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 Scans993
# of MS/MS Scans993
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 Matches14
Peptide Sequences10
Protein Groups2
Proteins2
Proteins (#Unique Peptides)1 (>2); 0 (=2); 1 (=1);
FDR (Peptide-Spectrum Matches)121.4%
FDR (Peptide Sequences)170.0%
FDR (Protein)200.0%
De Novo Only Spectra13
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.022C

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 473000

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: 4_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
1 6157 sp|P00760|TRY1_BOVIN 70.37 12 3 3 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
2 6158 tr|A0A835SGA5|A0A835SGA5_CHLIN 25.94 3 1 1 N 57283 MYND-type domain-containing protein OS=Chlamydomonas incerta OX=51695 GN=HXX76_011675 PE=4 SV=1
total 2 proteins

sp|P00760|TRY1_BOVIN
back to list

| 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.LGEDNINVVEGNEQFISASK.S Y 44.45 2162.0491 442.4 1082.5100 2 30.99 970 4 73 92
K.SIVHPSYNSN.T Y 31.46 1116.5200 -13.0 559.2600 2 16.08 414 1 93 102
K.SIVHPSYN.S Y 30.55 915.4450 0.5 458.7300 2 15.86 406 1 93 100
total 3 peptides
Best Unique PSM (Scan 970, m/z=1082.5100, z=2, RT=30.99, ppm=442.4):
tr|A0A835SGA5|A0A835SGA5_CHLIN
back to list

| 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
L.SPPRAGGAGGAGAAG.A Y 25.94 1152.5635 -137.1 577.2100 2 8.52 134 7 80 94
total 1 peptides
Best Unique PSM (Scan 134, m/z=577.2100, z=2, RT=8.52, ppm=-137.1):
 


Prepared with PEAKS ™ (bioinfor.com)