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 Matches38
Peptide Sequences30
Protein Groups6
Proteins6
Proteins (#Unique Peptides)2 (>2); 0 (=2); 4 (=1);
FDR (Peptide-Spectrum Matches)34.2%
FDR (Peptide Sequences)43.3%
FDR (Protein)66.7%
De Novo Only Spectra24
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0219C
Oxidation15.992M

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 241412400

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: 24_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
2 34478 tr|A0A1E1WVZ4|A0A1E1WVZ4_TITOB 128.59 38 4 4 Y 7197 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
1 32607 sp|P0DQU5|KA212_TITME 122.54 91 4 4 Y 4010 Potassium channel toxin OS=Tityus metuendus OX=2203750 PE=1 SV=1
17 7764 tr|A0A2I9LPY0|A0A2I9LPY0_9SCOR 28.48 1 1 1 N 118515 E1 ubiquitin-activating enzyme OS=Centruroides hentzi OX=88313 PE=3 SV=1
6 16299 sp|P0DQU4|NDB_TITME 22.46 33 1 1 N 1735 Probable bradykinin-potentiating peptide OS=Tityus metuendus OX=2203750 PE=1 SV=1
19 19612 tr|A0A1W7R9W7|A0A1W7R9W7_9SCOR 20.70 1 1 1 N 93955 Prominin-1-A OS=Hadrurus spadix OX=141984 PE=3 SV=1
21 19592 tr|A0A1W7R9E1|A0A1W7R9E1_9SCOR 20.24 1 1 1 N 73525 Transmembrane 9 superfamily member OS=Hadrurus spadix OX=141984 PE=3 SV=1
total 6 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 92.52 1487.6021 150.2 744.9200 2 13.36 330 2 46 58 Carbamidomethylation
R.GKGTGYC(+57.02)DEDVC(+57.02)KC(+57.02)SGW.K Y 45.55 1977.7655 -3.7 660.2600 3 20.45 600 2 46 62 Carbamidomethylation
K.GTGYC(+57.02)DEDVC(+57.02)K.C Y 25.07 1302.4856 -0.1 652.2500 2 15.17 398 2 48 58 Carbamidomethylation
P.FRYC(+57.02)NPR.N Y 19.73 1011.4708 -5.3 506.7400 2 13.58 338 1 30 36 Carbamidomethylation
total 4 peptides
Best Unique PSM (Scan 330, m/z=744.9200, z=2, RT=13.36, ppm=150.2):
sp|P0DQU5|KA212_TITME
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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.GYC(+57.02)ENYNC(+57.02)EC(+57.02)SKW Y 70.29 1768.6279 -12.7 885.3100 2 20.92 618 4 23 35 Carbamidomethylation
TAIGNC(+57.02)NPFTC(+57.02)DKEC(+57.02)K.T Y 68.14 1913.8070 -4.6 638.9400 3 20.50 602 2 1 16 Carbamidomethylation
TAIGNC(+57.02)NPFTC(+57.02)DKEC(+57.02)KTK.G Y 34.93 2142.9497 -5.4 715.3200 3 19.17 552 1 1 18 Carbamidomethylation
K.RGYC(+57.02)ENYNC(+57.02)EC(+57.02)SKW Y 26.13 1924.7291 -22.7 963.3500 2 18.92 542 1 22 35 Carbamidomethylation
total 4 peptides
Best Unique PSM (Scan 618, m/z=885.3100, z=2, RT=20.92, ppm=-12.7):
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 28.48 798.4963 -17.1 799.4900 1 18.57 528 1 91 98
total 1 peptides
Best Unique PSM (Scan 528, m/z=799.4900, z=1, RT=18.57, ppm=-17.1):
sp|P0DQU4|NDB_TITME
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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.APAAAE Y 22.46 528.2543 -3.0 529.2600 1 24.68 760 1 13 18
total 1 peptides
Best Unique PSM (Scan 760, m/z=529.2600, z=1, RT=24.68, ppm=-3.0):
tr|A0A1W7R9W7|A0A1W7R9W7_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.LETSSSLLGW.Y Y 20.70 1091.5499 957.8 547.3050 2 43.40 1448 1 48 57
total 1 peptides
Best Unique PSM (Scan 1448, m/z=547.3050, z=2, RT=43.40, ppm=957.8):
tr|A0A1W7R9E1|A0A1W7R9E1_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.QSSGAVP.F Y 20.24 644.3129 1675.9 646.4000 1 42.30 1406 1 432 438
total 1 peptides
Best Unique PSM (Scan 1406, m/z=646.4000, z=1, RT=42.30, ppm=1675.9):
 


Prepared with PEAKS ™ (bioinfor.com)