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 Scans1011
# of MS/MS Scans1011
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 Matches18
Peptide Sequences17
Protein Groups6
Proteins17
Proteins (#Unique Peptides)0 (>2); 0 (=2); 17 (=1);
FDR (Peptide-Spectrum Matches)133.3%
FDR (Peptide Sequences)129.4%
FDR (Protein)117.6%
De Novo Only Spectra44
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.026C
Oxidation15.991M

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 19152000

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: 19_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
14 15044 tr|A0A1E1WVX0|A0A1E1WVX0_TITOB 41.90 16 1 1 N 8616 Putative bradykinin-potentiating peptide OS=Tityus obscurus OX=1221240 PE=4 SV=1
2 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 37.77 16 1 1 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
8 6521 tr|C5Y0J0|C5Y0J0_SORBI 23.83 6 1 1 N 8990 Knottin scorpion toxin-like domain-containing protein OS=Sorghum bicolor OX=4558 GN=SORBI_3004G131400 PE=4 SV=1
8 25658 tr|A0A921UK76|A0A921UK76_SORBI 23.83 6 1 1 N 8990 Knottin scorpion toxin-like domain-containing protein OS=Sorghum bicolor OX=4558 GN=BDA96_04G140400 PE=4 SV=1
8 25659 tr|A0A8T0XF67|A0A8T0XF67_PANVG 23.83 6 1 1 N 8891 Knottin scorpion toxin-like domain-containing protein OS=Panicum virgatum OX=38727 GN=PVAP13_1KG272300 PE=4 SV=1
8 25660 tr|R0F8N9|R0F8N9_9BRAS 23.83 5 1 1 N 9938 Knottin scorpion toxin-like domain-containing protein OS=Capsella rubella OX=81985 GN=CARUB_v10006421mg PE=4 SV=1
8 20938 tr|A0A2I9LP31|A0A2I9LP31_9SCOR 23.83 1 1 1 N 97053 Junctophilin-1 OS=Centruroides hentzi OX=88313 PE=3 SV=1
8 11995 tr|A7HDZ9|A7HDZ9_ANADF 23.83 1 1 1 N 73428 Uncharacterized protein OS=Anaeromyxobacter sp. (strain Fw109-5) OX=404589 GN=Anae109_2744 PE=4 SV=1
8 5051 tr|A0A1W7RAA2|A0A1W7RAA2_9SCOR 23.83 1 1 1 N 81329 Junctophilin-1 OS=Hadrurus spadix OX=141984 PE=3 SV=1
6 25663 tr|A0A0K0LBV3|A0A0K0LBV3_9SCOR 22.26 6 1 1 N 10055 Sodium channel blocker AbNaTx25 OS=Androctonus bicolor OX=748906 PE=2 SV=1
6 13635 tr|E4VP15|E4VP15_MESEU 22.26 6 1 1 N 9980 Venom sodium channel toxin-1 OS=Mesobuthus eupeus OX=34648 PE=2 SV=1
6 5294 tr|A0A8C1H074|A0A8C1H074_CYPCA 22.26 1 1 1 N 39014 MYND-type domain-containing protein OS=Cyprinus carpio OX=7962 GN=LOC109079639 PE=4 SV=1
6 21803 tr|A0A2I9LPQ5|A0A2I9LPQ5_9SCOR 22.26 1 1 1 N 87600 Protein transport protein SEC23 OS=Centruroides hentzi OX=88313 PE=3 SV=1
6 9093 tr|A0A803LMD7|A0A803LMD7_CHEQI 22.26 0 1 1 N 131569 Knottin scorpion toxin-like domain-containing protein OS=Chenopodium quinoa OX=63459 PE=4 SV=1
6 6165 tr|A0A510ACK2|A0A510ACK2_MESMA 22.26 0 1 1 N 162123 Dscam11 OS=Mesobuthus martensii OX=34649 PE=2 SV=1
16 25652 tr|A0A5J9VAV3|A0A5J9VAV3_9POAL 20.87 10 1 1 N 9406 Knottin scorpion toxin-like domain-containing protein OS=Eragrostis curvula OX=38414 GN=EJB05_23706 PE=4 SV=1
5 25653 tr|A0A6J1R285|A0A6J1R285_9HYME 20.76 9 1 1 Y 11015 Defensin-like OS=Temnothorax curvispinosus OX=300111 GN=LOC112465437 PE=4 SV=1
total 17 proteins

