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 Matches55
Peptide Sequences41
Protein Groups14
Proteins21
Proteins (#Unique Peptides)3 (>2); 2 (=2); 16 (=1);
FDR (Peptide-Spectrum Matches)40.0%
FDR (Peptide Sequences)53.7%
FDR (Protein)38.1%
De Novo Only Spectra58
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0230C
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 30328100

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: 30_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 10567 tr|A0A1E1WVY8|A0A1E1WVY8_TITOB 133.51 58 6 6 Y 10060 Putative sodium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
2 46545 tr|A0A1E1WW05|A0A1E1WW05_TITOB 93.69 54 5 3 Y 8972 Putative sodium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
3 44510 tr|A0A1E1WVN4|A0A1E1WVN4_TITOB 84.10 35 3 3 Y 9938 Putative insulin-like protein growth factor binding protein OS=Tityus obscurus OX=1221240 PE=4 SV=1
4 46991 tr|A0A1E1WWK1|A0A1E1WWK1_TITOB 55.15 35 3 1 Y 9302 Putative sodium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
5 159 sp|P84685|SCX6_TITOB 45.88 25 3 1 Y 9385 Toxin To6 OS=Tityus obscurus OX=1221240 PE=1 SV=2
8 7764 tr|A0A2I9LPY0|A0A2I9LPY0_9SCOR 35.32 1 2 2 N 118515 E1 ubiquitin-activating enzyme OS=Centruroides hentzi OX=88313 PE=3 SV=1
8 10616 tr|A0A1W7R9A6|A0A1W7R9A6_9SCOR 35.32 1 2 2 N 117849 E1 ubiquitin-activating enzyme OS=Hadrurus spadix OX=141984 PE=3 SV=1
7 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 34.24 16 1 1 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
6 46720 sp|H1ZZI2|SCX13_TITOB 28.90 13 1 1 Y 10112 Sodium channel toxin To13 OS=Tityus obscurus OX=1221240 PE=3 SV=1
24 13712 tr|A0A2I9LPT1|A0A2I9LPT1_9SCOR 25.54 2 1 1 N 59583 T-complex protein 1 subunit theta OS=Centruroides hentzi OX=88313 PE=3 SV=1
18 20803 tr|A0A2I9LPL1|A0A2I9LPL1_9SCOR 24.83 2 1 1 N 34479 Large ribosomal subunit protein uL18 OS=Centruroides hentzi OX=88313 PE=3 SV=1
18 20804 tr|A0A1W7R9P7|A0A1W7R9P7_9SCOR 24.83 2 1 1 N 34693 Large ribosomal subunit protein uL18 OS=Hadrurus spadix OX=141984 PE=3 SV=1
20 6392 tr|A0A2I9LPF5|A0A2I9LPF5_9SCOR 24.32 3 1 1 N 22038 Peroxiredoxin 1 OS=Centruroides hentzi OX=88313 PE=3 SV=1
20 18696 tr|A0A1W7RAW8|A0A1W7RAW8_9SCOR 24.32 1 1 1 N 71142 ATP-binding cassette sub-family F member 2 OS=Hadrurus spadix OX=141984 PE=4 SV=1
20 11823 tr|A0A8K1K0X6|A0A8K1K0X6_HEMLE 24.32 1 1 1 N 51819 Citrate synthase OS=Hemiscorpius lepturus OX=520031 PE=2 SV=1
20 47094 tr|A0A1W7RAT1|A0A1W7RAT1_9SCOR 24.32 1 1 1 N 52665 Carboxypeptidase OS=Hadrurus spadix OX=141984 PE=3 SV=1
20 5164 tr|A0A7C3SY83|A0A7C3SY83_UNCHY 24.32 1 1 1 N 76375 Uncharacterized protein OS=Hydrogenedentes bacterium OX=2030809 GN=ENW01_15725 PE=4 SV=1
20 4959 tr|A0A1W7RAP5|A0A1W7RAP5_9SCOR 24.32 1 1 1 N 98016 Cubilin OS=Hadrurus spadix OX=141984 PE=4 SV=1
25 46999 tr|C5J8B0|C5J8B0_OPICY 23.99 4 1 1 N 20549 Hemocyanin-like peptide (Fragment) OS=Opisthacanthus cayaporum OX=573324 GN=HC PE=2 SV=1
9 6384 tr|A0A1W7RA79|A0A1W7RA79_9SCOR 22.25 1 1 1 N 65318 Matrix metalloproteinase-16 OS=Hadrurus spadix OX=141984 PE=3 SV=1
49 19658 tr|A0A1S5QN64|A0A1S5QN64_TITSE 21.99 1 1 1 N 68613 Serine protease 5 OS=Tityus serrulatus OX=6887 PE=2 SV=1
total 21 proteins

