1. Notes

2. Result Statistics

Figure 1. False discovery rate (FDR) curve. X axis is the number of peptide-spectrum matches (PSM) being kept. Y axis is the corresponding FDR.

Figure 2. PSM score distribution. (a) Distribution of PEAKS peptide score; (b) Scatterplot of PEAKS peptide score versus precursor mass error.

(a)

(b)

Figure 3. De novo result validation. Distribution of residue local confidence: (a) Residues in de novo sequences validated by confident database peptide assignment; (b) Residues in "de novo only" sequences.

(a)

(b)

Table 1. Statistics of data. # of MS scans 69077 # of MS/MS scans 38404 Table 2. Result filtration parameters. Peptide -10lgP ≥21.3 Peptide Ascore ≥0 Protein -10lgP ≥20 Proteins unique peptides ≥2 De novo ALC Score ≥50% Table 3. Statistics of filtered result. Peptide-Spectrum Matches 8620 Peptide sequences 3493 Protein groups 416 Proteins 733 Proteins (#Unique Peptides) 513 (>2); 220 (=2); 0 (=1); FDR (Peptide-Spectrum Matches) 1.0% FDR (Peptide Sequences) 1.6% De Novo Only Spectra 5597

Table 4. PTM profile. Name ∆Mass Position #PSM -10lgP Area AScore Oxidation 15.99 M 1395 89.81 1.95E5 1000.00 Carbamidomethyl 57.02 C 1049 84.11 1.28E5 1000.00

3. Experiment Control

Figure 4. Precursor mass error of peptide-spectrum matches (PSM) in filtered result. (a) Distribution of precursor mass error in ppm; (b) Scatterplot of precursor m/z versus precursor mass error in ppm.

(a)

(b)

Table 5. Number of identified peptides in each sample by the number of missed cleavages

Missed Cleavages 0 1 2 3 4+ Native 2687 203 14 0 0 Decellularized 533 53 3 0 0

4. Other Information

Table 6. Search parameters. Search Engine Name: PEAKS Parent Mass Error Tolerance: 10.0 ppm Fragment Mass Error Tolerance: 0.5 Da Precursor Mass Search Type: monoisotopic Enzyme: Trypsin Max Missed Cleavages: 3 Non-specific Cleavage: both Fixed Modifications:   Carbamidomethylation: 57.02 Variable Modifications:   Oxidation (M): 15.99 Max Variable PTM Per Peptide: 3 Database: Uniprot-RV-36080 Taxon: All Searched Entry: 36080 FDR Estimation: Enabled Merge Options: no merge Precursor Options: corrected Charge Options: no correction Filter Options: no filter Process: true

Table 7. Instrument parameters. Fractions: OB_FERNANDA_C1_20180720_09.raw, OB_FERNANDA_C2_20180 720_10.raw, OB_FERNANDA_C3_20180720_11.raw, OB_FERNANDA_C4_20 180720_12.raw, OB_FERNANDA_D1_20180720_13.raw, OB_FERNANDA_D2 _20180720_14.raw, OB_FERNANDA_D3_20180720_15.raw, OB_FERNANDA _D5_20180720_17.raw Ion Source: ESI(nano-spray) Fragmentation Mode: high energy CID (y and b ions) MS Scan Mode: FT-ICR/Orbitrap MS/MS Scan Mode: Linear Ion Trap