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.

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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 ( Da each) and phosphorylation of Ser21 and Ser23 ( 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 Da (C)

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

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

Cystatin SA 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 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 ( Da each). The raw data file and.PUF file for the data set are shown in (C). (A) (B) (C)

Cystatin SN 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 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 ( Da each). The raw data file and.PUF file for the data set are shown in (C). (A) (B) (C)

Cystatin C 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 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 ( Da each). The raw data file and.PUF file for the data set are shown in (C). (A) (B) (C)

(A) (B) Top-down mass spectrometry of truncated forms of intact Cystatin D with a C46R mutation, with masses Da and 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 ( 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 Da (C)

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