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 Scans1010
# of MS/MS Scans1010
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 Matches39
Peptide Sequences29
Protein Groups8
Proteins24
Proteins (#Unique Peptides)1 (>2); 8 (=2); 15 (=1);
FDR (Peptide-Spectrum Matches)38.5%
FDR (Peptide Sequences)51.7%
FDR (Protein)25.0%
De Novo Only Spectra32
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0211C
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 18263000

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: 18_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 108.56 19 5 5 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
5 20591 sp|P60211|KA181_TITOB 97.36 46 2 2 Y 6530 Potassium channel toxin alpha-KTx 18.1 OS=Tityus obscurus OX=1221240 PE=1 SV=2
2 26633 tr|A0A1E1WVQ0|A0A1E1WVQ0_TITOB 56.64 18 2 2 Y 6918 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
6 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 53.03 16 1 1 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
7 26646 sp|C0HL59|NDB4A_ISOMC 45.93 35 2 2 N 1700 Peptide Im-4 OS=Isometrus maculatus OX=497827 PE=1 SV=1
7 11772 sp|P0DQT2|TOAP3_TITOB 45.93 35 2 2 N 1700 Antimicrobial peptide ToAP3 OS=Tityus obscurus OX=1221240 PE=1 SV=1
7 11777 tr|A0A0U1S866|A0A0U1S866_ISOMC 45.93 9 2 2 N 7494 Uncharacterized protein OS=Isometrus maculatus OX=497827 PE=2 SV=1
7 11779 sp|P0CI90|NDB4T_LYCMC 45.93 8 2 2 N 8480 Antimicrobial peptide 143 OS=Lychas mucronatus OX=172552 PE=3 SV=1
7 11780 tr|A0A0U1SPC4|A0A0U1SPC4_ISOMC 45.93 8 2 2 N 8763 Antimicrobial peptide OS=Isometrus maculatus OX=497827 PE=2 SV=1
7 26647 sp|G8YYA6|NDB4C_ANDAM 45.93 8 2 2 N 8539 Antimicrobial peptide 2 OS=Androctonus amoreuxi OX=112024 PE=1 SV=1
3 36 tr|A0A1V1WBN0|A0A1V1WBN0_9SCOR 35.13 1 1 1 N 66291 Putative Neprilysin 1 (Fragment) OS=Superstitionia donensis OX=311983 PE=3 SV=1
20 32736 tr|A0A1E1WVV0|A0A1E1WVV0_TITOB 23.85 1 1 1 N 49029 Putative cysteine-rich protein OS=Tityus obscurus OX=1221240 PE=4 SV=1
20 21877 tr|A0A1W7RAN8|A0A1W7RAN8_9SCOR 23.85 1 1 1 N 50201 Rab GDP dissociation inhibitor OS=Hadrurus spadix OX=141984 PE=3 SV=1
20 23916 tr|A0A2I9LPI1|A0A2I9LPI1_9SCOR 23.85 1 1 1 N 50225 Rab GDP dissociation inhibitor OS=Centruroides hentzi OX=88313 PE=3 SV=1
17 46549 sp|E7CLP0|SCX9_RHOJU 22.09 10 1 1 Y 7188 Putative alpha-neurotoxin RjAa9 (Fragment) OS=Rhopalurus junceus OX=419285 PE=2 SV=1
17 2014 sp|E7CLN9|SCX44_RHOJU 22.09 9 1 1 Y 7536 Putative alpha-neurotoxin RjAa44 (Fragment) OS=Rhopalurus junceus OX=419285 PE=2 SV=1
17 2013 sp|E7CLN7|SCX13_RHOJU 22.09 9 1 1 Y 7564 Putative alpha-neurotoxin RjAa13 (Fragment) OS=Rhopalurus junceus OX=419285 PE=2 SV=1
17 2015 sp|E7CLN8|SCX16_RHOJU 22.09 9 1 1 Y 7624 Putative alpha-neurotoxin RjAa16 (Fragment) OS=Rhopalurus junceus OX=419285 PE=2 SV=1
17 45509 sp|P0DQU6|SCX_TITME 22.09 9 1 1 Y 7804 Sodium channel toxin OS=Tityus metuendus OX=2203750 PE=1 SV=1
17 44588 sp|B7SNV8|SCX8_PARGR 22.09 7 1 1 Y 9315 Toxin Pg8 OS=Parabuthus granulatus OX=242110 PE=1 SV=1
17 46550 tr|B8XH17|B8XH17_BUTOS 22.09 7 1 1 Y 9551 Putative depressant toxin Tx580 OS=Buthus occitanus israelis OX=539894 PE=2 SV=1
17 46551 sp|P0DUI1|SCX16_CENTE 22.09 7 1 1 Y 9746 Beta-toxin Ct16 OS=Centruroides tecomanus OX=1028682 PE=1 SV=1
17 10567 tr|A0A1E1WVY8|A0A1E1WVY8_TITOB 22.09 7 1 1 Y 10060 Putative sodium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
