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 Matches30
Peptide Sequences26
Protein Groups6
Proteins13
Proteins (#Unique Peptides)1 (>2); 1 (=2); 11 (=1);
FDR (Peptide-Spectrum Matches)66.7%
FDR (Peptide Sequences)76.9%
FDR (Protein)69.2%
De Novo Only Spectra14
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.026C
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 6.1214100

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: 6.1_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
1 6157 sp|P00760|TRY1_BOVIN 64.78 16 3 3 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
6 9168 tr|A0A498HG22|A0A498HG22_MALDO 28.96 1 1 1 Y 77829 UBX domain-containing protein OS=Malus domestica OX=3750 GN=DVH24_007674 PE=4 SV=1
6 13454 tr|M1D0T0|M1D0T0_SOLTU 28.96 17 1 1 Y 6426 Defensin protein OS=Solanum tuberosum OX=4113 GN=102604459 PE=4 SV=1
6 13455 tr|I0CCB1|I0CCB1_MALDO 28.96 13 1 1 Y 8273 Defensin OS=Malus domestica OX=3750 GN=DEF1 PE=2 SV=1
6 13456 tr|M1D0T1|M1D0T1_SOLTU 28.96 13 1 1 Y 8737 Defensin protein OS=Solanum tuberosum OX=4113 GN=102604459 PE=4 SV=1
6 13457 tr|M5Y0D4|M5Y0D4_PRUPE 28.96 13 1 1 Y 8614 Knottin scorpion toxin-like domain-containing protein OS=Prunus persica OX=3760 GN=PRUPE_1G341500 PE=4 SV=1
6 13458 tr|A0A314UVX1|A0A314UVX1_PRUYE 28.96 13 1 1 Y 8628 Defensin Ec-AMP-D2 OS=Prunus yedoensis var. nudiflora OX=2094558 GN=Pyn_27247 PE=4 SV=1
6 13459 tr|Q84UH1|Q84UH1_PRUPE 28.96 13 1 1 Y 8745 Defensin protein 1 OS=Prunus persica OX=3760 GN=DFN1 PE=2 SV=1
6 13460 tr|A0A5N5GWY9|A0A5N5GWY9_9ROSA 28.96 11 1 1 Y 9962 Defensin Ec-AMP-D2-like OS=Pyrus ussuriensis x Pyrus communis OX=2448454 GN=D8674_037096 PE=4 SV=1
2 4931 sp|E9PZQ0|RYR1_MOUSE 24.97 0 2 2 N 565047 Ryanodine receptor 1 OS=Mus musculus OX=10090 GN=Ryr1 PE=1 SV=1
4 13463 sp|D9U2B7|NDBP_LYCMC 24.63 10 1 1 N 9968 Bradykinin-potentiating peptide NDBP12 OS=Lychas mucronatus OX=172552 PE=3 SV=1
15 13467 tr|A0A1W7RB55|A0A1W7RB55_9SCOR 21.16 2 1 1 Y 71936 Angiotensin-converting enzyme OS=Hadrurus spadix OX=141984 PE=3 SV=1
16 5256 tr|A0A1W7R9Y4|A0A1W7R9Y4_9SCOR 21.08 1 1 1 N 138443 Polyprotein OS=Hadrurus spadix OX=141984 PE=4 SV=1
total 13 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 45.03 2162.0491 -57.2 1081.9700 2 30.39 946 4 73 92
S.NTLNNDIMLIK.L Y 23.83 1287.6857 -0.2 644.8500 2 27.92 854 1 102 112
K.SIVHPSYNS.N Y 23.50 1002.4771 -11.6 502.2400 2 16.88 444 1 93 101
total 3 peptides
Best Unique PSM (Scan 946, m/z=1081.9700, z=2, RT=30.39, ppm=-57.2):
tr|A0A498HG22|A0A498HG22_MALDO
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.TC(+57.02)ESQSNRFK.G Y 28.96 1255.5615 831.4 629.3100 2 27.65 844 1 549 558 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 844, m/z=629.3100, z=2, RT=27.65, ppm=831.4):
tr|M1D0T0|M1D0T0_SOLTU
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.TC(+57.02)ESQSNRFK.G Y 28.96 1255.5615 831.4 629.3100 2 27.65 844 1 13 22 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 844, m/z=629.3100, z=2, RT=27.65, ppm=831.4):
tr|I0CCB1|I0CCB1_MALDO
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.TC(+57.02)ESQSNRFK.G Y 28.96 1255.5615 831.4 629.3100 2 27.65 844 1 30 39 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 844, m/z=629.3100, z=2, RT=27.65, ppm=831.4):
tr|M1D0T1|M1D0T1_SOLTU
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.TC(+57.02)ESQSNRFK.G Y 28.96 1255.5615 831.4 629.3100 2 27.65 844 1 33 42 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 844, m/z=629.3100, z=2, RT=27.65, ppm=831.4):
tr|M5Y0D4|M5Y0D4_PRUPE
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.TC(+57.02)ESQSNRFK.G Y 28.96 1255.5615 831.4 629.3100 2 27.65 844 1 33 42 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 844, m/z=629.3100, z=2, RT=27.65, ppm=831.4):
tr|A0A314UVX1|A0A314UVX1_PRUYE
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.TC(+57.02)ESQSNRFK.G Y 28.96 1255.5615 831.4 629.3100 2 27.65 844 1 33 42 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 844, m/z=629.3100, z=2, RT=27.65, ppm=831.4):
tr|Q84UH1|Q84UH1_PRUPE
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.TC(+57.02)ESQSNRFK.G Y 28.96 1255.5615 831.4 629.3100 2 27.65 844 1 34 43 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 844, m/z=629.3100, z=2, RT=27.65, ppm=831.4):
tr|A0A5N5GWY9|A0A5N5GWY9_9ROSA
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.TC(+57.02)ESQSNRFK.G Y 28.96 1255.5615 831.4 629.3100 2 27.65 844 1 42 51 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 844, m/z=629.3100, z=2, RT=27.65, ppm=831.4):
sp|E9PZQ0|RYR1_MOUSE
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
K.EVGFFQ.S Y 16.91 725.3384 800.8 363.9669 2 5.31 14 1 3828 3833
S.DAEGEGE.G Y 16.11 705.2453 67.2 706.3000 1 13.39 314 1 4399 4405
total 2 peptides
Best Unique PSM (Scan 14, m/z=363.9669, z=2, RT=5.31, ppm=800.8):
sp|D9U2B7|NDBP_LYCMC
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.AEAPAPAAA.A Y 24.63 767.3813 -11.2 768.3800 1 13.81 330 2 65 73
total 1 peptides
Best Unique PSM (Scan 330, m/z=768.3800, z=1, RT=13.81, ppm=-11.2):
tr|A0A1W7RB55|A0A1W7RB55_9SCOR
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
K.IC(+57.02)ADGPIPAH.L Y 21.16 1049.4963 -887.0 525.2900 2 34.72 1108 1 260 269 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1108, m/z=525.2900, z=2, RT=34.72, ppm=-887.0):
tr|A0A1W7R9Y4|A0A1W7R9Y4_9SCOR
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
S.PLLAVNRNLAES.Y Y 21.08 1295.7197 -875.4 648.3000 2 6.28 50 1 265 276
total 1 peptides
Best Unique PSM (Scan 50, m/z=648.3000, z=2, RT=6.28, ppm=-875.4):
 


Prepared with PEAKS ™ (bioinfor.com)