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 Scans999
# of MS/MS Scans999
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 Matches20
Peptide Sequences15
Protein Groups2
Proteins7
Proteins (#Unique Peptides)0 (>2); 1 (=2); 6 (=1);
FDR (Peptide-Spectrum Matches)70.0%
FDR (Peptide Sequences)93.3%
FDR (Protein)57.1%
De Novo Only Spectra15
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.021C

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 3113100

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: 3_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 57.93 11 2 2 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
3 1 tr|A0A8D2LS65|A0A8D2LS65_VARKO 28.74 1 1 1 N 167367 Tenascin C OS=Varanus komodoensis OX=61221 PE=3 SV=1
3 2 tr|A0A8D2LTT5|A0A8D2LTT5_VARKO 28.74 0 1 1 N 187557 Tenascin C OS=Varanus komodoensis OX=61221 PE=3 SV=1
3 7 tr|A0A8D2LSP3|A0A8D2LSP3_VARKO 28.74 0 1 1 N 200563 Tenascin C OS=Varanus komodoensis OX=61221 PE=3 SV=1
3 9 tr|A0A8D2LS38|A0A8D2LS38_VARKO 28.74 0 1 1 N 210121 Tenascin C OS=Varanus komodoensis OX=61221 PE=3 SV=1
3 3 tr|A0A8D2LTQ1|A0A8D2LTQ1_VARKO 28.74 0 1 1 N 221181 Tenascin C OS=Varanus komodoensis OX=61221 PE=3 SV=1
3 10 tr|A0A8D2LTG4|A0A8D2LTG4_VARKO 28.74 0 1 1 N 231157 Tenascin C OS=Varanus komodoensis OX=61221 PE=3 SV=1
total 7 proteins

sp|P00760|TRY1_BOVIN
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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.LGEDNINVVEGNEQFISASK.S Y 48.16 2162.0491 206.5 1082.2550 2 30.81 976 4 73 92
K.LQGIVSW.G Y 19.53 801.4385 -7.2 802.4400 1 30.18 952 1 210 216
total 2 peptides
Best Unique PSM (Scan 976, m/z=1082.2550, z=2, RT=30.81, ppm=206.5):
tr|A0A8D2LS65|A0A8D2LS65_VARKO
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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
P.SAQPVEGR.I Y 28.74 842.4246 -70.2 422.1900 2 8.05 118 2 149 156
total 1 peptides
Best Unique PSM (Scan 118, m/z=422.1900, z=2, RT=8.05, ppm=-70.2):
tr|A0A8D2LTT5|A0A8D2LTT5_VARKO
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
P.SAQPVEGR.I Y 28.74 842.4246 -70.2 422.1900 2 8.05 118 2 149 156
total 1 peptides
Best Unique PSM (Scan 118, m/z=422.1900, z=2, RT=8.05, ppm=-70.2):
tr|A0A8D2LSP3|A0A8D2LSP3_VARKO
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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
P.SAQPVEGR.I Y 28.74 842.4246 -70.2 422.1900 2 8.05 118 2 149 156
total 1 peptides
Best Unique PSM (Scan 118, m/z=422.1900, z=2, RT=8.05, ppm=-70.2):
tr|A0A8D2LS38|A0A8D2LS38_VARKO
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
P.SAQPVEGR.I Y 28.74 842.4246 -70.2 422.1900 2 8.05 118 2 149 156
total 1 peptides
Best Unique PSM (Scan 118, m/z=422.1900, z=2, RT=8.05, ppm=-70.2):
tr|A0A8D2LTQ1|A0A8D2LTQ1_VARKO
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
P.SAQPVEGR.I Y 28.74 842.4246 -70.2 422.1900 2 8.05 118 2 149 156
total 1 peptides
Best Unique PSM (Scan 118, m/z=422.1900, z=2, RT=8.05, ppm=-70.2):
tr|A0A8D2LTG4|A0A8D2LTG4_VARKO
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
P.SAQPVEGR.I Y 28.74 842.4246 -70.2 422.1900 2 8.05 118 2 149 156
total 1 peptides
Best Unique PSM (Scan 118, m/z=422.1900, z=2, RT=8.05, ppm=-70.2):
 


Prepared with PEAKS ™ (bioinfor.com)