17 44589 sp|H1ZZI3|SCX14_TITOB 22.09 7 1 1 Y 10106 Toxin To14 OS=Tityus obscurus OX=1221240 PE=1 SV=1
total 24 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
T.LNNDIMLIK.L Y 56.07 1072.5951 -9.0 537.3000 2 26.56 834 1 104 112
S.NTLNNDIMLIK.L Y 50.54 1287.6857 -0.2 644.8500 2 28.47 904 3 102 112
R.LGEDNINVVEGNEQFISASK.S Y 47.31 2162.0491 -29.4 1082.0000 2 31.14 1004 3 73 92
K.LQGIVSW.G Y 28.31 801.4385 -7.2 802.4400 1 30.55 982 1 210 216
C.LISGWGNTK.S Y 21.85 974.5185 -13.4 488.2600 2 19.99 586 1 140 148
total 5 peptides
Best Unique PSM (Scan 834, m/z=537.3000, z=2, RT=26.56, ppm=-9.0):
sp|P60211|KA181_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
A.TGPQTTC(+57.02)QAAM(+15.99)C(+57.02)EAGC(+57.02)K.G Y 69.11 1885.7427 -19.8 943.8600 2 15.50 414 1 27 43 Carbamidomethylation; Oxidation (M)
K.SMESC(+57.02)QGDTC(+57.02)K.C Y 56.50 1301.4686 -2.5 651.7400 2 10.66 222 1 48 58 Carbamidomethylation
total 2 peptides
Best Unique PSM (Scan 414, m/z=943.8600, z=2, RT=15.50, ppm=-19.8):
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
K.C(+57.02)TC(+57.02)YG Y 37.84 659.2043 -2.4 660.2100 1 5.77 32 2 57 61 Carbamidomethylation
R.TPC(+57.02)FIK.H Y 37.59 764.3891 -8.3 765.3900 1 17.44 490 2 39 44 Carbamidomethylation
total 2 peptides
Best Unique PSM (Scan 32, m/z=660.2100, z=1, RT=5.77, ppm=-2.4):
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 53.03 1250.5271 -1.3 626.2700 2 13.73 344 2 32 41 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 344, m/z=626.2700, z=2, RT=13.73, ppm=-1.3):
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
L.ISAIK Y 31.90 530.3428 -0.1 531.3500 1 10.36 210 1 13 17
G.LISAIK Y 28.04 643.4268 -6.4 644.4300 1 16.71 462 1 12 17
total 2 peptides
Best Unique PSM (Scan 210, m/z=531.3500, z=1, RT=10.36, ppm=-0.1):
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
L.ISAIK Y 31.90 530.3428 -0.1 531.3500 1 10.36 210 1 13 17
G.LISAIK Y 28.04 643.4268 -6.4 644.4300 1 16.71 462 1 12 17
total 2 peptides
Best Unique PSM (Scan 210, m/z=531.3500, z=1, RT=10.36, ppm=-0.1):
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
L.ISAIK.G Y 31.90 530.3428 -0.1 531.3500 1 10.36 210 1 25 29
G.LISAIK.G Y 28.04 643.4268 -6.4 644.4300 1 16.71 462 1 24 29
total 2 peptides
Best Unique PSM (Scan 210, m/z=531.3500, z=1, RT=10.36, ppm=-0.1):
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
L.ISAIK.G Y 31.90 530.3428 -0.1 531.3500 1 10.36 210 1 34 38
G.LISAIK.G Y 28.04 643.4268 -6.4 644.4300 1 16.71 462 1 33 38
total 2 peptides
Best Unique PSM (Scan 210, m/z=531.3500, z=1, RT=10.36, ppm=-0.1):
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
L.ISAIK.G Y 31.90 530.3428 -0.1 531.3500 1 10.36 210 1 35 39
G.LISAIK.G Y 28.04 643.4268 -6.4 644.4300 1 16.71 462 1 34 39
total 2 peptides
Best Unique PSM (Scan 210, m/z=531.3500, z=1, RT=10.36, ppm=-0.1):
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
L.ISAIK.G Y 31.90 530.3428 -0.1 531.3500 1 10.36 210 1 36 40
G.LISAIK.G Y 28.04 643.4268 -6.4 644.4300 1 16.71 462 1 35 40
total 2 peptides
Best Unique PSM (Scan 210, m/z=531.3500, z=1, RT=10.36, ppm=-0.1):
tr|A0A1V1WBN0|A0A1V1WBN0_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
I.MAAYK.N Y 35.13 582.2836 -1.5 583.2900 1 5.10 6 3 272 276
total 1 peptides
Best Unique PSM (Scan 6, m/z=583.2900, z=1, RT=5.10, ppm=-1.5):
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
I.YKGGK.K Y 23.85 551.3067 47.3 552.3400 1 5.30 14 1 214 218
