1. Notes

2. Result Statistics

Figure 1. False discovery rate (FDR) curve. X axis is the number of peptides being kept. Y axis is the corresponding FDR.



Figure 2. 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.
#Frames #Features#PrecursorsIdentified #Peptides#Sequences#Proteins*
MS1 MS/MS #Chimera #Original #PSMs #Scans #Features**Groups All Top
Total103851815190048386914213413482999964115101
Sample 3103851815190048386914213413482999964115101
* proteins with significant peptides are used in counts.
** features are identified by DB search only.

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;

(a)
Table 2. Result filtration parameters.
Peptide -10lgP≥ 30.05
Protein -10lgP≥ 15
Proteins unique peptides≥ 1
De novo score(%)≥ 50%
Table 3. Statistics of filtered result.
FDR (Peptide-Spectrum Matches)0.7%
FDR (Peptide Sequences)1.0%
FDR (Protein Group)1.0%
De Novo Only Spectra12299
Table 4. PTM profile.
Name ∆Mass Position # peptides # proteins # modification
sites
Carbamidomethylation57.02
C
20
17
33 (33)
Acetylation (Protein N-term)42.01
Protein N-term
6
6
3 (6)
Oxidation (M)15.99
M
4
3
4 (5)

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 Cleavages01234+
Sample 35441500

4. Other Information

Table 6. Search parameters.
Search Engine Name: PEAKS
Parent Mass Error Tolerance: 20.0 ppm
Fragment Mass Error Tolerance: 0.05 Da
Precursor Mass Search Type: monoisotopic
Enzyme: Trypsin
Max Missed Cleavages: 2
Digest Mode: Specific
Peptide Length Range: 6 - 55
Fixed Modifications:
  Carbamidomethylation (+57.02)
Variable Modifications:
  Acetylation (Protein N-term) (+42.01)
  Oxidation (M) (+15.99)
Max Variable PTM Per Peptide: 2
Database: Velella_singlebestonly_minlen100_2STEP
Taxon: all species
Searched Entries: 194010
Deep Learning Boost: Yes
FDR Estimation: Enabled