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 Scans1001
# of MS/MS Scans1001
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 Matches57
Peptide Sequences35
Protein Groups15
Proteins20
Proteins (#Unique Peptides)1 (>2); 2 (=2); 17 (=1);
FDR (Peptide-Spectrum Matches)38.6%
FDR (Peptide Sequences)45.7%
FDR (Protein)75.0%
De Novo Only Spectra24
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0234C
Oxidation15.993M

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 27275210

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: 27_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 181.71 60 8 2 Y 10060 Putative sodium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
2 44589 sp|H1ZZI3|SCX14_TITOB 171.58 46 7 1 Y 10106 Toxin To14 OS=Tityus obscurus OX=1221240 PE=1 SV=1
3 44510 tr|A0A1E1WVN4|A0A1E1WVN4_TITOB 107.94 49 5 5 Y 9938 Putative insulin-like protein growth factor binding protein OS=Tityus obscurus OX=1221240 PE=4 SV=1
5 27165 tr|A0A1E1WVV5|A0A1E1WVV5_TITOB 55.05 25 2 2 Y 7194 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
20 45511 sp|A0A1D3IY23|TOACP_TITOB 43.49 14 1 1 N 7368 Peptide ToAcP OS=Tityus obscurus OX=1221240 PE=1 SV=1
20 27184 tr|A0A1E1WWD3|A0A1E1WWD3_TITOB 43.49 9 1 1 N 11661 Putative venom toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
37 16312 tr|A0A2I9LP26|A0A2I9LP26_9SCOR 25.31 1 1 1 N 97687 Alpha-1,4 glucan phosphorylase OS=Centruroides hentzi OX=88313 PE=3 SV=1
37 23927 tr|A0A1W7RAF7|A0A1W7RAF7_9SCOR 25.31 1 1 1 N 98263 Alpha-1,4 glucan phosphorylase OS=Hadrurus spadix OX=141984 PE=3 SV=1
21 45517 tr|A0A0E0B974|A0A0E0B974_9ORYZ 24.70 8 1 1 Y 8840 Knottin scorpion toxin-like domain-containing protein OS=Oryza glumipatula OX=40148 PE=4 SV=1
21 45518 tr|A0A0E0QXT4|A0A0E0QXT4_ORYRU 24.70 8 1 1 Y 8841 Knottin scorpion toxin-like domain-containing protein OS=Oryza rufipogon OX=4529 PE=4 SV=1
21 45519 tr|A0A0E0M6M9|A0A0E0M6M9_ORYPU 24.70 8 1 1 Y 8814 Knottin scorpion toxin-like domain-containing protein OS=Oryza punctata OX=4537 PE=4 SV=1
9 6351 tr|A0A509ZVT9|A0A509ZVT9_MESMA 22.92 0 1 1 N 164057 Dscam2 (Fragment) OS=Mesobuthus martensii OX=34649 PE=2 SV=1
8 7523 tr|A0A2I9LNX9|A0A2I9LNX9_9SCOR 22.89 1 1 1 N 84169 N-acetylated-alpha-linked acidic dipeptidase OS=Centruroides hentzi OX=88313 PE=3 SV=1
8 6165 tr|A0A510ACK2|A0A510ACK2_MESMA 22.89 0 1 1 N 162123 Dscam11 OS=Mesobuthus martensii OX=34649 PE=2 SV=1
14 5284 tr|A0A7L2Z8I1|A0A7L2Z8I1_JACJC 22.23 1 1 1 N 110337 SYNE3 protein (Fragment) OS=Jacana jacana OX=54508 GN=Syne3 PE=3 SV=1
12 45530 tr|A0A1W7RA16|A0A1W7RA16_9SCOR 21.98 2 1 1 N 32629 Phospholipase A2 OS=Hadrurus spadix OX=141984 PE=3 SV=1
23 101 tr|A0A2I9LPU7|A0A2I9LPU7_9SCOR 21.20 1 1 1 N 114433 Metalloendopeptidase OS=Centruroides hentzi OX=88313 PE=3 SV=1
10 4976 tr|A0A1W7R9N2|A0A1W7R9N2_9SCOR 21.04 0 1 1 N 577007 Ryanodine receptor OS=Hadrurus spadix OX=141984 PE=4 SV=1
24 15120 tr|S8B2S7|S8B2S7_PENO1 20.45 3 1 1 N 26719 Dickkopf N-terminal cysteine-rich domain-containing protein OS=Penicillium oxalicum (strain 114-2 / CGMCC 5302) OX=933388 GN=PDE_03698 PE=3 SV=1
25 15291 tr|A0A835YNU6|A0A835YNU6_9CHLO 20.29 1 1 1 N 64935 MYND-type domain-containing protein OS=Edaphochlamys debaryana OX=47281 GN=HYH03_000373 PE=4 SV=1
total 20 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 N 77.42 1716.7123 -44.8 859.3250 2 23.74 724 3 65 79 Carbamidomethylation
