1. 8893 10046 13550 14721 14751 4972 4211 3511 12864 13479 13481 4971 4212 3710 13473 21376 10690 12862 11121 9515 9481 8701 7513 6737 4841 a) b) c) d) e) 0 20 40 60 80 100 Relative Intensity 80 40 0 Relative Intensity 0 20 Relative Intensity 100 200 0 Relative Intensity 60 40 20 0 Relative Intensity Supplemental Figure 1. Region-specific mass spectra from shrimp tissue section. a) hepatopancreas, b) nervous system, c) tail muscle, d) cuticle, and e) heart.

2. ETD Sequence Tag tblastn search L. vannamei EST database Translate EST match Match predicted c,z ions with ETD spectrum in Protein Prospector blast EST sequence Supplemental Figure 2. Workflow used to interpret ETD spectra of shrimp tail muscle proteins.

3. 10020030040050060070080090010001100120013001400150016001700180019002000 m/z 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 Relative Abundance 909.57 855.51 1818.02 1338.70 1568.09 1023.71 1108.66 1209.71 1282.66 1152.72 784.53 519.32 1494.00 390.31 1641.02 811.56 261.25 1977.08 1444.46 475.33 740.52 1882.25 1066.76 546.37 605.77 430.43 146.19346.37 201.17 c3c3 c4c4 c5c5 c8c8 c9c9 c 11 c 14 z 23 +2 z 19 +2 c 13 c 12 z 27 +2 z 24 +2 z 22 +2 z 21 +2 Supplemental Figure 3. ETD mass spectrum of m/z 909.6 corresponding to [M+8H] 8+ ion of protein of 7268.8 Da identified as flightin fragment 1-65.

4. 10020030040050060070080090010001100120013001400150016001700180019002000 m/z 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 Relative Abundance 838.59 855.53 216.19 1338.65 1992.81 1023.64 1616.95 1210.76 1129.73 784.50 1447.88 1109.64 1294.69 1814.80 1559.07 1677.98 1775.95 765.56 1707.91 1039.69 1504.40 666.27 1928.82 346.32 1405.70 752.02 901.79 1831.99 390.34 938.22 546.71 723.47 475.25 635.45 146.26 261.38 c3c3 c4c4 c8c8 c9c9 c 11 c 14 z 19 +2 c 13 z2z2 z7z7 c5c5 z 27 +2 z 12 z 13 z 26 +2 c2c2 Supplemental Figure 4. ETD mass spectrum of m/z 838.7 corresponding to [M+12H] 12+ ion of protein of 10052.4 Da identified as flightin fragment 1-89.

5. 10020030040050060070080090010001100120013001400150016001700180019002000 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 Relative Abundance 855.56 1589.24 1338.85 797.55 1995.47 1210.80 1023.67 390.42 768.28 961.07 1295.68 1817.22 918.17 1153.77 1928.28 1640.68 1108.63 1512.24 1268.54 1838.15 1382.13 1723.17 677.51 519.26 475.49 146.20 569.60 381.33 398.35 261.33 329.35 c3c3 c4c4 c9c9 c 11 c 14 z 15 +2 c 13 z3z3 c5c5 c2c2 c 12 z 16 +2 z 27 +2 z 28 +2 Supplemental Figure 5. ETD mass spectrum of m/z 983.1 corresponding to [M+15H] 15+ ion of protein of 14732.2 Da identified as flightin.

6. 10020030040050060070080090010001100120013001400150016001700180019002000 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 Relative Abundance 1162.82 775.50 684.51 855.54 1550.79 1210.75 390.30 1339.661494.91 342.45670.09 747.74 519.25 1023.70 927.28 1993.07 1292.52 216.18 569.44 1816.18 1096.53 1367.721937.48 261.31 1750.10 159.17 1878.57 475.35 c3c3 c4c4 c9c9 c 11 c 14 z 18 +2 c 13 z5z5 c5c5 z4z4 z 12 Supplemental Figure 6. ETD mass spectrum of m/z 775.4 corresponding to [M+12H] 12+ ion of protein of 9292.3 Da identified as flightin fragment 1-82.

7. Supplemental Figure 7. ETD mass spectrum of m/z 822.3 corresponding to [M+6H] 6+ ion of protein of 4927.8 Da identified as Troponin-I. T V K K K E F E L E D D K G A T K P D W A A G G P G A A K K E G E E G A P A E G D A P A E E A A A Processed Protein Sequence: M +6

8. 10020030040050060070080090010001100120013001400150016001700180019002000 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 Relative Abundance 542.44 174.23 671.52 893.65 441.38 1595.95 1148.86 1334.88 1786.34 962.74 328.40 1263.78 799.34 1886.22 498.40 1077.80 1464.99 1713.55 1033.66284.37 1553.98 1976.53 1639.92 732.82 Supplemental Figure 8. ETD mass spectrum of m/z 894.3 corresponding to [M+15H] 15+ ion of protein of 13399.5 Da identified as a Titin fragment. c3c3 c4c4 c7c7 c 10 z 33 +2 c5c5 c1c1 c6c6 z 35 +2 c8c8 c9c9 c 11 c 12 c 13 c 14 M +15 R G P L T E K Y D A D A E M A P P K F T V P I K S Q S M Q E G E R A F F E A R V E P R N D P N L R I E W Y H N G K P L Q S G H R F R T N F E L G H V T L E L L H T Y A E D S G E Y V C R A Y N K L G Q D I T R A S L K S K A G Q S V V L Q Processed Protein Sequence:

9. 10020030040050060070080090010001100120013001400150016001700180019002000 m/z 0 10 20 30 40 50 Relative Abundance 779.25 277.23 1136.69 1558.87 390.33 960.00 537.28 720.52 1422.52 1920.06 1264.70 636.43 1347.90 653.64 978.65 1250.40 1739.03 867.71 1536.75 1691.91 610.07 1079.691801.62 149.16 433.42 c3c3 c4c4 c8c8 z 32 +2 c5c5 c2c2 c 24 2+ M +11 c 10 c 17 c 11 Supplemental Figure 9. ETD mass spectrum of m/z 779.9 corresponding to [M+11H] 11+ ion of protein of 8567.9 Da identified as Ubiquitin. MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV LRLRGG Processed Protein Sequence: z 50 +2 z 11 +2 z 12 +2 z 17 +2 c 31 2+ c9c9 c1c1 z8z8 z 22 +2 z 30 +2