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 Scans1004
# of MS/MS Scans1004
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 Matches76
Peptide Sequences55
Protein Groups14
Proteins21
Proteins (#Unique Peptides)5 (>2); 1 (=2); 15 (=1);
FDR (Peptide-Spectrum Matches)21.1%
FDR (Peptide Sequences)27.3%
FDR (Protein)33.3%
De Novo Only Spectra23
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0238C
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 45448300

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: 45_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 23721 tr|A0A1E1WVU0|A0A1E1WVU0_TITOB 115.22 41 6 6 Y 9716 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
1 71794 tr|A0A1E1WVT2|A0A1E1WVT2_TITOB 107.00 36 5 5 Y 9668 Putative sodium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
3 70278 tr|A0A1E1WWE7|A0A1E1WWE7_TITOB 87.46 25 4 4 Y 13264 Putative phospholipase A2 (Fragment) OS=Tityus obscurus OX=1221240 PE=3 SV=1
4 32736 tr|A0A1E1WVV0|A0A1E1WVV0_TITOB 82.54 7 3 3 Y 49029 Putative cysteine-rich protein OS=Tityus obscurus OX=1221240 PE=4 SV=1
5 6157 sp|P00760|TRY1_BOVIN 79.72 8 2 2 Y 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
6 10567 tr|A0A1E1WVY8|A0A1E1WVY8_TITOB 77.25 38 3 3 Y 10060 Putative sodium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
9 9350 tr|C9X4G4|C9X4G4_TITDI 53.74 11 1 1 Y 10469 Uncharacterized protein (Fragment) OS=Tityus discrepans OX=57059 PE=2 SV=1
27 27300 tr|A0A1E1WWF5|A0A1E1WWF5_TITOB 47.37 3 1 1 Y 43159 Putative metalloproteinase (Fragment) OS=Tityus obscurus OX=1221240 PE=3 SV=1
11 71787 sp|P84691|SC61_TITOB 38.13 90 1 1 N 1079 Toxin To61 (Fragment) OS=Tityus obscurus OX=1221240 PE=1 SV=1
11 71788 tr|A0A7L4XUQ7|A0A7L4XUQ7_TITPA 38.13 12 1 1 N 8023 Neurotoxin TpaCR3 OS=Tityus pachyurus OX=288781 PE=2 SV=1
11 51271 sp|H1ZZH7|SCX8_TITOB 38.13 10 1 1 N 9866 Toxin To8 OS=Tityus obscurus OX=1221240 PE=2 SV=1
11 71789 tr|A0A1E1WVW4|A0A1E1WVW4_TITOB 38.13 10 1 1 N 9795 Putative sodium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
28 20749 tr|A0A1E1WVN0|A0A1E1WVN0_TITOB 35.62 3 1 1 N 31480 Putative lectin OS=Tityus obscurus OX=1221240 PE=4 SV=1
28 7751 tr|A0A1E1WVQ4|A0A1E1WVQ4_TITOB 35.62 3 1 1 N 31627 Putative lectin OS=Tityus obscurus OX=1221240 PE=4 SV=1
29 22605 tr|A0A1E1WVV4|A0A1E1WVV4_TITOB 31.62 11 1 1 Y 9994 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
29 48468 sp|Q0GY43|KIK2_TITDI 31.62 11 1 1 Y 9960 Potassium channel toxin TdiKIK OS=Tityus discrepans OX=57059 PE=1 SV=1
29 17899 tr|A0A2I9LP49|A0A2I9LP49_9SCOR 31.62 11 1 1 Y 10286 KTx OS=Centruroides hentzi OX=88313 PE=4 SV=1
46 11886 tr|A0A1E1WVT1|A0A1E1WVT1_TITOB 21.51 1 1 1 N 82894 Putative endothelin-converting enzyme (Fragment) OS=Tityus obscurus OX=1221240 PE=3 SV=1
46 7482 tr|A0A812TXT4|A0A812TXT4_9DINO 21.51 1 1 1 N 100858 Uncharacterized protein OS=Symbiodinium natans OX=878477 GN=SNAT2548_LOCUS30740 PE=4 SV=1
31 55857 tr|A0A2N5ZQN8|A0A2N5ZQN8_9BACT 20.46 0 1 1 N 158113 Ig-like domain-containing protein OS=Candidatus Parcubacteria bacterium OX=2762014 GN=C0584_04300 PE=4 SV=1
30 22714 tr|A0A9D6ZEH8|A0A9D6ZEH8_UNCDE 20.21 2 1 1 Y 45906 SMP-30/Gluconolactonase/LRE-like region domain-containing protein OS=Deltaproteobacteria bacterium OX=2026735 GN=HY907_00960 PE=4 SV=1
total 21 proteins

