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 Scans1006
# of MS/MS Scans1006
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 Matches68
Peptide Sequences25
Protein Groups7
Proteins9
Proteins (#Unique Peptides)2 (>2); 1 (=2); 6 (=1);
FDR (Peptide-Spectrum Matches)16.2%
FDR (Peptide Sequences)44.0%
FDR (Protein)55.6%
De Novo Only Spectra25
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0259C
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 14178000

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: 14_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 136.08 48 8 7 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
2 6157 sp|P00760|TRY1_BOVIN 66.08 11 3 3 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
3 17889 sp|P0C1X6|KA183_TITDI 42.96 21 3 2 Y 6633 Potassium channel toxin alpha-KTx 18.3 OS=Tityus discrepans OX=57059 PE=1 SV=2
11 8954 tr|A0A933ZE42|A0A933ZE42_UNCDE 28.96 0 1 1 Y 107880 TNFR-Cys domain-containing protein OS=Deltaproteobacteria bacterium OX=2026735 GN=HY898_09650 PE=4 SV=1
11 7526 tr|A0A1W7RAU8|A0A1W7RAU8_9SCOR 28.96 0 1 1 Y 180469 Protein ced-11 OS=Hadrurus spadix OX=141984 PE=4 SV=1
13 46992 tr|A0A1E1WW12|A0A1E1WW12_TITOB 23.65 10 1 1 Y 7716 Putative sodium channel toxin (Fragment) OS=Tityus obscurus OX=1221240 PE=4 SV=1
13 46991 tr|A0A1E1WWK1|A0A1E1WWK1_TITOB 23.65 8 1 1 Y 9302 Putative sodium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
14 23697 tr|A0A0Q3HLL6|A0A0Q3HLL6_BRADI 21.39 10 1 1 Y 7864 Knottin scorpion toxin-like domain-containing protein OS=Brachypodium distachyon OX=15368 GN=BRADI_1g76294v3 PE=4 SV=1
16 77084 tr|A0A1W7RB70|A0A1W7RB70_9SCOR 20.07 5 1 1 N 22710 Alpha-crystallin B chain OS=Hadrurus spadix OX=141984 PE=3 SV=1
total 9 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.SDC(+57.02)KPDLC(+57.02)EK.A Y 66.17 1250.5271 198.6 626.3950 2 12.55 302 23 32 41 Carbamidomethylation
K.GKPMDFC(+57.02)KGDTC(+57.02)K.C Y 56.68 1542.6628 -16.0 515.2200 3 13.97 356 15 48 60 Carbamidomethylation
K.PMDFC(+57.02)KGDTC(+57.02)K.C Y 44.51 1357.5465 -0.7 679.7800 2 14.17 364 4 50 60 Carbamidomethylation
A.EAGDGPKSDC(+57.02)KPDLC(+57.02)EK.A Y 37.59 1904.8243 -46.7 953.3750 2 15.01 400 1 25 41 Carbamidomethylation
M.DFC(+57.02)KGDTC(+57.02)K.C Y 36.65 1129.4532 -6.9 565.7300 2 10.73 224 2 52 60 Carbamidomethylation
K.PDLC(+57.02)EK.A Y 29.74 760.3425 0.2 761.3500 1 12.33 288 1 36 41 Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)KGDTC(+57.02)K.C Y 28.34 1558.6578 4.9 780.3400 2 11.93 272 2 48 60 Oxidation (M); Carbamidomethylation
D.C(+57.02)KPDLC(+57.02)EK.A Y 21.88 1048.4681 -2.6 525.2400 2 12.43 294 9 34 41 Carbamidomethylation
K.GKPMDFC(+57.02)K.G N 15.29 981.4412 -16.0 491.7200 2 13.10 320 1 48 55 Carbamidomethylation
total 9 peptides
Best Unique PSM (Scan 302, m/z=626.3950, z=2, RT=12.55, ppm=198.6):
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 40.36 2162.0491 44.5 1082.0800 2 30.95 994 2 73 92
R.LGEDNINVVEGNEQF.I Y 35.66 1675.7689 9.9 838.9000 2 31.70 1022 1 73 87
K.LQGIVSW.G Y 23.65 801.4385 -7.2 802.4400 1 30.68 984 1 210 216
total 3 peptides
Best Unique PSM (Scan 994, m/z=1082.0800, z=2, RT=30.95, ppm=44.5):
sp|P0C1X6|KA183_TITDI
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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.PMDFC(+57.02)KDGTC(+57.02)K.C Y 29.28 1357.5465 -0.7 679.7800 2 13.78 348 2 49 59 Carbamidomethylation
M.DFC(+57.02)KDGTC(+57.02)K.C Y 17.16 1129.4532 -6.9 565.7300 2 14.07 360 1 51 59 Carbamidomethylation
L.GKPMDFC(+57.02)K.D N 15.29 981.4412 -16.0 491.7200 2 13.10 320 1 47 54 Carbamidomethylation
total 3 peptides
Best Unique PSM (Scan 348, m/z=679.7800, z=2, RT=13.78, ppm=-0.7):
tr|A0A933ZE42|A0A933ZE42_UNCDE
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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.C(+57.02)STC(+57.02)K.S Y 28.96 654.2465 70.6 655.3000 1 5.90 38 1 733 737 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 38, m/z=655.3000, z=1, RT=5.90, ppm=70.6):
tr|A0A1W7RAU8|A0A1W7RAU8_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.C(+57.02)STC(+57.02)K.I Y 28.96 654.2465 70.6 655.3000 1 5.90 38 1 1139 1143 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 38, m/z=655.3000, z=1, RT=5.90, ppm=70.6):
tr|A0A1E1WW12|A0A1E1WW12_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.NC(+57.02)YC(+57.02)YDV Y 23.65 992.3368 89.3 497.2200 2 33.37 1084 1 63 69 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1084, m/z=497.2200, z=2, RT=33.37, ppm=89.3):
tr|A0A1E1WWK1|A0A1E1WWK1_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.NC(+57.02)YC(+57.02)YDV.A Y 23.65 992.3368 89.3 497.2200 2 33.37 1084 1 63 69 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1084, m/z=497.2200, z=2, RT=33.37, ppm=89.3):
tr|A0A0Q3HLL6|A0A0Q3HLL6_BRADI
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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.C(+57.02)GGPGPK.T Y 21.39 671.3061 -49.7 672.2800 1 11.17 242 1 55 61 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 242, m/z=672.2800, z=1, RT=11.17, ppm=-49.7):
tr|A0A1W7RB70|A0A1W7RB70_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
E.EKTESSSVYR.E Y 20.07 1184.5673 32.2 593.3100 2 37.48 1238 1 137 146
total 1 peptides
Best Unique PSM (Scan 1238, m/z=593.3100, z=2, RT=37.48, ppm=32.2):
 


Prepared with PEAKS ™ (bioinfor.com)