tr|A0A1E1WVY8|A0A1E1WVY8_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.AAC(+57.02)YC(+57.02)YGLPDDSPTK.T Y 72.04 1716.7123 -33.2 859.3350 2 23.74 720 2 65 79 Carbamidomethylation
R.NC(+57.02)MLDC(+57.02)NILDDK.G Y 46.12 1509.6262 -0.5 755.8200 2 28.71 902 1 32 43 Carbamidomethylation
C.KKDDYPVDTAK.R Y 45.27 1278.6455 767.3 427.5495 3 11.98 274 3 20 30
Y.C(+57.02)YGLPDDSPTK.T Y 41.12 1251.5441 -286.6 626.6000 2 21.57 638 2 69 79 Carbamidomethylation
R.KADSGYC(+57.02)YK.L Y 37.98 1090.4753 -9.1 546.2400 2 10.27 208 3 54 62 Carbamidomethylation
R.C(+57.02)NPNL.R Y 32.64 616.2639 -1.9 617.2700 1 12.82 306 2 84 88 Carbamidomethylation
total 6 peptides
Best Unique PSM (Scan 720, m/z=859.3350, z=2, RT=23.74, ppm=-33.2):
tr|A0A1E1WW05|A0A1E1WW05_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.IYC(+57.02)PDDAVC(+57.02)KDTC(+57.02)K.N Y 45.66 1743.7266 0.9 582.2500 3 19.04 542 2 34 47 Carbamidomethylation
K.GC(+57.02)YC(+57.02)YDVAPSTK.M Y 44.14 1419.5798 3.9 710.8000 2 19.72 568 2 63 74 Carbamidomethylation
K.IYC(+57.02)PDDAVC(+57.02)K.D Y 42.67 1239.5264 -0.7 620.7700 2 18.86 536 2 34 43 Carbamidomethylation
G.EAIDGYPLSK.N N 26.82 1091.5498 -3.9 546.7800 2 22.81 684 2 19 28
K.M(+15.99)YPGRLPC(+57.02)N N 25.12 1122.4950 0.4 562.2550 2 18.26 514 2 75 83 Oxidation (M); Carbamidomethylation
total 5 peptides
Best Unique PSM (Scan 542, m/z=582.2500, z=3, RT=19.04, ppm=0.9):
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.VPDNSSDNTGIC(+57.02)K.K Y 51.99 1405.6144 -6.4 703.8100 2 14.37 364 1 78 90 Carbamidomethylation
R.KDC(+57.02)PAGIVK.D Y 39.84 986.5219 -16.6 494.2600 2 12.50 294 2 35 43 Carbamidomethylation
R.C(+57.02)EETVC(+57.02)SLKQ.R Y 36.57 1252.5427 2.2 627.2800 2 16.36 440 2 24 33 Carbamidomethylation
total 3 peptides
Best Unique PSM (Scan 364, m/z=703.8100, z=2, RT=14.37, ppm=-6.4):
tr|A0A1E1WWK1|A0A1E1WWK1_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.IYC(+57.02)PNDEVC(+57.02)K.D Y 33.36 1296.5479 -17.2 649.2700 2 17.72 492 2 34 43 Carbamidomethylation
T.EALDGYPLSK.N N 26.82 1091.5498 -3.9 546.7800 2 22.81 684 2 19 28
K.M(+15.99)YPGRLPC(+57.02)N.A N 25.12 1122.4950 0.4 562.2550 2 18.26 514 2 75 83 Oxidation (M); Carbamidomethylation
total 3 peptides
Best Unique PSM (Scan 492, m/z=649.2700, z=2, RT=17.72, ppm=-17.2):
sp|P84685|SCX6_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.EALDGYPLSK.N N 26.82 1091.5498 -3.9 546.7800 2 22.81 684 2 19 28
E.M(+15.99)YPGRLPC(+57.02)N.P N 25.12 1122.4950 0.4 562.2550 2 18.26 514 2 75 83 Oxidation (M); Carbamidomethylation
R.LPC(+57.02)NPY Y 19.50 762.3370 -5.6 763.3400 1 19.67 566 1 80 85 Carbamidomethylation
total 3 peptides
Best Unique PSM (Scan 566, m/z=763.3400, z=1, RT=19.67, ppm=-5.6):
tr|A0A2I9LPY0|A0A2I9LPY0_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.NVILGGVK.S Y 27.55 798.4963 -4.5 799.5000 1 19.62 564 1 91 98
N.VILGGVK.S Y 15.54 684.4534 -0.9 685.4600 1 17.51 484 1 92 98
total 2 peptides
Best Unique PSM (Scan 564, m/z=799.5000, z=1, RT=19.62, ppm=-4.5):
tr|A0A1W7R9A6|A0A1W7R9A6_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.NVILGGVK.S Y 27.55 798.4963 -4.5 799.5000 1 19.62 564 1 91 98
N.VILGGVK.S Y 15.54 684.4534 -0.9 685.4600 1 17.51 484 1 92 98
total 2 peptides
Best Unique PSM (Scan 564, m/z=799.5000, z=1, RT=19.62, ppm=-4.5):
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 34.24 1250.5271 -1.3 626.2700 2 13.30 324 2 32 41 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 324, m/z=626.2700, z=2, RT=13.30, ppm=-1.3):
