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 Scans987
# of MS/MS Scans987
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 Sequences38
Protein Groups14
Proteins18
Proteins (#Unique Peptides)2 (>2); 2 (=2); 14 (=1);
FDR (Peptide-Spectrum Matches)25.5%
FDR (Peptide Sequences)31.6%
FDR (Protein)27.8%
De Novo Only Spectra31
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0224C
Oxidation15.994M

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 432810000

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: 43_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 70267 tr|A0A1E1WVN8|A0A1E1WVN8_TITOB 118.06 43 6 6 Y 12853 Venom protein OS=Tityus obscurus OX=1221240 PE=4 SV=1
3 10567 tr|A0A1E1WVY8|A0A1E1WVY8_TITOB 67.29 27 2 2 Y 10060 Putative sodium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
3 44589 sp|H1ZZI3|SCX14_TITOB 67.29 27 2 2 Y 10106 Toxin To14 OS=Tityus obscurus OX=1221240 PE=1 SV=1
12 70268 tr|A0A1E1WVR3|A0A1E1WVR3_TITOB 66.12 13 1 1 Y 12355 Putative secreted protein (Fragment) OS=Tityus obscurus OX=1221240 PE=4 SV=1
12 70269 tr|A0A1E1WVN2|A0A1E1WVN2_TITOB 66.12 13 1 1 Y 12454 Putative secreted protein (Fragment) OS=Tityus obscurus OX=1221240 PE=4 SV=1
2 23721 tr|A0A1E1WVU0|A0A1E1WVU0_TITOB 43.94 11 3 3 N 9716 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
13 9350 tr|C9X4G4|C9X4G4_TITDI 43.68 11 1 1 Y 10469 Uncharacterized protein (Fragment) OS=Tityus discrepans OX=57059 PE=2 SV=1
6 10556 tr|A0A1L4BJ76|A0A1L4BJ76_HEMLE 28.65 2 1 1 N 50571 Venom toxin OS=Hemiscorpius lepturus OX=520031 PE=2 SV=1
41 101 tr|A0A2I9LPU7|A0A2I9LPU7_9SCOR 26.59 0 1 1 Y 114433 Metalloendopeptidase OS=Centruroides hentzi OX=88313 PE=3 SV=1
22 70275 tr|A0A8R7U1Y0|A0A8R7U1Y0_TRIUA 26.47 5 1 1 Y 12796 Knottin scorpion toxin-like domain-containing protein OS=Triticum urartu OX=4572 PE=4 SV=1
5 7541 tr|A0A2I9LP25|A0A2I9LP25_9SCOR 25.76 2 2 1 N 72654 Heat shock 70 kDa protein OS=Centruroides hentzi OX=88313 PE=3 SV=1
23 70278 tr|A0A1E1WWE7|A0A1E1WWE7_TITOB 24.68 9 1 1 Y 13264 Putative phospholipase A2 (Fragment) OS=Tityus obscurus OX=1221240 PE=3 SV=1
15 70280 tr|A0A2I9LNN6|A0A2I9LNN6_9SCOR 24.17 3 1 1 N 23285 ADP-ribosylation factor-like protein 6-interacting protein 1 OS=Centruroides hentzi OX=88313 PE=4 SV=1
14 13777 tr|A0A2I9LNY7|A0A2I9LNY7_9SCOR 22.92 2 1 1 N 61114 EH domain-containing protein 3 OS=Centruroides hentzi OX=88313 PE=4 SV=1
35 44682 tr|A0A2I9LNW1|A0A2I9LNW1_9SCOR 22.47 1 1 1 N 68693 Ceramide transfer protein OS=Centruroides hentzi OX=88313 PE=4 SV=1
35 44650 tr|A0A1W7RAQ4|A0A1W7RAQ4_9SCOR 22.47 1 1 1 N 69427 Ceramide transfer protein OS=Hadrurus spadix OX=141984 PE=4 SV=1
32 22603 tr|A0A834SYJ6|A0A834SYJ6_9FABA 20.26 8 1 1 N 7090 Putative defensin-like protein 244 OS=Senna tora OX=362788 GN=G2W53_032207 PE=4 SV=1
32 22605 tr|A0A1E1WVV4|A0A1E1WVV4_TITOB 20.26 5 1 1 N 9994 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
total 18 proteins