total 1 peptides
Best Unique PSM (Scan 14, m/z=552.3400, z=1, RT=5.30, ppm=47.3):
tr|A0A1W7RAN8|A0A1W7RAN8_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
V.YKGGK.I Y 23.85 551.3067 47.3 552.3400 1 5.30 14 1 111 115
total 1 peptides
Best Unique PSM (Scan 14, m/z=552.3400, z=1, RT=5.30, ppm=47.3):
tr|A0A2I9LPI1|A0A2I9LPI1_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
V.YKGGK.I Y 23.85 551.3067 47.3 552.3400 1 5.30 14 1 111 115
total 1 peptides
Best Unique PSM (Scan 14, m/z=552.3400, z=1, RT=5.30, ppm=47.3):
sp|E7CLP0|SCX9_RHOJU
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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
T.SGYC(+57.02)YK.L Y 22.09 776.3163 -4.6 777.3200 1 8.85 152 1 32 37 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 152, m/z=777.3200, z=1, RT=8.85, ppm=-4.6):
sp|E7CLN9|SCX44_RHOJU
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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.SGYC(+57.02)YK.L Y 22.09 776.3163 -4.6 777.3200 1 8.85 152 1 32 37 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 152, m/z=777.3200, z=1, RT=8.85, ppm=-4.6):
sp|E7CLN7|SCX13_RHOJU
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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.SGYC(+57.02)YK.L Y 22.09 776.3163 -4.6 777.3200 1 8.85 152 1 32 37 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 152, m/z=777.3200, z=1, RT=8.85, ppm=-4.6):
sp|E7CLN8|SCX16_RHOJU
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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.SGYC(+57.02)YK.L Y 22.09 776.3163 -4.6 777.3200 1 8.85 152 1 32 37 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 152, m/z=777.3200, z=1, RT=8.85, ppm=-4.6):
sp|P0DQU6|SCX_TITME
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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.SGYC(+57.02)YK.L Y 22.09 776.3163 -4.6 777.3200 1 8.85 152 1 38 43 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 152, m/z=777.3200, z=1, RT=8.85, ppm=-4.6):
sp|B7SNV8|SCX8_PARGR
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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.SGYC(+57.02)YK.L Y 22.09 776.3163 -4.6 777.3200 1 8.85 152 1 53 58 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 152, m/z=777.3200, z=1, RT=8.85, ppm=-4.6):
tr|B8XH17|B8XH17_BUTOS
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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.SGYC(+57.02)YK.W Y 22.09 776.3163 -4.6 777.3200 1 8.85 152 1 51 56 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 152, m/z=777.3200, z=1, RT=8.85, ppm=-4.6):
sp|P0DUI1|SCX16_CENTE
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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.SGYC(+57.02)YK.L Y 22.09 776.3163 -4.6 777.3200 1 8.85 152 1 52 57 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 152, m/z=777.3200, z=1, RT=8.85, ppm=-4.6):
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
D.SGYC(+57.02)YK.L Y 22.09 776.3163 -4.6 777.3200 1 8.85 152 1 57 62 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 152, m/z=777.3200, z=1, RT=8.85, ppm=-4.6):
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
D.SGYC(+57.02)YK.L Y 22.09 776.3163 -4.6 777.3200 1 8.85 152 1 57 62 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 152, m/z=777.3200, z=1, RT=8.85, ppm=-4.6):
 


Prepared with PEAKS ™ (bioinfor.com)