B RPL19B Q12499 Nucleolar protein 58 NOP58 1 14 2.71E-53 19.03023 21.85605 Q12159 RNA annealing protein YRA1 YRA1 1 7 1.38E-26 19.01947 21.25084 P02406 60S ribosomal protein L28 RPL28 1 4 3.02E-11 18.98782 21.02817 P32445 Single-stranded DNA-binding protein RIM1, RIM1 1 4 2.54E-13 18.97418 19.36329 mitochondrial P02407; 40S ribosomal protein S17-A;40S ribosomal RPS17A 2 4 5.48E-47 18.9605 21.31744 P14127 protein S17-B ;RPS17B P32787 Mitochondrial genome maintenance protein MGM1 14 3.54E-14 18.95359 19.76912 MGM101 01 P05317 60S acidic ribosomal protein P0 RPP0 1 9 1.09E-33 18.93509 23.51797 P0C2H6 60S ribosomal protein L27-A;60S ribosomal RPL27A; 2 5 1.82E-19 18.8845 21.94292 ;P0C2H7
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