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 29365 # of MS/MS scans 85674 Table 2. Result filtration parameters. Peptide -10lgP ≥20 Peptide Ascore ≥0 Protein -10lgP ≥20 Proteins unique peptides ≥2 De novo ALC Score ≥50% Table 3. Statistics of filtered result. Peptide-Spectrum Matches 34123 Peptide sequences 20634 Protein groups 2213 Proteins 5110 Proteins (#Unique Peptides) 4116 (>2); 994 (=2); 0 (=1); FDR (Peptide-Spectrum Matches) 0.1% FDR (Peptide Sequences) 0.2% FDR (Protein) 0.0% De Novo Only Spectra 8827

Table 4. PTM profile. Name ∆Mass Position #PSM -10lgP Area AScore Carbamidomethyl 57.02 C 6515 81.68 3.32E7 1000.00 Oxidation 15.99 M 860 72.55 3.59E6 1000.00 Phe->Tyr 15.99 Y 286 65.82 2.37E6 1000.00 Tyr->Phe -15.99 F 94 58.44 2.15E7 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+ Sample 2 16034 3813 659 128 0

4. Other Information

Table 6. Search parameters. Search Engine Name: PEAKS Parent Mass Error Tolerance: 20.0 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   Phe->Tyr substitution: 15.99   Tyr->Phe substitution: -15.99 Max Variable PTM Per Peptide: 3 Database: arabidopsis Taxon: All Contaminant Database: contaminants Searched Entry: 89449 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: 20190523-08-H2.raw Ion Source: ESI(nano-spray) Fragmentation Mode: CID, CAD(y and b ions) MS Scan Mode: FT-ICR/Orbitrap MS/MS Scan Mode: Linear Ion Trap