Summary

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 Scans982
# of MS/MS Scans982
Table 2. Result filtration parameters.
Peptide -10lgP≥15
Protein -10lgP≥20
Proteins unique peptides≥0
De novo ALC Score≥50%
Table 3. Statistics of filtered result.
Peptide-Spectrum Matches8
Peptide Sequences8
Protein Groups2
Proteins2
Proteins (#Unique Peptides)0 (>2); 0 (=2); 2 (=1);
FDR (Peptide-Spectrum Matches)137.5%
FDR (Peptide Sequences)112.5%
FDR (Protein)200.0%
De Novo Only Spectra15
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.022C
Oxidation15.991M

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 Cleavages01234+
Sample 162000

4. Other Information

Table 6. Search parameters.
Search Engine Name: PEAKS 7.0
Parent Mass Error Tolerance: 0.5 Da
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: Scopion2023
Taxon: All
Searched Entry: 15746
FDR Estimation: Enabled
Merge Options: 0.1 min. 0.5 Da
Precursor Options: corrected
Charge Options: no correction
Filter Options: no filter
Process: true
Table 7. Instrument parameters.
Fractions: 1_Seg1Ev1.mzXML
Ion Source: ESI(nano-spray)
Fragmentation Mode: CID, CAD(y and b ions)
MS Scan Mode: 3D Ion Trap
MS/MS Scan Mode: 3D Ion Trap

Protein List

Protein Group Protein ID Accession -10lgP Coverage (%) #Peptides #Unique PTM Avg. Mass Description
8 4925 tr|A0A1W7RA78|A0A1W7RA78_9SCOR 22.07 1 1 1 N 75289 alpha-glucosidase OS=Hadrurus spadix OX=141984 PE=4 SV=1
9 4926 tr|A0A1W7R9X0|A0A1W7R9X0_9SCOR 20.02 1 1 1 N 94388 Prospero OS=Hadrurus spadix OX=141984 PE=4 SV=1
total 2 proteins

tr|A0A1W7RA78|A0A1W7RA78_9SCOR
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| Protein Coverage | Supporting Peptides | Best Unique PSM |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
S.SNLLTGPLA.E Y 22.07 884.4967 -540.1 443.0168 2 10.84 220 1 623 631
total 1 peptides
Best Unique PSM (Scan 220, m/z=443.0168, z=2, RT=10.84, ppm=-540.1):
tr|A0A1W7R9X0|A0A1W7R9X0_9SCOR
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| Protein Coverage | Supporting Peptides | Best Unique PSM |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
R.SPGGPQGVGP.E Y 20.02 851.4137 -1268.3 426.1742 2 9.69 178 1 240 249
total 1 peptides
Best Unique PSM (Scan 178, m/z=426.1742, z=2, RT=9.69, ppm=-1268.3):
 


Prepared with PEAKS ™ (bioinfor.com)