tr|A0A1E1WVN8|A0A1E1WVN8_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.FFDC(+57.02)LYNTATK.E Y 65.78 1378.6227 321.1 690.5400 2 29.61 942 5 36 46 Carbamidomethylation
K.C(+57.02)ASEQNIPIDSK.E Y 50.52 1360.6293 -2.8 681.3200 2 17.64 486 3 55 66 Carbamidomethylation
R.RDFIC(+57.02)DR.N Y 39.15 980.4498 675.6 491.5634 2 15.55 410 3 69 75 Carbamidomethylation
K.YC(+57.02)AHIDAVK.F Y 29.56 1075.5121 -6.2 538.7600 2 16.02 426 1 27 35 Carbamidomethylation
K.TVDIC(+57.02)M(+15.99)KQ Y 18.61 1009.4573 998.7 506.2400 2 14.15 356 2 103 110 Carbamidomethylation; Oxidation (M)
R.DFIC(+57.02)DR.N Y 17.06 824.3487 -20.9 413.1730 2 18.12 504 1 70 75 Carbamidomethylation
total 6 peptides
Best Unique PSM (Scan 942, m/z=690.5400, z=2, RT=29.61, ppm=321.1):
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 46.41 1716.7123 -4.0 859.3600 2 23.90 726 1 65 79 Carbamidomethylation
R.KADSGYC(+57.02)YK.L Y 41.75 1090.4753 -9.1 546.2400 2 10.84 230 3 54 62 Carbamidomethylation
total 2 peptides
Best Unique PSM (Scan 726, m/z=859.3600, z=2, RT=23.90, ppm=-4.0):
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
K.AAC(+57.02)YC(+57.02)YGLPDDSPTK.T Y 46.41 1716.7123 -4.0 859.3600 2 23.90 726 1 65 79 Carbamidomethylation
R.KADSGYC(+57.02)YK.L Y 41.75 1090.4753 -9.1 546.2400 2 10.84 230 3 54 62 Carbamidomethylation
total 2 peptides
Best Unique PSM (Scan 726, m/z=859.3600, z=2, RT=23.90, ppm=-4.0):
tr|A0A1E1WVR3|A0A1E1WVR3_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.VTDLTGFVDLTC(+57.02)NR.I Y 66.12 1609.7770 30.1 805.9200 2 33.56 1088 1 53 66 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1088, m/z=805.9200, z=2, RT=33.56, ppm=30.1):
tr|A0A1E1WVN2|A0A1E1WVN2_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.VTDLTGFVDLTC(+57.02)NR.I Y 66.12 1609.7770 30.1 805.9200 2 33.56 1088 1 54 67 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1088, m/z=805.9200, z=2, RT=33.56, ppm=30.1):
tr|A0A1E1WVU0|A0A1E1WVU0_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
S.LIPDETLR.N Y 26.08 955.5338 -8.8 478.7700 2 21.97 654 2 32 39
L.VSLIPDETLR.N Y 22.30 1141.6343 9.8 571.8300 2 28.29 892 2 30 39
I.PDETLR.N Y 20.11 729.3657 -4.1 730.3700 1 24.70 756 1 34 39
total 3 peptides
Best Unique PSM (Scan 654, m/z=478.7700, z=2, RT=21.97, ppm=-8.8):
tr|C9X4G4|C9X4G4_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
K.FFC(+57.02)DASNETK.V Y 43.68 1217.5023 2.6 609.7600 2 18.02 500 1 51 60 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 500, m/z=609.7600, z=2, RT=18.02, ppm=2.6):
tr|A0A1L4BJ76|A0A1L4BJ76_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
K.YSDEETR.I Y 28.65 898.3668 -1.5 450.1900 2 12.66 300 2 51 57
total 1 peptides
Best Unique PSM (Scan 300, m/z=450.1900, z=2, RT=12.66, ppm=-1.5):
tr|A0A2I9LPU7|A0A2I9LPU7_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.YC(+57.02)GYK.V Y 26.59 689.2843 -2.3 690.2900 1 9.21 166 1 525 529 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 166, m/z=690.2900, z=1, RT=9.21, ppm=-2.3):
tr|A0A8R7U1Y0|A0A8R7U1Y0_TRIUA
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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.KIC(+57.02)TDK.E Y 26.47 763.3898 -48.6 764.3600 1 9.01 158 1 40 45 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 158, m/z=764.3600, z=1, RT=9.01, ppm=-48.6):
tr|A0A2I9LP25|A0A2I9LP25_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.KEGEK.N Y 17.40 589.3071 1545.2 591.2250 1 7.79 112 1 217 221
V.NGILK.V N 16.71 543.3380 1665.1 545.2500 1 13.14 318 1 509 513
total 2 peptides
Best Unique PSM (Scan 112, m/z=591.2250, z=1, RT=7.79, ppm=1545.2):
tr|A0A1E1WWE7|A0A1E1WWE7_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
R.KGC(+57.02)EC(+57.02)DEEFR.N Y 24.68 1328.5125 9.8 665.2700 2 12.90 310 1 58 67 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 310, m/z=665.2700, z=2, RT=12.90, ppm=9.8):
tr|A0A2I9LNN6|A0A2I9LNN6_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.NFAGPK.V Y 24.17 632.3282 1446.3 634.2500 1 5.61 26 2 197 202
total 1 peptides
Best Unique PSM (Scan 26, m/z=634.2500, z=1, RT=5.61, ppm=1446.3):
tr|A0A2I9LNY7|A0A2I9LNY7_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.KEMPSVFGK.D Y 22.92 1021.5266 938.6 512.2500 2 16.57 446 1 316 324
total 1 peptides
Best Unique PSM (Scan 446, m/z=512.2500, z=2, RT=16.57, ppm=938.6):
tr|A0A2I9LNW1|A0A2I9LNW1_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.FTQYVK.D Y 22.47 784.4119 -25.9 393.2031 2 18.89 532 1 583 588
total 1 peptides
Best Unique PSM (Scan 532, m/z=393.2031, z=2, RT=18.89, ppm=-25.9):
tr|A0A1W7RAQ4|A0A1W7RAQ4_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.FTQYVK.D Y 22.47 784.4119 -25.9 393.2031 2 18.89 532 1 591 596
total 1 peptides
Best Unique PSM (Scan 532, m/z=393.2031, z=2, RT=18.89, ppm=-25.9):
tr|A0A834SYJ6|A0A834SYJ6_9FABA
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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.EFLGK.Y Y 20.26 592.3220 1.2 593.3300 1 14.69 376 1 31 35
total 1 peptides
Best Unique PSM (Scan 376, m/z=593.3300, z=1, RT=14.69, ppm=1.2):
tr|A0A1E1WVV4|A0A1E1WVV4_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.EFLGK.I Y 20.26 592.3220 1.2 593.3300 1 14.69 376 1 30 34
total 1 peptides
Best Unique PSM (Scan 376, m/z=593.3300, z=1, RT=14.69, ppm=1.2):
 


Prepared with PEAKS ™ (bioinfor.com)