sp|H1ZZI2|SCX13_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
W.C(+57.02)DNIPDTVVTWK.N Y 28.90 1446.6813 2.9 724.3500 2 28.38 890 2 69 80 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 890, m/z=724.3500, z=2, RT=28.38, ppm=2.9):
tr|A0A2I9LPT1|A0A2I9LPT1_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
R.LIPGGGASE.I Y 25.54 799.4075 -1144.4 799.5000 1 19.33 554 1 408 416
total 1 peptides
Best Unique PSM (Scan 554, m/z=799.5000, z=1, RT=19.33, ppm=-1144.4):
tr|A0A2I9LPL1|A0A2I9LPL1_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.YNTPK.Y Y 24.83 621.3122 0.9 622.3200 1 5.51 22 2 44 48
total 1 peptides
Best Unique PSM (Scan 22, m/z=622.3200, z=1, RT=5.51, ppm=0.9):
tr|A0A1W7R9P7|A0A1W7R9P7_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.YNTPK.Y Y 24.83 621.3122 0.9 622.3200 1 5.51 22 2 44 48
total 1 peptides
Best Unique PSM (Scan 22, m/z=622.3200, z=1, RT=5.51, ppm=0.9):
tr|A0A2I9LPF5|A0A2I9LPF5_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
P.LLADK.S Y 24.32 558.3377 26.9 559.3600 1 20.53 598 1 103 107
total 1 peptides
Best Unique PSM (Scan 598, m/z=559.3600, z=1, RT=20.53, ppm=26.9):
tr|A0A1W7RAW8|A0A1W7RAW8_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.IIADK.T Y 24.32 558.3377 26.9 559.3600 1 20.53 598 1 381 385
total 1 peptides
Best Unique PSM (Scan 598, m/z=559.3600, z=1, RT=20.53, ppm=26.9):
tr|A0A8K1K0X6|A0A8K1K0X6_HEMLE
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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.ILADK.I Y 24.32 558.3377 26.9 559.3600 1 20.53 598 1 38 42
total 1 peptides
Best Unique PSM (Scan 598, m/z=559.3600, z=1, RT=20.53, ppm=26.9):
tr|A0A1W7RAT1|A0A1W7RAT1_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
R.LLADK.R Y 24.32 558.3377 26.9 559.3600 1 20.53 598 1 297 301
total 1 peptides
Best Unique PSM (Scan 598, m/z=559.3600, z=1, RT=20.53, ppm=26.9):
tr|A0A7C3SY83|A0A7C3SY83_UNCHY
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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
V.LLADK.I Y 24.32 558.3377 26.9 559.3600 1 20.53 598 1 135 139
total 1 peptides
Best Unique PSM (Scan 598, m/z=559.3600, z=1, RT=20.53, ppm=26.9):
tr|A0A1W7RAP5|A0A1W7RAP5_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
E.IIADK.K Y 24.32 558.3377 26.9 559.3600 1 20.53 598 1 198 202
total 1 peptides
Best Unique PSM (Scan 598, m/z=559.3600, z=1, RT=20.53, ppm=26.9):
tr|C5J8B0|C5J8B0_OPICY
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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.PVDERDPR.L Y 23.99 982.4832 2.3 492.2500 2 11.14 242 1 26 33
total 1 peptides
Best Unique PSM (Scan 242, m/z=492.2500, z=2, RT=11.14, ppm=2.3):
tr|A0A1W7RA79|A0A1W7RA79_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
D.GIADGYPR.L Y 22.25 847.4188 0.8 424.7170 2 10.58 220 2 325 332
total 1 peptides
Best Unique PSM (Scan 220, m/z=424.7170, z=2, RT=10.58, ppm=0.8):
tr|A0A1S5QN64|A0A1S5QN64_TITSE
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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
V.RPPLF.P Y 21.99 628.3696 -11.0 629.3700 1 18.67 528 1 321 325
total 1 peptides
Best Unique PSM (Scan 528, m/z=629.3700, z=1, RT=18.67, ppm=-11.0):
 


Prepared with PEAKS ™ (bioinfor.com)