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 Scans1007
# of MS/MS Scans1007
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 Matches29
Peptide Sequences22
Protein Groups8
Proteins15
Proteins (#Unique Peptides)2 (>2); 0 (=2); 13 (=1);
FDR (Peptide-Spectrum Matches)51.7%
FDR (Peptide Sequences)68.2%
FDR (Protein)60.0%
De Novo Only Spectra36
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 20174100

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: 20_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 73.33 11 3 3 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
2 26633 tr|A0A1E1WVQ0|A0A1E1WVQ0_TITOB 54.75 26 3 3 Y 6918 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
16 20825 tr|A0A8S1EK64|A0A8S1EK64_9PELO 29.64 5 1 1 N 15010 Knottin scorpion toxin-like domain-containing protein OS=Caenorhabditis bovis OX=2654633 GN=CBOVIS_LOCUS6577 PE=4 SV=1
3 22611 sp|P60210|KAX44_TITOB 28.13 16 1 1 N 3878 Potassium channel toxin alpha-KTx 4.4 OS=Tityus obscurus OX=1221240 PE=1 SV=1
3 26645 sp|P59925|KAX43_TITDI 28.13 16 1 1 N 3826 Potassium channel toxin alpha-KTx 4.3 OS=Tityus discrepans OX=57059 PE=1 SV=1
18 26646 sp|C0HL59|NDB4A_ISOMC 24.72 35 1 1 N 1700 Peptide Im-4 OS=Isometrus maculatus OX=497827 PE=1 SV=1
18 11772 sp|P0DQT2|TOAP3_TITOB 24.72 35 1 1 N 1700 Antimicrobial peptide ToAP3 OS=Tityus obscurus OX=1221240 PE=1 SV=1
18 11777 tr|A0A0U1S866|A0A0U1S866_ISOMC 24.72 9 1 1 N 7494 Uncharacterized protein OS=Isometrus maculatus OX=497827 PE=2 SV=1
18 11779 sp|P0CI90|NDB4T_LYCMC 24.72 8 1 1 N 8480 Antimicrobial peptide 143 OS=Lychas mucronatus OX=172552 PE=3 SV=1
18 11780 tr|A0A0U1SPC4|A0A0U1SPC4_ISOMC 24.72 8 1 1 N 8763 Antimicrobial peptide OS=Isometrus maculatus OX=497827 PE=2 SV=1
18 26647 sp|G8YYA6|NDB4C_ANDAM 24.72 8 1 1 N 8539 Antimicrobial peptide 2 OS=Androctonus amoreuxi OX=112024 PE=1 SV=1
4 6351 tr|A0A509ZVT9|A0A509ZVT9_MESMA 23.72 1 1 1 N 164057 Dscam2 (Fragment) OS=Mesobuthus martensii OX=34649 PE=2 SV=1
19 26648 tr|A0A8S3Y771|A0A8S3Y771_PARAO 22.27 6 1 1 N 23350 (apollo) hypothetical protein OS=Parnassius apollo OX=110799 GN=PAPOLLO_LOCUS25573 PE=4 SV=1
19 26649 tr|A0A8S3Y833|A0A8S3Y833_PARAO 22.27 5 1 1 N 28556 (apollo) hypothetical protein OS=Parnassius apollo OX=110799 GN=PAPOLLO_LOCUS25573 PE=4 SV=1
5 26651 tr|A0A1V1WBL6|A0A1V1WBL6_9SCOR 21.41 8 1 1 N 8967 Putative NDBP OS=Superstitionia donensis OX=311983 PE=4 SV=1
total 15 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 46.05 2162.0491 -85.0 1081.9399 2 30.87 990 3 73 92
D.NINVVEGNEQFISASK.S Y 42.00 1747.8740 6.6 874.9500 2 26.94 846 1 77 92
K.LQGIVSW.G Y 18.85 801.4385 -0.9 802.4450 1 30.26 968 1 210 216
total 3 peptides
Best Unique PSM (Scan 990, m/z=1081.9399, z=2, RT=30.87, ppm=-85.0):
tr|A0A1E1WVQ0|A0A1E1WVQ0_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
Q.THSDIIC(+57.02)NTTR.Q Y 35.57 1316.6143 -6.7 659.3100 2 14.57 378 1 25 35 Carbamidomethylation
S.DIIC(+57.02)NTTR.Q Y 24.88 991.4757 -10.4 496.7400 2 16.42 448 1 28 35 Carbamidomethylation
T.PC(+57.02)FIK.H Y 20.22 663.3414 2.0 664.3500 1 17.70 498 2 40 44 Carbamidomethylation
total 3 peptides
Best Unique PSM (Scan 378, m/z=659.3100, z=2, RT=14.57, ppm=-6.7):
tr|A0A8S1EK64|A0A8S1EK64_9PELO
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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.KLQNVLR.R Y 29.64 869.5447 -74.6 435.7472 2 11.87 270 1 107 113