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
K.HVQSLVSLIPDETLR.N Y 64.73 1705.9363 -6.4 853.9700 2 33.17 1082 1 25 39
Y.C(+57.02)MMHC(+57.02)QDIEK.H Y 39.18 1350.5189 4.9 676.2700 2 15.79 426 2 63 72 Carbamidomethylation
Q.SLVSLIPDETLR.N Y 36.23 1341.7504 -3.7 671.8800 2 34.23 1122 1 28 39
S.LVSLIPDETLR.N Y 34.73 1254.7183 5.7 628.3700 2 32.04 1040 2 29 39
H.VQSLVSLIPDETLR.N Y 29.00 1568.8773 -20.3 785.4300 2 35.88 1184 2 26 39
K.TQFGC(+57.02)PAYGGY.C Y 26.03 1219.4968 78.6 1220.6000 1 25.09 778 1 52 62 Carbamidomethylation
total 6 peptides
Best Unique PSM (Scan 1082, m/z=853.9700, z=2, RT=33.17, ppm=-6.4):
tr|A0A1E1WVT2|A0A1E1WVT2_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.KEGYLLGSDGC(+57.02)K.M Y 55.94 1325.6285 -2.3 663.8200 2 17.33 484 7 21 32 Carbamidomethylation
Y.C(+57.02)YNVPDSVTLWESDTNEC(+57.02)G.K Y 48.40 2244.8940 -92.9 1123.3500 2 35.61 1174 1 65 83 Carbamidomethylation
K.EGYLLGSDGC(+57.02)K.M Y 41.66 1197.5336 -6.7 599.7700 2 21.19 630 2 22 32 Carbamidomethylation
Y.NVPDSVTLWESDTNEC(+57.02)G.K Y 36.05 1921.7999 512.8 962.4000 2 32.86 1070 3 67 83 Carbamidomethylation
L.GSDGC(+57.02)K.M Y 19.79 622.2380 -8.6 623.2400 1 17.41 486 2 27 32 Carbamidomethylation
total 5 peptides
Best Unique PSM (Scan 484, m/z=663.8200, z=2, RT=17.33, ppm=-2.3):
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
K.GC(+57.02)EC(+57.02)DEEFR.N Y 51.35 1200.4176 -10.1 601.2100 2 15.14 400 3 59 67 Carbamidomethylation
R.KGC(+57.02)EC(+57.02)DEEFR.N Y 49.57 1328.5125 9.8 665.2700 2 13.09 322 2 58 67 Carbamidomethylation
R.NC(+57.02)LFK.T Y 19.84 680.3315 -12.9 681.3300 1 15.61 418 1 68 72 Carbamidomethylation
Y.GIGEIFFSDILNNY.C Y 18.82 1600.7772 5.2 801.4000 2 48.43 1650 1 80 93
total 4 peptides
Best Unique PSM (Scan 400, m/z=601.2100, z=2, RT=15.14, ppm=-10.1):
tr|A0A1E1WVV0|A0A1E1WVV0_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.DIILQWADELR.S Y 65.07 1370.7194 4.4 686.3700 2 39.95 1336 3 138 148
K.YSDITVDHSMC(+57.02)KPK.N Y 22.47 1679.7648 591.4 561.2600 3 18.42 526 2 23 36 Carbamidomethylation
K.NWVNLFR.A Y 18.70 947.4977 915.8 475.1900 2 31.09 1004 1 168 174
total 3 peptides
Best Unique PSM (Scan 1336, m/z=686.3700, z=2, RT=39.95, ppm=4.4):
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
K.LQGIVSWGSGC(+57.02)AQK.N Y 65.17 1489.7347 -6.2 745.8700 2 25.49 794 1 210 223 Carbamidomethylation
K.QTIASN Y 29.08 632.3129 -0.3 633.3200 1 5.35 16 2 241 246
total 2 peptides
Best Unique PSM (Scan 794, m/z=745.8700, z=2, RT=25.49, ppm=-6.2):
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
R.NC(+57.02)MLDC(+57.02)NILDDK.G Y 51.05 1509.6262 -0.5 755.8200 2 28.74 914 1 32 43 Carbamidomethylation
C.KKDDYPVDTAK.R Y 39.41 1278.6455 0.0 640.3300 2 12.21 288 1 20 30
Y.C(+57.02)YGLPDDSPTK.T Y 19.49 1251.5441 1.2 626.7800 2 21.51 642 1 69 79 Carbamidomethylation
total 3 peptides
Best Unique PSM (Scan 914, m/z=755.8200, z=2, RT=28.74, ppm=-0.5):
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 53.74 1217.5023 -13.9 609.7500 2 18.37 524 2 51 60 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 524, m/z=609.7500, z=2, RT=18.37, ppm=-13.9):
tr|A0A1E1WWF5|A0A1E1WWF5_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.YYC(+57.02)NNPTDLSSK.A Y 47.37 1460.6241 -12.8 731.3100 2 19.17 554 1 251 262 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 554, m/z=731.3100, z=2, RT=19.17, ppm=-12.8):
