1. Supplemental Top-down mass spectrometry of intact human salivary Cystatins S, S1, and S2. Parent molecular ions were subjected to CAD on a hybrid linear ion-trap FTICR mass spectrometer (A, D, and G). Amino acid sequence and protein sequence coverage is displayed with the graphical output of ProSight PC 2.0 to illustrate assigned ions from the CAD data set (B, E, and H). The location of b and y fragment ions are shown in blue, and highlighted in orange are cysteine residues oxidized to disulfides (-1.00782509 Da each) and phosphorylation of Ser21 and Ser23 (+79.966333 Da). The raw data file and.PUF file for each data set are shown in (C), (F), and (I). (A) (B) P-Score: 1.71E-57 Matching fragments: 44 Non-matching fragments: 63 Fragments explained: 41% Cystatin S 14175.8569 Da (C)

2. (D) (E) P-Score: 2.58E-54 Matching fragments: 54 Non-matching fragments: 120 Fragments explained: 31% Cystatin S1 14255.8567 Da (F)

3. (G) (H) P-Score: 8.06E-32 Matching fragments: 26 Non-matching fragments: 73 Fragments explained: 26% Cystatin S2 14335.8110 Da (I)

4. Cystatin SA 14336.9856 Da P-Score: 2.81E-46 Matching fragments: 42 Non-matching fragments: 80 Fragments explained: 34% Top-down mass spectrometry of intact Cystatin SA, mass 14336.9856 Da. A parent molecular ion (inset) was subjected to CAD on a hybrid linear ion-trap FTICR mass spectrometer (A). Amino acid sequence and protein sequence coverage is displayed with the graphical output of ProSight PC 2.0 to illustrate assigned ions from the CAD experiment (B). The location of b and y fragment ions are shown in blue, and highlighted in orange are cysteine residues oxidized to disulfides (-1.00782509 Da each). The raw data file and.PUF file for the data set are shown in (C). (A) (B) (C)

5. Cystatin SN 14303.1553 Da P-Score: 4.3E-29 Matching fragments: 24 Non-matching fragments: 54 Fragments explained: 30% Top-down mass spectrometry of intact Cystatin SN, mass 14303.1553 Da. (A) A parent molecular ion (inset) was subjected to CAD on a hybrid linear ion-trap FTICR mass spectrometer. (B) Amino acid and protein sequence coverage is displayed with the graphical output of ProSight PC 2.0 to illustrate assigned ions from the CAD experiment. The location of b and y fragment ions are shown in blue, and highlighted in orange are cysteine residues oxidized to disulfides (-1.00782509 Da each). The raw data file and.PUF file for the data set are shown in (C). (A) (B) (C)

6. Cystatin C 13334.5829 Da P-Score: 1.25E-34 Matching fragments: 29 Non-matching fragments: 100 Fragments explained: 22% Top-down mass spectrometry of intact Cystatin C, mass 13334.5829 Da. (A) A parent molecular ion (inset) was subjected to CAD on a hybrid linear ion-trap FTICR mass spectrometer. (B) Amino acid and protein sequence coverage is displayed with the graphical output of ProSight PC 2.0 to illustrate assigned ions from the CAD experiment. The location of b and y fragment ions are shown in blue, and highlighted in orange are cysteine residues oxidized to disulfides (-1.00782509 Da each). The raw data file and.PUF file for the data set are shown in (C). (A) (B) (C)

7. (A) (B) Top-down mass spectrometry of truncated forms of intact Cystatin D with a C46R mutation, with masses 13154.4675 Da and 13596.7015 Da respectively. (A and D) Parent molecular ions (insets) were subjected to CAD on a hybrid linear ion-trap FTICR mass spectrometer. Amino acid and protein sequence coverage is displayed with the graphical output of ProSight PC 2.0 to illustrate assigned ions from the CAD experiments (B and E). The location of b and y fragment ions are shown in blue, the C46R SNP is reflected in the sequence (SVQR), and highlighted in orange are cysteine residues oxidized to disulfides (-1.00782509 Da each). The raw data file for the CAD data set is shown in (C) and (F). P-Score: 3.44E-18 Matching fragments: 21 Non-matching fragments: 46 Fragments explained: 31% Cystatin D 13154.4675 Da (C)

8. (D) (E) P-Score: 2E-22 Matching fragments: 19 Non-matching fragments: 18 Fragments explained: 51% Cystatin D 13596.7015 Da (F)