a) b) c) d) e) Relative Intensity Relative Intensity 0 20 Relative Intensity Relative Intensity 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.

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.

m/z Relative Abundance c3c3 c4c4 c5c5 c8c8 c9c9 c 11 c 14 z z c 13 c 12 z z z z Supplemental Figure 3. ETD mass spectrum of m/z corresponding to [M+8H] 8+ ion of protein of Da identified as flightin fragment 1-65.

m/z Relative Abundance c3c3 c4c4 c8c8 c9c9 c 11 c 14 z c 13 z2z2 z7z7 c5c5 z z 12 z 13 z c2c2 Supplemental Figure 4. ETD mass spectrum of m/z corresponding to [M+12H] 12+ ion of protein of Da identified as flightin fragment 1-89.

m/z Relative Abundance c3c3 c4c4 c9c9 c 11 c 14 z c 13 z3z3 c5c5 c2c2 c 12 z z z Supplemental Figure 5. ETD mass spectrum of m/z corresponding to [M+15H] 15+ ion of protein of Da identified as flightin.

m/z Relative Abundance c3c3 c4c4 c9c9 c 11 c 14 z c 13 z5z5 c5c5 z4z4 z 12 Supplemental Figure 6. ETD mass spectrum of m/z corresponding to [M+12H] 12+ ion of protein of Da identified as flightin fragment 1-82.

Supplemental Figure 7. ETD mass spectrum of m/z corresponding to [M+6H] 6+ ion of protein of 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

m/z Relative Abundance Supplemental Figure 8. ETD mass spectrum of m/z corresponding to [M+15H] 15+ ion of protein of Da identified as a Titin fragment. c3c3 c4c4 c7c7 c 10 z c5c5 c1c1 c6c6 z 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:

m/z Relative Abundance c3c3 c4c4 c8c8 z c5c5 c2c2 c M +11 c 10 c 17 c 11 Supplemental Figure 9. ETD mass spectrum of m/z corresponding to [M+11H] 11+ ion of protein of Da identified as Ubiquitin. MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV LRLRGG Processed Protein Sequence: z z z z c c9c9 c1c1 z8z8 z z 30 +2