total 1 peptides
Best Unique PSM (Scan 270, m/z=435.7472, z=2, RT=11.87, ppm=-74.6):
sp|P60210|KAX44_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
VFINVK.C Y 28.13 718.4377 -7.0 719.4400 1 19.40 566 3 1 6
total 1 peptides
Best Unique PSM (Scan 566, m/z=719.4400, z=1, RT=19.40, ppm=-7.0):
sp|P59925|KAX43_TITDI
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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
VFINVK.C Y 28.13 718.4377 -7.0 719.4400 1 19.40 566 3 1 6
total 1 peptides
Best Unique PSM (Scan 566, m/z=719.4400, z=1, RT=19.40, ppm=-7.0):
sp|C0HL59|NDB4A_ISOMC
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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
G.LISAIK Y 24.72 643.4268 -6.4 644.4300 1 16.52 452 1 12 17
total 1 peptides
Best Unique PSM (Scan 452, m/z=644.4300, z=1, RT=16.52, ppm=-6.4):
sp|P0DQT2|TOAP3_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
G.LISAIK Y 24.72 643.4268 -6.4 644.4300 1 16.52 452 1 12 17
total 1 peptides
Best Unique PSM (Scan 452, m/z=644.4300, z=1, RT=16.52, ppm=-6.4):
tr|A0A0U1S866|A0A0U1S866_ISOMC
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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
G.LISAIK.G Y 24.72 643.4268 -6.4 644.4300 1 16.52 452 1 24 29
total 1 peptides
Best Unique PSM (Scan 452, m/z=644.4300, z=1, RT=16.52, ppm=-6.4):
sp|P0CI90|NDB4T_LYCMC
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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
G.LISAIK.G Y 24.72 643.4268 -6.4 644.4300 1 16.52 452 1 33 38
total 1 peptides
Best Unique PSM (Scan 452, m/z=644.4300, z=1, RT=16.52, ppm=-6.4):
tr|A0A0U1SPC4|A0A0U1SPC4_ISOMC
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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
G.LISAIK.G Y 24.72 643.4268 -6.4 644.4300 1 16.52 452 1 34 39
total 1 peptides
Best Unique PSM (Scan 452, m/z=644.4300, z=1, RT=16.52, ppm=-6.4):
sp|G8YYA6|NDB4C_ANDAM
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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
G.LISAIK.G Y 24.72 643.4268 -6.4 644.4300 1 16.52 452 1 35 40
total 1 peptides
Best Unique PSM (Scan 452, m/z=644.4300, z=1, RT=16.52, ppm=-6.4):
tr|A0A509ZVT9|A0A509ZVT9_MESMA
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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
A.TPLSASTIK.V Y 23.72 916.5229 -171.8 459.1900 2 19.68 578 2 983 991
total 1 peptides
Best Unique PSM (Scan 578, m/z=459.1900, z=2, RT=19.68, ppm=-171.8):
tr|A0A8S3Y771|A0A8S3Y771_PARAO
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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
I.ILSLKDVLGDFLT.M Y 22.27 1432.8176 -78.3 717.3600 2 29.57 942 1 172 184
total 1 peptides
Best Unique PSM (Scan 942, m/z=717.3600, z=2, RT=29.57, ppm=-78.3):
tr|A0A8S3Y833|A0A8S3Y833_PARAO
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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
I.ILSLKDVLGDFLT.M Y 22.27 1432.8176 -78.3 717.3600 2 29.57 942 1 216 228
total 1 peptides
Best Unique PSM (Scan 942, m/z=717.3600, z=2, RT=29.57, ppm=-78.3):
tr|A0A1V1WBL6|A0A1V1WBL6_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
L.SSADLK.F Y 21.41 619.3177 88.9 620.3800 1 18.83 544 2 64 69
total 1 peptides
Best Unique PSM (Scan 544, m/z=620.3800, z=1, RT=18.83, ppm=88.9):
 


Prepared with PEAKS ™ (bioinfor.com)