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 Scans1009
# of MS/MS Scans1009
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 Matches29
Peptide Sequences23
Protein Groups6
Proteins8
Proteins (#Unique Peptides)1 (>2); 3 (=2); 4 (=1);
FDR (Peptide-Spectrum Matches)34.5%
FDR (Peptide Sequences)43.5%
FDR (Protein)12.5%
De Novo Only Spectra20
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0211C

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 22156200

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: 22_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 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 89.28 37 3 3 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
2 15044 tr|A0A1E1WVX0|A0A1E1WVX0_TITOB 65.80 21 2 2 N 8616 Putative bradykinin-potentiating peptide OS=Tityus obscurus OX=1221240 PE=4 SV=1
3 27165 tr|A0A1E1WVV5|A0A1E1WVV5_TITOB 48.70 28 2 2 Y 7194 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
8 7764 tr|A0A2I9LPY0|A0A2I9LPY0_9SCOR 28.39 1 1 1 N 118515 E1 ubiquitin-activating enzyme OS=Centruroides hentzi OX=88313 PE=3 SV=1
8 10616 tr|A0A1W7R9A6|A0A1W7R9A6_9SCOR 28.39 1 1 1 N 117849 E1 ubiquitin-activating enzyme OS=Hadrurus spadix OX=141984 PE=3 SV=1
4 4991 tr|A0A159W474|A0A159W474_MESMA 25.32 1 2 2 N 174842 Dscam OS=Mesobuthus martensii OX=34649 GN=Dscam PE=2 SV=1
14 27169 tr|A0A8T2F9B8|A0A8T2F9B8_ARASU 22.48 8 1 1 N 8678 Knottin scorpion toxin-like superfamily OS=Arabidopsis suecica OX=45249 GN=ISN44_As03g029200 PE=4 SV=1
14 27170 tr|A0A921R469|A0A921R469_SORBI 22.48 7 1 1 N 9222 Knottin scorpion toxin-like domain-containing protein OS=Sorghum bicolor OX=4558 GN=BDA96_04G082100 PE=4 SV=1
total 8 proteins

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.GKPMDFC(+57.02)KGDTC(+57.02)K.C Y 53.83 1542.6628 3.4 515.2300 3 14.77 388 3 48 60 Carbamidomethylation
K.SDC(+57.02)KPDLC(+57.02)EK.A Y 46.25 1250.5271 -1.3 626.2700 2 13.53 340 2 32 41 Carbamidomethylation
K.PMDFC(+57.02)KGDTC(+57.02)K.C Y 36.97 1357.5465 -0.7 679.7800 2 14.93 394 1 50 60 Carbamidomethylation
total 3 peptides
Best Unique PSM (Scan 388, m/z=515.2300, z=3, RT=14.77, ppm=3.4):
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.KVLTPAEEAPAEAPA.A Y 46.86 1492.7772 -7.9 747.3900 2 21.08 632 2 55 69
N.KVLTPAEEAPAEAPAA.A Y 37.88 1563.8143 -18.4 782.9000 2 21.53 648 2 55 70
total 2 peptides
Best Unique PSM (Scan 632, m/z=747.3900, z=2, RT=21.08, ppm=-7.9):
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
R.GKGTGYC(+57.02)DKDVC(+57.02)K.C Y 35.53 1486.6544 -6.0 744.3300 2 10.61 224 2 46 58 Carbamidomethylation
A.SPFGK.C Y 26.33 534.2802 -13.8 535.2800 1 9.32 172 1 28 32
total 2 peptides
Best Unique PSM (Scan 224, m/z=744.3300, z=2, RT=10.61, ppm=-6.0):
tr|A0A2I9LPY0|A0A2I9LPY0_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.NVILGGVK.S Y 28.39 798.4963 -4.5 799.5000 1 19.22 562 1 91 98
total 1 peptides
Best Unique PSM (Scan 562, m/z=799.5000, z=1, RT=19.22, ppm=-4.5):
tr|A0A1W7R9A6|A0A1W7R9A6_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.NVILGGVK.S Y 28.39 798.4963 -4.5 799.5000 1 19.22 562 1 91 98
total 1 peptides
Best Unique PSM (Scan 562, m/z=799.5000, z=1, RT=19.22, ppm=-4.5):
tr|A0A159W474|A0A159W474_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
T.NIQLII.Q Y 17.14 712.4483 1157.2 714.2800 1 30.06 962 1 894 899
K.YLVFIFLR.I Y 16.36 1069.6324 -1072.3 535.2500 2 38.96 1294 1 8 15
total 2 peptides
Best Unique PSM (Scan 962, m/z=714.2800, z=1, RT=30.06, ppm=1157.2):
tr|A0A8T2F9B8|A0A8T2F9B8_ARASU
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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
MASSGK.C Y 22.48 579.2686 1595.3 581.2000 1 13.02 320 1 1 6
total 1 peptides
Best Unique PSM (Scan 320, m/z=581.2000, z=1, RT=13.02, ppm=1595.3):
tr|A0A921R469|A0A921R469_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
MASSGK.N Y 22.48 579.2686 1595.3 581.2000 1 13.02 320 1 1 6
total 1 peptides
Best Unique PSM (Scan 320, m/z=581.2000, z=1, RT=13.02, ppm=1595.3):
 


Prepared with PEAKS ™ (bioinfor.com)