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 Scans998
# of MS/MS Scans998
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 Matches27
Peptide Sequences20
Protein Groups6
Proteins12
Proteins (#Unique Peptides)0 (>2); 2 (=2); 10 (=1);
FDR (Peptide-Spectrum Matches)51.9%
FDR (Peptide Sequences)70.0%
FDR (Protein)16.7%
De Novo Only Spectra18
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0212C
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 15125300

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: 15_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 6157 sp|P00760|TRY1_BOVIN 99.60 14 2 2 Y 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
2 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 63.29 37 2 2 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
30 6165 tr|A0A510ACK2|A0A510ACK2_MESMA 24.01 0 1 1 N 162123 Dscam11 OS=Mesobuthus martensii OX=34649 PE=2 SV=1
4 11856 tr|A0A0U4RZC4|A0A0U4RZC4_ODODO 23.09 7 1 1 N 9440 Sodium channel toxin NaTx11 OS=Odontobuthus doriae OX=342590 GN=NaTx11 PE=2 SV=1
4 20635 sp|P0DQN8|DEL1A_HOTJU 23.09 9 1 1 N 7491 Delta-buthitoxin-Hj1a OS=Hottentotta judaicus OX=6863 PE=1 SV=1
4 20636 tr|D5HR49|D5HR49_9SCOR 23.09 9 1 1 N 7750 Neurotoxin 9 (Fragment) OS=Androctonus bicolor OX=748906 PE=4 SV=1
4 20637 tr|A0A0B5GD34|A0A0B5GD34_MESEU 23.09 7 1 1 N 9272 Analgesic-antitumor-like protein OS=Mesobuthus eupeus OX=34648 PE=4 SV=1
4 20639 tr|B8XGZ6|B8XGZ6_BUTOS 23.09 7 1 1 N 9334 Putative alpha toxin Tx772 OS=Buthus occitanus israelis OX=539894 PE=2 SV=1
4 20638 sp|Q2YHM1|SCX8R_ANDMA 23.09 7 1 1 N 9598 Neurotoxin 8-related gene product 1/2/3 OS=Androctonus mauritanicus mauritanicus OX=6860 GN=NTVIIIrgp1 PE=3 SV=1
4 268 sp|Q86SE0|SCX2_ANDAM 23.09 7 1 1 N 9283 Toxin Aam2 OS=Androctonus amoreuxi OX=112024 PE=1 SV=1
15 13480 tr|A0A6J1T5F7|A0A6J1T5F7_FRAOC 21.09 2 1 1 Y 46072 Sarcoplasmic reticulum histidine-rich calcium-binding protein-like isoform X1 OS=Frankliniella occidentalis OX=133901 GN=LOC113211635 PE=4 SV=2
16 17969 tr|A0A2E4D844|A0A2E4D844_9BACT 20.65 1 1 1 N 149598 LysM domain-containing protein OS=Halobacteriovoraceae bacterium OX=2026745 GN=CME62_04835 PE=4 SV=1
total 12 proteins

sp|P00760|TRY1_BOVIN
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
K.LQGIVSWGSGC(+57.02)AQK.N Y 72.27 1489.7347 -6.2 745.8700 2 25.48 772 2 210 223 Carbamidomethylation
R.LGEDNINVVEGNEQFISASK.S Y 54.66 2162.0491 211.1 1082.2600 2 31.37 992 3 73 92
total 2 peptides
tr|A0A1E1WVU5|A0A1E1WVU5_TITOB
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| Protein Coverage | Supporting Peptides |
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 53.27 1250.5271 -20.3 417.8412 3 12.93 304 4 32 41 Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)KGDTC(+57.02)K.C Y 20.03 1558.6578 -19.1 520.5500 3 12.24 278 1 48 60 Oxidation (M); Carbamidomethylation
total 2 peptides
tr|A0A510ACK2|A0A510ACK2_MESMA
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
P.QLLEVK.E Y 24.01 728.4432 54.2 729.4900 1 13.28 318 1 74 79
total 1 peptides
tr|A0A0U4RZC4|A0A0U4RZC4_ODODO
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
P.IKVPGK.C Y 23.09 640.4272 -6.9 641.4301 1 10.63 218 3 76 81
total 1 peptides
sp|P0DQN8|DEL1A_HOTJU
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
P.IKVPGK.C Y 23.09 640.4272 -6.9 641.4301 1 10.63 218 3 59 64
total 1 peptides
tr|D5HR49|D5HR49_9SCOR
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
P.IKVPGK.C Y 23.09 640.4272 -6.9 641.4301 1 10.63 218 3 61 66
total 1 peptides
tr|A0A0B5GD34|A0A0B5GD34_MESEU
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
P.IKVPGK.C Y 23.09 640.4272 -6.9 641.4301 1 10.63 218 3 76 81
total 1 peptides
tr|B8XGZ6|B8XGZ6_BUTOS
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
P.IKVPGK.C Y 23.09 640.4272 -6.9 641.4301 1 10.63 218 3 77 82
total 1 peptides
sp|Q2YHM1|SCX8R_ANDMA
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
P.IKVPGK.C Y 23.09 640.4272 -6.9 641.4301 1 10.63 218 3 77 82
total 1 peptides
sp|Q86SE0|SCX2_ANDAM
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
P.IKVPGK.C Y 23.09 640.4272 -6.9 641.4301 1 10.63 218 3 77 82
total 1 peptides
tr|A0A6J1T5F7|A0A6J1T5F7_FRAOC
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
M(+15.99)RRATASALR.L Y 21.09 1147.6244 645.7 575.1900 2 25.81 784 1 1 10 Oxidation (M)
total 1 peptides
tr|A0A2E4D844|A0A2E4D844_9BACT
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
R.FEQFVSKY.K Y 20.65 1046.5072 17.5 524.2700 2 36.26 1174 1 463 470
total 1 peptides
 


Prepared with PEAKS ™ (bioinfor.com)