Supplemental Information. Comprehensive Quantification. of the Modified Proteome Reveals Oxidative. Heart Damage in Mitochondrial Heteroplasmy

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1 Cell Reports, Volume 23 Supplemental Information Comprehensive Quantification of the Modified Proteome Reveals Oxidative Heart Damage in Mitochondrial Heteroplasmy Navratan Bagwan, Elena Bonzon-Kulichenko, Enrique Calvo, Ana Victoria Lechuga- Vieco, Spiros Michalakopoulos, Marco Trevisan-Herraz, Iakes Ezkurdia, José Manuel Rodríguez, Ricardo Magni, Ana Latorre-Pellicer, José Antonio Enríquez, and Jesús Vázquez

2 Relative Intensity Relative Intensity Large----mass---Small Intensity (log) Intensity (log) Relative Intensity Intensity (log) A B C MZ= , Charge= 2+, Scan= ppm.5 ppm Oxidation in W 6 Error in ppm MZ= , Charge= D MZ= , Charge= 4+, Scan= 684 Oxidation in P E m/z b1 MZ= , Charge= 2+, Scan=42483 b series y series y1 y Error in ppm MZ= , Charge= m/z b9 y12 Unmodified fragments 5 4 Oxidation in Y m/z Fig. S1 b1 b series y series b9 y12 y Error in ppm 18.6 MZ= , Charge= 2+ Increased mass in y series from y m/z b1 y6 b series y series y6 y12 Unmodified fragments y

3 Figure S1. Related to Figure 1. Peptide identification performance of Comet-PTM. (A-B) Comparison of scores obtained from Comet-PTM and CS in the population of PSM that produced the same match with the two engines. A match was considered identical when the peptide sequence was the same and the difference between ΔMass obtained by Comet-PTM and the theoretical mass of the modification selected in CS was within 5 ppm (A) or.5 ppm (B). Note that the scores were practically identical, and the dispersion around the identity line was diminished when the tolerance decreased; this demonstrates that the small differences in the score are a consequence of the error in the estimation of ΔMass and not in the design of the score in Comet-PTM. (C-E) Vseq analyses of 3 peptides containing oxidations incorrectly assigned to Met by CS. Comet-PTM correctly assigns the oxidation to Trp (C) Pro (D) or Tyr (E).

4 DMass(Kynurenin): Da DMass(Pro > Thr): Da DPCNSSIASIR Pituitary homeobox3 isoform X1 EAMEHPYFYPVVK Casein kinase II subunit alpha EGFHFEETIPGFK Glucose 1,6-bisphosphate synthase IIPGGAAAEDGR Disks large homolog 2 isoform X1 DTCNSSIASIR Pituitary homeobox2 isoform c EAMEHTYFYPVVK Casein kinase II subunit alpha isoform X1 EGFHFEETI TGFK Phosphoglucomutase-1 isoform X1 IITGGAAAEDGR Disks large homolog 2 isoform X1 VDNSSITGESEPQ PR VDNSSITGESEPQ TR ATPase, H+/K+ transporting alpha polypeptide Na+/K+ transporting ATPase subunit alpha 3 YAAEIHIVHWNPK Carbonic anhydrase 3 isoform CRA-b YAAEIHIVHWN TK Carbonic anhydrase 2 isoform X1 Figure S2. Related to Figure 2. List of peptides containing a Pro > Thr substitution assigned as a kynurenin modification in Pro. Peptide sequences together with their corresponding proteins are listed, highlighting (in red) the position of Pro and Thr residues.

5 Relative intensity Error ppm b2 m/z , charge 2+ y8* y7* y1 y3* y6* b3 y4* y5* y2* b4 y9* b5 b6 b9 m/z , charge 2+ y4* b2 y9* y1 y2* b3 b4 y3* b7 y5* y7* y6* y8* y1* m/z SAVENCQDSWR b1 FirstScan: PTM Xcorr: Bseries= Escore:.569 Yseries= W1 FASENDIPEWK b1 11 FirstScan: 5198 PTM Xcorr: Bseries= Escore: Yseries= W1 11 b series y series y1 y Figure S3. Related to Figure 2. Detection of a Trp iodination. Vseq results for 2 representative peptides containing iodinated Trp. Both the MS2 spectra (left panels) and the V-shaped heatmap distributions for the main fragmentation series (right panels), demonstrate the location of the modification in Trp.

6 PSM (%) Heart Liver Muscle NM: non-modified CAM: carbamidomethyl D Mass DEA: deamidation MC: missed cleavage Figure S4. Related to Figure 4. ΔMass distribution of modified peptides identified in the 3 mouse tissues. Assignations of the most frequent ΔMass peaks are indicated.

7 Frequency Frequency Position Position Frequency Position Frequency Frequency Position Position Oxidation M C F P W Y Phosphorylation S T Y Fig. S Deamidation M A C D E F GH I K N P Q R S T VWY C N Q A CDE F GH I KMNPQRS T VWY 12 6 Heart Liver Muscle A D E F G H I K N P Q R S T V Y Methylmalonylation S A C D E F G H I K N P Q R S T V Y Iodination 4 Y A D E F G H I K MN P Q R S T V WY

8 Figure S5. Related to Figure 4. Distribution of amino acids containing the most frequent modifications. The horizontal and vertical bar graphs have the same meaning as in Figure 2E.

9 Thermo raw files CometPTM.txt" cometptm output files SHIFTS Input (SHIFTS) Best Non-Modified PSMs s Calculation Calibration All PSMs PSMs with calibrated Masses Calculation of systematic machine error (m/z) Dmass peaks identification (Gaussian peak modelling) PSMs to peak apex assignment Global, Local and Peak FDR FDR threshold Identified PSMs Fig. S6 Isotopic correction.txt SHIFTS output files

10 Figure S6. Related to Experimental Procedures. Scheme of SHIFTS algorithm. Schematic representation of SHIFTS (Systematic, Hypothesis-free Identification of modifications with controlled FDR based on ultra-tolerant database Search), depicting how the output from Comet-PTM is processed, including mass recalibration, peak detection and FDR calculation.