R.NC(+57.02)MLDC(+57.02)NILDDK.G Y 69.55 1509.6262 330.7 756.0700 2 28.58 904 2 32 43 Carbamidomethylation
R.KADSGYC(+57.02)YK.L N 67.12 1090.4753 183.5 546.3450 2 9.27 170 6 54 62 Carbamidomethylation
R.NC(+57.02)M(+15.99)LDC(+57.02)NILDDK.G Y 67.05 1525.6211 42.2 763.8500 2 24.84 766 2 32 43 Carbamidomethylation; Oxidation (M)
C.KKDDYPVDTAK.R N 66.29 1278.6455 0.0 640.3300 2 11.93 274 2 20 30
C.KKDDYPVDTAKR.N N 62.82 1434.7466 -0.8 718.3800 2 11.68 264 1 20 31
Y.C(+57.02)YGLPDDSPTK.T N 60.52 1251.5441 1.2 626.7800 2 21.42 636 3 69 79 Carbamidomethylation
R.C(+57.02)NPNL.R Y 29.69 616.2639 -1.9 617.2700 1 13.00 316 3 84 88 Carbamidomethylation
K.ADSGYC(+57.02)YK.L N 29.35 962.3804 -15.5 482.1900 2 12.53 298 1 55 62 Carbamidomethylation
total 9 peptides
Best Unique PSM (Scan 904, m/z=756.0700, z=2, RT=28.58, ppm=330.7):
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 N 77.42 1716.7123 -44.8 859.3250 2 23.74 724 3 65 79 Carbamidomethylation
R.KADSGYC(+57.02)YK.L N 67.12 1090.4753 183.5 546.3450 2 9.27 170 6 54 62 Carbamidomethylation
C.KKDDYPVDTAK.R N 66.29 1278.6455 0.0 640.3300 2 11.93 274 2 20 30
C.KKDDYPVDTAKR.N N 62.82 1434.7466 -0.8 718.3800 2 11.68 264 1 20 31
Y.C(+57.02)YGLPDDSPTK.T N 60.52 1251.5441 1.2 626.7800 2 21.42 636 3 69 79 Carbamidomethylation
R.C(+57.02)NPNV.R Y 38.97 602.2482 -9.1 603.2500 1 8.77 148 2 84 88 Carbamidomethylation
K.ADSGYC(+57.02)YK.L N 29.35 962.3804 -15.5 482.1900 2 12.53 298 1 55 62 Carbamidomethylation
total 7 peptides
Best Unique PSM (Scan 148, m/z=603.2500, z=1, RT=8.77, ppm=-9.1):
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 60.46 1405.6144 -6.4 703.8100 2 15.27 402 2 78 90 Carbamidomethylation
R.KDC(+57.02)PAGIVK.D Y 44.28 986.5219 -16.6 494.2600 2 12.69 304 2 35 43 Carbamidomethylation
R.C(+57.02)EETVC(+57.02)SLKQ.R Y 37.26 1252.5427 2.2 627.2800 2 16.59 452 2 24 33 Carbamidomethylation
R.NISGIC(+57.02)GK.G Y 29.92 847.4222 24.3 848.4500 1 14.68 380 1 65 72 Carbamidomethylation
K.GLVC(+57.02)K.V Y 27.19 575.3101 4.5 576.3200 1 8.56 140 1 73 77 Carbamidomethylation
total 5 peptides
Best Unique PSM (Scan 402, m/z=703.8100, z=2, RT=15.27, ppm=-6.4):
tr|A0A1E1WVV5|A0A1E1WVV5_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.GTGYC(+57.02)DKDVC(+57.02)K.C Y 44.58 1301.5380 -32.4 434.8392 3 12.33 290 4 48 58 Carbamidomethylation
A.SPFGK.C Y 20.94 534.2802 1876.5 536.2900 1 9.85 192 1 28 32
total 2 peptides
Best Unique PSM (Scan 290, m/z=434.8392, z=3, RT=12.33, ppm=-32.4):
sp|A0A1D3IY23|TOACP_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.LGFSEEDLK.A Y 43.49 1036.5077 -2.1 519.2600 2 24.02 734 1 40 48
total 1 peptides
Best Unique PSM (Scan 734, m/z=519.2600, z=2, RT=24.02, ppm=-2.1):
tr|A0A1E1WWD3|A0A1E1WWD3_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.LGFSEEDLK.A Y 43.49 1036.5077 -2.1 519.2600 2 24.02 734 1 40 48
total 1 peptides
Best Unique PSM (Scan 734, m/z=519.2600, z=2, RT=24.02, ppm=-2.1):
tr|A0A2I9LP26|A0A2I9LP26_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
G.IFAQK.I Y 25.31 605.3536 -117.2 606.2900 1 6.03 42 1 166 170
total 1 peptides
Best Unique PSM (Scan 42, m/z=606.2900, z=1, RT=6.03, ppm=-117.2):
tr|A0A1W7RAF7|A0A1W7RAF7_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
G.IFAQK.I Y 25.31 605.3536 -117.2 606.2900 1 6.03 42 1 166 170
total 1 peptides
