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 | #Precursors | Identified | #Peptides | #Sequences | #Proteins* | MS1 | MS/MS | #Chimera | #Original | #PSMs | #Scans | #Features** | Groups | All | Top | Total | 1039 | 5187 | 56913 | 5503 | 75838 | 401 | 401 | 210 | 303 | 300 | 163 | 318 | 281 | Sample 6 | 1039 | 5187 | 56913 | 5503 | 75838 | 401 | 401 | 210 | 303 | 300 | 163 | 318 | 281 | * 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 | ≥ 36.88 | Protein -10lgP | ≥ 15 | Proteins unique peptides | ≥ 1 | De novo score(%) | ≥ 50% |
|
Table 3.
Statistics of filtered result.
FDR (Peptide-Spectrum Matches) | 1.0% | FDR (Peptide Sequences) | 1.0% | FDR (Protein Group) | 1.0% | De Novo Only Spectra | 16741 |
|
Table 4.
PTM profile.
Name |
∆Mass |
Position |
# peptides |
# proteins |
# modification
sites |
Carbamidomethylation | 57.02 | C | 66 | 63 | 133 (133) | Oxidation (M) | 15.99 | M | 14 | 15 | 7 (24) | Acetylation (Protein N-term) | 42.01 | Protein N-term | 6 | 7 | 2 (7) |
|
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+ | Sample 6 | 191 | 102 | 10 | 0 | 0 |
|
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
|
|