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 Scans1002
# of MS/MS Scans1002
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 Matches51
Peptide Sequences27
Protein Groups6
Proteins7
Proteins (#Unique Peptides)2 (>2); 0 (=2); 5 (=1);
FDR (Peptide-Spectrum Matches)29.4%
FDR (Peptide Sequences)55.6%
FDR (Protein)100.0%
De Novo Only Spectra22
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0233C
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 26196200

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: 26_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
2 44510 tr|A0A1E1WVN4|A0A1E1WVN4_TITOB 139.09 49 6 6 Y 9938 Putative insulin-like protein growth factor binding protein OS=Tityus obscurus OX=1221240 PE=4 SV=1
1 20591 sp|P60211|KA181_TITOB 129.16 46 4 4 Y 6530 Potassium channel toxin alpha-KTx 18.1 OS=Tityus obscurus OX=1221240 PE=1 SV=2
4 44511 tr|A0A1E1WVR0|A0A1E1WVR0_TITOB 42.67 20 1 1 Y 7174 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
3 44520 tr|H2CYP9|H2CYP9_PANCV 27.18 3 1 1 N 22307 5-demethoxyubiquinone hydroxylase, mitochondrial OS=Pandinus cavimanus OX=217261 PE=2 SV=1
3 20719 tr|A0A978VM66|A0A978VM66_ZIZJJ 27.18 1 1 1 N 55950 Knottin scorpion toxin-like domain-containing protein OS=Ziziphus jujuba var. spinosa OX=714518 GN=FEM48_Zijuj03G0006100 PE=4 SV=1
13 9273 tr|A0A835IPW1|A0A835IPW1_9MAGN 26.79 2 1 1 N 49583 Knottin scorpion toxin-like domain-containing protein OS=Coptis chinensis OX=261450 GN=IFM89_016673 PE=4 SV=1
15 44519 tr|A0A7J8I025|A0A7J8I025_MOLMO 21.05 1 1 1 N 62115 EGF-like domain-containing protein OS=Molossus molossus OX=27622 GN=HJG59_010803 PE=3 SV=1
total 7 proteins

tr|A0A1E1WVN4|A0A1E1WVN4_TITOB
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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
K.GLVC(+57.02)KVPDNSSDNTGIC(+57.02)K.K Y 73.14 1962.9139 -2.9 655.3100 3 20.10 590 1 73 90 Carbamidomethylation
R.KDC(+57.02)PAGIVK.D Y 59.32 986.5219 -16.6 494.2600 2 12.95 314 4 35 43 Carbamidomethylation
K.VPDNSSDNTGIC(+57.02)K.K Y 53.62 1405.6144 -6.4 703.8100 2 15.02 396 2 78 90 Carbamidomethylation
R.C(+57.02)EETVC(+57.02)SLKQ.R Y 34.43 1252.5427 2.2 627.2800 2 16.65 458 3 24 33 Carbamidomethylation
R.NISGIC(+57.02)GK.G Y 30.15 847.4222 1074.5 849.3400 1 14.40 372 1 65 72 Carbamidomethylation
K.GLVC(+57.02)K.V Y 22.67 575.3101 -12.9 576.3100 1 8.19 126 2 73 77 Carbamidomethylation
total 6 peptides
Best Unique PSM (Scan 590, m/z=655.3100, z=3, RT=20.10, ppm=-2.9):
sp|P60211|KA181_TITOB
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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
K.SMESC(+57.02)QGDTC(+57.02)K.C Y 80.57 1301.4686 327.9 651.9550 2 10.12 204 10 48 58 Carbamidomethylation
A.TGPQTTC(+57.02)QAAMC(+57.02)EAGC(+57.02)K.G Y 71.26 1869.7478 -17.3 935.8650 2 18.28 524 8 27 43 Carbamidomethylation
A.TGPQTTC(+57.02)QAAM(+15.99)C(+57.02)EAGC(+57.02)K.G Y 36.99 1885.7427 -9.1 943.8700 2 15.92 430 1 27 43 Carbamidomethylation; Oxidation (M)
C.QAAMC(+57.02)EAGC(+57.02)K.G Y 25.56 1124.4413 -14.1 563.2200 2 11.72 266 1 34 43 Carbamidomethylation
A.TGPQTTC(+57.02).Q Y 17.75 763.3171 -5.7 764.3200 1 7.31 92 2 27 33 Carbamidomethylation
total 5 peptides
Best Unique PSM (Scan 204, m/z=651.9550, z=2, RT=10.12, ppm=327.9):
tr|A0A1E1WVR0|A0A1E1WVR0_TITOB
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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
K.GKPTGYC(+57.02)NKDVC(+57.02)K.C Y 42.67 1525.7017 2.5 763.8600 2 11.24 248 3 46 58 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 248, m/z=763.8600, z=2, RT=11.24, ppm=2.5):
tr|H2CYP9|H2CYP9_PANCV
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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
E.QLIPK.Y Y 27.18 597.3849 63.2 598.4300 1 5.98 40 4 80 84
total 1 peptides
Best Unique PSM (Scan 40, m/z=598.4300, z=1, RT=5.98, ppm=63.2):
tr|A0A978VM66|A0A978VM66_ZIZJJ
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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
M.QLLPK.T Y 27.18 597.3849 63.2 598.4300 1 5.98 40 4 109 113
total 1 peptides
Best Unique PSM (Scan 40, m/z=598.4300, z=1, RT=5.98, ppm=63.2):
tr|A0A835IPW1|A0A835IPW1_9MAGN
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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
K.VDNLNSED.K Y 26.79 904.3774 8.9 453.2000 2 37.44 1224 1 109 116
total 1 peptides
Best Unique PSM (Scan 1224, m/z=453.2000, z=2, RT=37.44, ppm=8.9):
tr|A0A7J8I025|A0A7J8I025_MOLMO
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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.FASPPR.L Y 21.05 673.3547 1318.8 675.2500 1 20.00 586 1 63 68
total 1 peptides
Best Unique PSM (Scan 586, m/z=675.2500, z=1, RT=20.00, ppm=1318.8):
 


Prepared with PEAKS ™ (bioinfor.com)