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 Scans992
# of MS/MS Scans992
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 Matches26
Peptide Sequences21
Protein Groups8
Proteins15
Proteins (#Unique Peptides)1 (>2); 1 (=2); 13 (=1);
FDR (Peptide-Spectrum Matches)61.5%
FDR (Peptide Sequences)76.2%
FDR (Protein)26.7%
De Novo Only Spectra20
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.029C
Oxidation15.992M

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 9135300

4. Other Information

Table 6. Search parameters.
Search Engine Name: PEAKS 7.0
Parent Mass Error Tolerance: 0.1 Da
Fragment Mass Error Tolerance: 0.1 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: 9_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 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 101.62 37 4 4 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
2 9349 tr|A0A1E1WVM2|A0A1E1WVM2_TITOB 61.08 8 2 2 N 19508 Corticotropin-releasing factor domain-containing protein OS=Tityus obscurus OX=1221240 PE=4 SV=1
3 6157 sp|P00760|TRY1_BOVIN 42.07 8 1 1 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
13 45510 sp|C0HLM0|SCX2_TITMA 31.86 14 1 1 N 7830 Toxin Tma2 OS=Tityus macrochirus OX=2599738 PE=1 SV=1
13 45508 sp|C0HLM1|SCX3_TITMA 31.86 14 1 1 N 7836 Toxin Tma3 OS=Tityus macrochirus OX=2599738 PE=1 SV=1
13 44589 sp|H1ZZI3|SCX14_TITOB 31.86 11 1 1 N 10106 Toxin To14 OS=Tityus obscurus OX=1221240 PE=1 SV=1
17 16584 tr|A0A2I9LNW9|A0A2I9LNW9_9SCOR 27.06 1 1 1 N 57810 Cytochrome P450 OS=Centruroides hentzi OX=88313 PE=3 SV=1
14 19668 tr|A0A1W7RAC7|A0A1W7RAC7_9SCOR 23.97 1 1 1 N 82445 Heat shock protein 83 OS=Hadrurus spadix OX=141984 PE=3 SV=1
14 13644 tr|Q5WQZ6|Q5WQZ6_OPICA 23.97 1 1 1 N 83121 Heat shock protein 83 OS=Opistophthalmus carinatus OX=190115 GN=HSP90 PE=2 SV=1
15 23801 tr|R0H4W2|R0H4W2_9BRAS 21.42 14 1 1 N 9047 Knottin scorpion toxin-like domain-containing protein OS=Capsella rubella OX=81985 GN=CARUB_v10007092mg PE=4 SV=1
11 109873 tr|A0A7D4W9M1|A0A7D4W9M1_HELAN 20.52 15 1 1 N 7817 Putative gamma-thionin (Fragment) OS=Helianthus annuus OX=4232 PE=4 SV=1
11 109874 sp|P22357|SF18_HELAN 20.52 7 1 1 N 15363 Anther-specific protein SF18 (Fragment) OS=Helianthus annuus OX=4232 PE=2 SV=1
11 44659 tr|A0A9K3DR31|A0A9K3DR31_HELAN 20.52 6 1 1 N 16978 Defensin, plant, knottin, scorpion toxin-like superfamily OS=Helianthus annuus OX=4232 GN=HanXRQr2_Chr16g0732561 PE=4 SV=1
11 5120 tr|A0A9K3DPA5|A0A9K3DPA5_HELAN 20.52 6 1 1 N 17826 Defensin, plant, knottin, scorpion toxin-like superfamily OS=Helianthus annuus OX=4232 GN=HanXRQr2_Chr16g0732551 PE=4 SV=1
11 5121 tr|A0A251RX36|A0A251RX36_HELAN 20.52 3 1 1 N 34729 Putative gamma-thionin OS=Helianthus annuus OX=4232 GN=HannXRQ_Chr16g0506041 PE=4 SV=1
total 15 proteins