tr|A0A1E1WVX0|A0A1E1WVX0_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
N.KVLTPAEEAPAE.A Y 41.90 1253.6503 -3.8 627.8300 2 18.15 516 1 55 66
total 1 peptides
Best Unique PSM (Scan 516, m/z=627.8300, z=2, RT=18.15, ppm=-3.8):
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 37.77 1250.5271 -1.3 626.2700 2 13.38 328 2 32 41 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 328, m/z=626.2700, z=2, RT=13.38, ppm=-1.3):
tr|C5Y0J0|C5Y0J0_SORBI
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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.TATAR.V Y 23.83 518.2812 -35.7 519.2700 1 29.67 956 1 23 27
total 1 peptides
Best Unique PSM (Scan 956, m/z=519.2700, z=1, RT=29.67, ppm=-35.7):
tr|A0A921UK76|A0A921UK76_SORBI
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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.TATAR.V Y 23.83 518.2812 -35.7 519.2700 1 29.67 956 1 23 27
total 1 peptides
Best Unique PSM (Scan 956, m/z=519.2700, z=1, RT=29.67, ppm=-35.7):
tr|A0A8T0XF67|A0A8T0XF67_PANVG
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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.TATAR.V Y 23.83 518.2812 -35.7 519.2700 1 29.67 956 1 25 29
total 1 peptides
Best Unique PSM (Scan 956, m/z=519.2700, z=1, RT=29.67, ppm=-35.7):
tr|R0F8N9|R0F8N9_9BRAS
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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.TATAR.G Y 23.83 518.2812 -35.7 519.2700 1 29.67 956 1 31 35
total 1 peptides
Best Unique PSM (Scan 956, m/z=519.2700, z=1, RT=29.67, ppm=-35.7):
tr|A0A2I9LP31|A0A2I9LP31_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.TATAR.G Y 23.83 518.2812 -35.7 519.2700 1 29.67 956 1 399 403
total 1 peptides
Best Unique PSM (Scan 956, m/z=519.2700, z=1, RT=29.67, ppm=-35.7):
tr|A7HDZ9|A7HDZ9_ANADF
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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.TATAR.G Y 23.83 518.2812 -35.7 519.2700 1 29.67 956 1 182 186
total 1 peptides
Best Unique PSM (Scan 956, m/z=519.2700, z=1, RT=29.67, ppm=-35.7):
tr|A0A1W7RAA2|A0A1W7RAA2_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.TATAR.G Y 23.83 518.2812 -35.7 519.2700 1 29.67 956 1 392 396
total 1 peptides
Best Unique PSM (Scan 956, m/z=519.2700, z=1, RT=29.67, ppm=-35.7):
tr|A0A0K0LBV3|A0A0K0LBV3_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.LIEVK.T Y 22.26 600.3846 1462.6 602.2700 1 14.92 388 1 15 19
total 1 peptides
Best Unique PSM (Scan 388, m/z=602.2700, z=1, RT=14.92, ppm=1462.6):
tr|E4VP15|E4VP15_MESEU
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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.LIEVK.T Y 22.26 600.3846 1462.6 602.2700 1 14.92 388 1 15 19
total 1 peptides
Best Unique PSM (Scan 388, m/z=602.2700, z=1, RT=14.92, ppm=1462.6):
tr|A0A8C1H074|A0A8C1H074_CYPCA
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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.LLEVK.E Y 22.26 600.3846 1462.6 602.2700 1 14.92 388 1 330 334
total 1 peptides
Best Unique PSM (Scan 388, m/z=602.2700, z=1, RT=14.92, ppm=1462.6):
tr|A0A2I9LPQ5|A0A2I9LPQ5_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.ILEVK.T Y 22.26 600.3846 1462.6 602.2700 1 14.92 388 1 409 413
total 1 peptides
Best Unique PSM (Scan 388, m/z=602.2700, z=1, RT=14.92, ppm=1462.6):
tr|A0A803LMD7|A0A803LMD7_CHEQI
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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.ILEVK.W Y 22.26 600.3846 1462.6 602.2700 1 14.92 388 1 951 955
total 1 peptides
Best Unique PSM (Scan 388, m/z=602.2700, z=1, RT=14.92, ppm=1462.6):
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
Q.LLEVK.E Y 22.26 600.3846 1462.6 602.2700 1 14.92 388 1 75 79
total 1 peptides
Best Unique PSM (Scan 388, m/z=602.2700, z=1, RT=14.92, ppm=1462.6):
tr|A0A5J9VAV3|A0A5J9VAV3_9POAL
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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.SAGPLGGGR.G Y 20.87 770.4034 -223.3 386.1230 2 9.24 166 1 78 86
total 1 peptides
Best Unique PSM (Scan 166, m/z=386.1230, z=2, RT=9.24, ppm=-223.3):
tr|A0A6J1R285|A0A6J1R285_9HYME
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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.AC(+57.02)AANC(+57.02)IAR.N Y 20.76 1005.4484 -957.8 503.2500 2 48.12 1648 6 69 77 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1648, m/z=503.2500, z=2, RT=48.12, ppm=-957.8):
 


Prepared with PEAKS ™ (bioinfor.com)