Best Unique PSM (Scan 42, m/z=606.2900, z=1, RT=6.03, ppm=-117.2):
tr|A0A0E0B974|A0A0E0B974_9ORYZ
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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.C(+57.02)YLNC(+57.02)K.I Y 24.70 856.3572 -25.2 429.1751 2 15.17 398 1 42 47 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 398, m/z=429.1751, z=2, RT=15.17, ppm=-25.2):
tr|A0A0E0QXT4|A0A0E0QXT4_ORYRU
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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.C(+57.02)YLNC(+57.02)K.I Y 24.70 856.3572 -25.2 429.1751 2 15.17 398 1 42 47 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 398, m/z=429.1751, z=2, RT=15.17, ppm=-25.2):
tr|A0A0E0M6M9|A0A0E0M6M9_ORYPU
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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.C(+57.02)YLNC(+57.02)K.I Y 24.70 856.3572 -25.2 429.1751 2 15.17 398 1 42 47 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 398, m/z=429.1751, z=2, RT=15.17, ppm=-25.2):
tr|A0A509ZVT9|A0A509ZVT9_MESMA
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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.LPDNH.R Y 22.92 594.2762 179.3 595.3900 1 18.81 536 2 539 543
total 1 peptides
Best Unique PSM (Scan 536, m/z=595.3900, z=1, RT=18.81, ppm=179.3):
tr|A0A2I9LNX9|A0A2I9LNX9_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
A.QLLEV.A Y 22.89 600.3483 57.4 601.3900 1 18.91 540 2 392 396
total 1 peptides
Best Unique PSM (Scan 540, m/z=601.3900, z=1, RT=18.91, ppm=57.4):
tr|A0A510ACK2|A0A510ACK2_MESMA
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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.QLLEV.K Y 22.89 600.3483 57.4 601.3900 1 18.91 540 2 74 78
total 1 peptides
Best Unique PSM (Scan 540, m/z=601.3900, z=1, RT=18.91, ppm=57.4):
tr|A0A7L2Z8I1|A0A7L2Z8I1_JACJC
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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.VPDGQSLF.E Y 22.23 861.4232 1024.2 432.1600 2 13.95 352 1 835 842
total 1 peptides
Best Unique PSM (Scan 352, m/z=432.1600, z=2, RT=13.95, ppm=1024.2):
tr|A0A1W7RA16|A0A1W7RA16_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.GFETK.Y Y 21.98 580.2856 -160.1 581.2000 1 13.10 320 1 170 174
total 1 peptides
Best Unique PSM (Scan 320, m/z=581.2000, z=1, RT=13.10, ppm=-160.1):
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
R.LSQGDIAQTNL.L Y 21.20 1158.5880 -157.5 580.2100 2 39.45 1300 1 321 331
total 1 peptides
Best Unique PSM (Scan 1300, m/z=580.2100, z=2, RT=39.45, ppm=-157.5):
tr|A0A1W7R9N2|A0A1W7R9N2_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
M.QDKLSK.S Y 21.04 717.4021 1278.9 360.1671 2 11.88 272 1 4101 4106
total 1 peptides
Best Unique PSM (Scan 272, m/z=360.1671, z=2, RT=11.88, ppm=1278.9):
tr|S8B2S7|S8B2S7_PENO1
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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.TMTSVIPR.C Y 20.45 903.4848 1019.0 453.2100 2 37.47 1226 1 233 240
total 1 peptides
Best Unique PSM (Scan 1226, m/z=453.2100, z=2, RT=37.47, ppm=1019.0):
tr|A0A835YNU6|A0A835YNU6_9CHLO
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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
M.LGDVPGDQR.I Y 20.29 955.4723 1060.4 479.2500 2 11.98 276 1 524 532
total 1 peptides
Best Unique PSM (Scan 276, m/z=479.2500, z=2, RT=11.98, ppm=1060.4):
 


Prepared with PEAKS ™ (bioinfor.com)