tr|A0A1E1WVU5|A0A1E1WVU5_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.SDC(+57.02)KPDLC(+57.02)EK.A Y 63.42 1250.5271 -1.3 626.2700 2 13.64 330 3 32 41 Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)K.G Y 42.63 997.4361 -10.7 499.7200 2 11.74 258 1 48 55 Oxidation (M); Carbamidomethylation
S.DC(+57.02)KPDLC(+57.02)EK.A Y 36.14 1163.4951 -8.3 582.7500 2 14.12 348 1 33 41 Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)KGDTC(+57.02)K.C Y 19.33 1558.6578 0.2 520.5600 3 12.27 278 2 48 60 Oxidation (M); Carbamidomethylation
total 4 peptides
Best Unique PSM (Scan 330, m/z=626.2700, z=2, RT=13.64, ppm=-1.3):
tr|A0A1E1WVM2|A0A1E1WVM2_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.DYSKEDINRPNPD.L Y 47.93 1561.7008 -8.1 521.5700 3 17.07 458 3 26 38
V.GDYSKEDINRPNPD.L Y 26.28 1618.7223 -35.1 810.3400 2 17.67 480 1 25 38
total 2 peptides
Best Unique PSM (Scan 458, m/z=521.5700, z=3, RT=17.07, ppm=-8.1):
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 42.07 2162.0491 79.2 1082.1174 2 30.86 970 2 73 92
total 1 peptides
Best Unique PSM (Scan 970, m/z=1082.1174, z=2, RT=30.86, ppm=79.2):
sp|C0HLM0|SCX2_TITMA
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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
KKDDYPVDTA.E Y 31.86 1150.5505 -4.4 576.2800 2 14.33 356 1 1 10
total 1 peptides
Best Unique PSM (Scan 356, m/z=576.2800, z=2, RT=14.33, ppm=-4.4):
sp|C0HLM1|SCX3_TITMA
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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
KKDDYPVDTA.K Y 31.86 1150.5505 -4.4 576.2800 2 14.33 356 1 1 10
total 1 peptides
Best Unique PSM (Scan 356, m/z=576.2800, z=2, RT=14.33, ppm=-4.4):
sp|H1ZZI3|SCX14_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
C.KKDDYPVDTA.K Y 31.86 1150.5505 -4.4 576.2800 2 14.33 356 1 20 29
total 1 peptides
Best Unique PSM (Scan 356, m/z=576.2800, z=2, RT=14.33, ppm=-4.4):
tr|A0A2I9LNW9|A0A2I9LNW9_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
K.ESEDI.Q Y 27.06 591.2388 6.7 592.2500 1 6.49 60 1 344 348
total 1 peptides
Best Unique PSM (Scan 60, m/z=592.2500, z=1, RT=6.49, ppm=6.7):
tr|A0A1W7RAC7|A0A1W7RAC7_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
K.HSQFIGYPIK.L Y 23.97 1188.6292 -19.9 595.3100 2 38.02 1232 1 206 215
total 1 peptides
Best Unique PSM (Scan 1232, m/z=595.3100, z=2, RT=38.02, ppm=-19.9):
tr|Q5WQZ6|Q5WQZ6_OPICA
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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.HSQFIGYPIK.L Y 23.97 1188.6292 -19.9 595.3100 2 38.02 1232 1 206 215
total 1 peptides
Best Unique PSM (Scan 1232, m/z=595.3100, z=2, RT=38.02, ppm=-19.9):
tr|R0H4W2|R0H4W2_9BRAS
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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.SMLKVNDAQRR.F Y 21.42 1316.6982 35.9 659.3800 2 53.43 1812 1 28 38
total 1 peptides
Best Unique PSM (Scan 1812, m/z=659.3800, z=2, RT=53.43, ppm=35.9):
tr|A0A7D4W9M1|A0A7D4W9M1_HELAN
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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.NPGPPPGAPGT Y 20.52 960.4664 40.6 481.2600 2 24.03 714 2 61 71
total 1 peptides
Best Unique PSM (Scan 714, m/z=481.2600, z=2, RT=24.03, ppm=40.6):
sp|P22357|SF18_HELAN
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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.NPGPPPGAPGT.P Y 20.52 960.4664 40.6 481.2600 2 24.03 714 2 70 80
total 1 peptides
Best Unique PSM (Scan 714, m/z=481.2600, z=2, RT=24.03, ppm=40.6):
tr|A0A9K3DR31|A0A9K3DR31_HELAN
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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.NPGPPPGAPGT.P Y 20.52 960.4664 40.6 481.2600 2 24.03 714 2 92 102
total 1 peptides
Best Unique PSM (Scan 714, m/z=481.2600, z=2, RT=24.03, ppm=40.6):
tr|A0A9K3DPA5|A0A9K3DPA5_HELAN
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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.NPGPPPGAPGT.P Y 20.52 960.4664 40.6 481.2600 2 24.03 714 2 92 102
total 1 peptides
Best Unique PSM (Scan 714, m/z=481.2600, z=2, RT=24.03, ppm=40.6):
tr|A0A251RX36|A0A251RX36_HELAN
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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.NPGPPPGAPGT.P Y 20.52 960.4664 40.6 481.2600 2 24.03 714 2 92 102
total 1 peptides
Best Unique PSM (Scan 714, m/z=481.2600, z=2, RT=24.03, ppm=40.6):
 


Prepared with PEAKS ™ (bioinfor.com)