sp|P84691|SC61_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
KEGYLLGSR.G Y 38.13 1021.5556 -9.9 511.7800 2 16.62 456 2 1 9
total 1 peptides
Best Unique PSM (Scan 456, m/z=511.7800, z=2, RT=16.62, ppm=-9.9):
tr|A0A7L4XUQ7|A0A7L4XUQ7_TITPA
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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.KEGYLLGSR.G Y 38.13 1021.5556 -9.9 511.7800 2 16.62 456 2 8 16
total 1 peptides
Best Unique PSM (Scan 456, m/z=511.7800, z=2, RT=16.62, ppm=-9.9):
sp|H1ZZH7|SCX8_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.KEGYLLGSR.G Y 38.13 1021.5556 -9.9 511.7800 2 16.62 456 2 21 29
total 1 peptides
Best Unique PSM (Scan 456, m/z=511.7800, z=2, RT=16.62, ppm=-9.9):
tr|A0A1E1WVW4|A0A1E1WVW4_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.KEGYLLGSR.G Y 38.13 1021.5556 -9.9 511.7800 2 16.62 456 2 21 29
total 1 peptides
Best Unique PSM (Scan 456, m/z=511.7800, z=2, RT=16.62, ppm=-9.9):
tr|A0A1E1WVN0|A0A1E1WVN0_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.IIDDLLHK.V Y 35.62 965.5546 -9.4 483.7800 2 23.70 726 1 29 36
total 1 peptides
Best Unique PSM (Scan 726, m/z=483.7800, z=2, RT=23.70, ppm=-9.4):
tr|A0A1E1WVQ4|A0A1E1WVQ4_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.IIDDLLHK.V Y 35.62 965.5546 -9.4 483.7800 2 23.70 726 1 29 36
total 1 peptides
Best Unique PSM (Scan 726, m/z=483.7800, z=2, RT=23.70, ppm=-9.4):
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.SEYAC(+57.02)PVIDK.F Y 31.62 1180.5433 1.8 591.2800 2 19.70 574 1 57 66 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 574, m/z=591.2800, z=2, RT=19.70, ppm=1.8):
sp|Q0GY43|KIK2_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.SEYAC(+57.02)PVIDK.F Y 31.62 1180.5433 1.8 591.2800 2 19.70 574 1 57 66 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 574, m/z=591.2800, z=2, RT=19.70, ppm=1.8):
tr|A0A2I9LP49|A0A2I9LP49_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.SEYAC(+57.02)PVIDK.F Y 31.62 1180.5433 1.8 591.2800 2 19.70 574 1 57 66 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 574, m/z=591.2800, z=2, RT=19.70, ppm=1.8):
tr|A0A1E1WVT1|A0A1E1WVT1_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
D.EEASR.L Y 21.51 590.2660 1807.3 592.3400 1 15.46 412 1 249 253
total 1 peptides
Best Unique PSM (Scan 412, m/z=592.3400, z=1, RT=15.46, ppm=1807.3):
tr|A0A812TXT4|A0A812TXT4_9DINO
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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.EEASR.A Y 21.51 590.2660 1807.3 592.3400 1 15.46 412 1 602 606
total 1 peptides
Best Unique PSM (Scan 412, m/z=592.3400, z=1, RT=15.46, ppm=1807.3):
tr|A0A2N5ZQN8|A0A2N5ZQN8_9BACT
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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.NLNTGDP.I Y 20.46 729.3293 45.8 730.3700 1 34.70 1140 1 182 188
total 1 peptides
Best Unique PSM (Scan 1140, m/z=730.3700, z=1, RT=34.70, ppm=45.8):
tr|A0A9D6ZEH8|A0A9D6ZEH8_UNCDE
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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.AC(+57.02)AAAC(+57.02)RTSGY.T Y 20.21 1186.4860 -17.3 594.2400 2 34.12 1118 1 32 42 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1118, m/z=594.2400, z=2, RT=34.12, ppm=-17.3):
 


Prepared with PEAKS ™ (bioinfor.com)