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 Matches44
Peptide Sequences36
Protein Groups10
Proteins11
Proteins (#Unique Peptides)2 (>2); 2 (=2); 7 (=1);
FDR (Peptide-Spectrum Matches)36.4%
FDR (Peptide Sequences)44.4%
FDR (Protein)63.6%
De Novo Only Spectra27
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0225C
Oxidation15.994M

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 25315000

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: 25_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 34478 tr|A0A1E1WVZ4|A0A1E1WVZ4_TITOB 130.52 28 3 3 Y 7197 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
3 20591 sp|P60211|KA181_TITOB 91.97 46 2 2 Y 6530 Potassium channel toxin alpha-KTx 18.1 OS=Tityus obscurus OX=1221240 PE=1 SV=2
2 15044 tr|A0A1E1WVX0|A0A1E1WVX0_TITOB 61.81 32 4 4 N 8616 Putative bradykinin-potentiating peptide OS=Tityus obscurus OX=1221240 PE=4 SV=1
24 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 54.52 16 1 1 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
4 6157 sp|P00760|TRY1_BOVIN 32.08 8 1 1 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
5 18066 tr|A0A2I9LPE3|A0A2I9LPE3_9SCOR 30.79 1 2 2 N 103040 Paramyosin OS=Centruroides hentzi OX=88313 PE=4 SV=1
25 111 tr|A0A1V1WBH9|A0A1V1WBH9_9SCOR 25.76 4 1 1 Y 26319 Putative phospholipase OS=Superstitionia donensis OX=311983 PE=3 SV=1
31 115689 tr|V4KSG7|V4KSG7_EUTSA 21.89 5 1 1 Y 11155 Knottin scorpion toxin-like domain-containing protein OS=Eutrema salsugineum OX=72664 GN=EUTSA_v10011889mg PE=3 SV=1
27 47017 tr|A0A397ZYR2|A0A397ZYR2_BRACM 21.06 7 1 1 Y 9423 Knottin scorpion toxin-like domain-containing protein OS=Brassica campestris OX=3711 GN=BRARA_C02325 PE=4 SV=1
43 6529 tr|A0A510A1Z8|A0A510A1Z8_MESMA 20.68 0 1 1 N 157093 Dscam6 OS=Mesobuthus martensii OX=34649 PE=2 SV=1
43 7833 tr|A0A510A7E6|A0A510A7E6_MESMA 20.68 0 1 1 N 169621 Dscam13 (Fragment) OS=Mesobuthus martensii OX=34649 PE=2 SV=1
total 11 proteins

tr|A0A1E1WVZ4|A0A1E1WVZ4_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)DEDVC(+57.02)K.C Y 88.78 1487.6021 2.3 744.8100 2 13.47 336 2 46 58 Carbamidomethylation
K.GTGYC(+57.02)DEDVC(+57.02)K.C Y 50.27 1302.4856 -0.1 652.2500 2 15.56 416 1 48 58 Carbamidomethylation
R.YC(+57.02)NPR.N Y 49.82 708.3013 -107.4 355.1199 2 5.60 26 6 32 36 Carbamidomethylation
total 3 peptides
Best Unique PSM (Scan 336, m/z=744.8100, z=2, RT=13.47, ppm=2.3):
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)QAAMC(+57.02)EAGC(+57.02)K.G Y 66.61 1869.7478 9.5 935.8900 2 18.78 538 2 27 43 Carbamidomethylation
K.SMESC(+57.02)QGDTC(+57.02)K.C Y 50.72 1301.4686 -2.5 651.7400 2 10.79 230 1 48 58 Carbamidomethylation
total 2 peptides
Best Unique PSM (Scan 538, m/z=935.8900, z=2, RT=18.78, ppm=9.5):
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
K.VLTPAEEAPAEAPAAAE.R Y 38.08 1635.7991 89.5 818.9800 2 24.73 760 1 56 72
M.LKEYANK.V Y 25.24 864.4705 0.0 433.2425 2 6.37 56 1 49 55
N.KVLTPAEEAPAEAPAAAE.R Y 19.92 1763.8940 -16.2 882.9400 2 22.25 668 1 55 72
E.APAAAE.R Y 17.82 528.2543 -3.0 529.2600 1 24.36 746 1 67 72
total 4 peptides
Best Unique PSM (Scan 760, m/z=818.9800, z=2, RT=24.73, ppm=89.5):
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 54.52 1250.5271 -1.3 626.2700 2 13.68 344 1 32 41 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 344, m/z=626.2700, z=2, RT=13.68, ppm=-1.3):
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
R.LGEDNINVVEGNEQFISASK.S Y 32.08 2162.0491 -20.2 1082.0100 2 30.52 972 2 73 92
total 1 peptides
Best Unique PSM (Scan 972, m/z=1082.0100, z=2, RT=30.52, ppm=-20.2):
tr|A0A2I9LPE3|A0A2I9LPE3_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
D.AELAK.L Y 23.07 530.3064 -6.9 531.3100 1 45.84 1544 1 94 98
I.VQAEE.D Y 15.45 574.2598 22.5 575.2800 1 44.94 1510 1 778 782
total 2 peptides
Best Unique PSM (Scan 1544, m/z=531.3100, z=1, RT=45.84, ppm=-6.9):
tr|A0A1V1WBH9|A0A1V1WBH9_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.IC(+57.02)SAASEAER.F Y 25.76 1092.4869 90.1 547.3000 2 56.05 1934 1 95 104 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1934, m/z=547.3000, z=2, RT=56.05, ppm=90.1):
tr|V4KSG7|V4KSG7_EUTSA
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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.TC(+57.02)PNR.K Y 21.89 646.2857 88.2 647.3500 1 8.55 142 1 82 86 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 142, m/z=647.3500, z=1, RT=8.55, ppm=88.2):
tr|A0A397ZYR2|A0A397ZYR2_BRACM
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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.C(+57.02)ISTGY.K Y 21.06 699.2898 -10.1 700.2900 1 16.43 450 1 46 51 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 450, m/z=700.2900, z=1, RT=16.43, ppm=-10.1):
tr|A0A510A1Z8|A0A510A1Z8_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.VGDFVT.S Y 20.68 636.3119 32.8 637.3400 1 38.11 1252 1 469 474
total 1 peptides
Best Unique PSM (Scan 1252, m/z=637.3400, z=1, RT=38.11, ppm=32.8):
tr|A0A510A7E6|A0A510A7E6_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
S.VGDFVT.R Y 20.68 636.3119 32.8 637.3400 1 38.11 1252 1 467 472
total 1 peptides
Best Unique PSM (Scan 1252, m/z=637.3400, z=1, RT=38.11, ppm=32.8):
 


Prepared with PEAKS ™ (bioinfor.com)