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)

Table 1. Statistics of data. #Scans #Features Identified #Peptides #Sequences #Proteins* MS1 MS2 #PSMs #Scans #Features Groups All Top Total 15027 71603 60693 640 635 7481 324 323 106 1055 398 BuCaMH04_B15 15027 71603 60693 640 635 7481 324 323 106 1055 398 * proteins with significant peptides are used in counts.

Figure 3. Sample overlap for Proteins and Peptides (up to 8 samples). (a) All Proteins; (b) Top Proteins; (c) Peptides;

(a) Not applicable to only one sample

(b) Not applicable to only one sample

(c) Not applicable to only one sample

Figure 4. Distribution of peptide feature detection. (a) Feature m/z distribution; (b) Feature RT distribution.

(a)

(b)

Figure 5. Distribution of identified peptide features. (a) Feature abundance distribution; (b) De novo sequencing validation.

(a)

(b)

Table 2. Result filtration parameters. Peptide -10lgP ≥50.5 PTM Ascore ≥0 Protein -10lgP ≥20 Proteins unique peptides ≥0 De novo score(%) ≥50% Table 3. Statistics of filtered result. FDR (Peptide-Spectrum Matches) 0.0% FDR (Peptide Sequences) 0.0% FDR (Protein Group) 8.3% De Novo Only Spectra 13577

Table 4. PTM profile. Name ∆Mass Position #PSM -10lgP Abundance AScore Carbamidomethyl 57.02 C 178 123.10 2.41E7 1000.00

3. Experiment Control

Figure 6. 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+ BuCaMH04_B15 294 28 2 0 0

4. Other Information

Table 6. Search parameters. Search Engine Name: PEAKS Parent Mass Error Tolerance: 10.0 ppm Fragment Mass Error Tolerance: 0.6 Da Precursor Mass Search Type: monoisotopic Enzyme: Trypsin Max Missed Cleavages: 2 Digest Mode: Semispecific Fixed Modifications:   Carbamidomethylation: 57.02 Variable Modifications:   Oxidation (M): 15.99 Max Variable PTM Per Peptide: 3 Database: NCBI_Serpentes_BuCaMH04 Taxon: All Contaminant Database: cRAP_contaminants Searched Entry: 410235 FDR Estimation: Enabled Merge Options: no merge Precursor Options: corrected Charge Options: no correction Filter Charge: 2 - 8 Process: true Associate chimera: yes

Table 7. Instrument parameters. Fractions: BuCaMH04.raw Ion Source: ESI(nano-spray) Fragmentation Mode: CID, CAD(y and b ions) MS Scan Mode: FT-ICR/Orbitrap MS/MS Scan Mode: FT-ICR/Orbitrap