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 Scans997
# of MS/MS Scans997
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 Sequences22
Protein Groups6
Proteins7
Proteins (#Unique Peptides)0 (>2); 5 (=2); 2 (=1);
FDR (Peptide-Spectrum Matches)37.0%
FDR (Peptide Sequences)45.5%
FDR (Protein)0.0%
De Novo Only Spectra9
Table 4. PTM profile.
Name ∆Mass #PSM Position
Oxidation15.992M
Carbamidomethyl57.021C

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 7183100

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: 7_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 58.17 11 2 2 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
2 16299 sp|P0DQU4|NDB_TITME 43.75 61 2 2 N 1735 Probable bradykinin-potentiating peptide OS=Tityus metuendus OX=2203750 PE=1 SV=1
16 7483 tr|A0A1W7R9Y6|A0A1W7R9Y6_9SCOR 26.80 2 1 1 N 40842 Plasminogen activator inhibitor 1 RNA-binding protein OS=Hadrurus spadix OX=141984 PE=3 SV=1
3 13710 tr|Q1JV20|Q1JV20_PANIM 25.19 2 2 2 N 48913 Zinc finger protein Pi-Zic OS=Pandinus imperator OX=55084 GN=Pi-Zic PE=2 SV=1
4 5311 tr|A0A249JQT4|A0A249JQT4_ANTPA 24.03 1 2 2 Y 224552 Sodium channel protein OS=Antrozous pallidus OX=9440 GN=SCN9A PE=2 SV=1
4 18 sp|Q15858|SCN9A_HUMAN 24.03 1 2 2 Y 226370 Sodium channel protein type 9 subunit alpha OS=Homo sapiens OX=9606 GN=SCN9A PE=1 SV=3
17 16312 tr|A0A2I9LP26|A0A2I9LP26_9SCOR 22.30 1 1 1 N 97687 Alpha-1,4 glucan phosphorylase OS=Centruroides hentzi OX=88313 PE=3 SV=1
total 7 proteins

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 50.44 2162.0491 238.9 1082.2900 2 30.31 954 4 73 92
K.SAASLNSR.V Y 15.44 804.4089 -425.0 403.0408 2 7.50 96 1 115 122
total 2 peptides
Best Unique PSM (Scan 954, m/z=1082.2900, z=2, RT=30.31, ppm=238.9):
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.APAEAPAAAE Y 30.11 896.4239 -12.5 897.4200 1 13.92 338 1 9 18
E.EAPAEAPAA.A Y 27.27 825.3868 1206.7 827.3900 1 14.60 364 3 8 16
total 2 peptides
Best Unique PSM (Scan 338, m/z=897.4200, z=1, RT=13.92, ppm=-12.5):
tr|A0A1W7R9Y6|A0A1W7R9Y6_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.GTKHAPVNK.S Y 26.80 950.5297 -25.5 476.2600 2 36.54 1186 1 50 58
total 1 peptides
Best Unique PSM (Scan 1186, m/z=476.2600, z=2, RT=36.54, ppm=-25.5):
tr|Q1JV20|Q1JV20_PANIM
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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
Q.APNGY.G Y 17.40 520.2281 -1740.4 520.3300 1 23.32 690 2 44 48
A.AAVAA.A Y 15.58 401.2274 -2678.5 401.1600 1 6.86 72 1 28 32
total 2 peptides
Best Unique PSM (Scan 690, m/z=520.3300, z=1, RT=23.32, ppm=-1740.4):
tr|A0A249JQT4|A0A249JQT4_ANTPA
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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.SEC(+57.02)FALM(+15.99).N Y 16.43 872.3408 164.9 437.2496 2 57.35 1970 1 1355 1361 Carbamidomethylation; Oxidation (M)
A.LDPPLLI.A Y 15.19 779.4792 -1547.8 779.2800 1 17.36 466 1 1796 1802
total 2 peptides
Best Unique PSM (Scan 1970, m/z=437.2496, z=2, RT=57.35, ppm=164.9):
sp|Q15858|SCN9A_HUMAN
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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.SEC(+57.02)FALM(+15.99).N Y 16.43 872.3408 164.9 437.2496 2 57.35 1970 1 1368 1374 Carbamidomethylation; Oxidation (M)
A.LDPPLLI.A Y 15.19 779.4792 -1547.8 779.2800 1 17.36 466 1 1809 1815
total 2 peptides
Best Unique PSM (Scan 1970, m/z=437.2496, z=2, RT=57.35, ppm=164.9):
tr|A0A2I9LP26|A0A2I9LP26_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.DYGVTVNP.S Y 22.30 863.4025 764.7 865.0700 1 11.03 230 1 553 560
total 1 peptides
Best Unique PSM (Scan 230, m/z=865.0700, z=1, RT=11.03, ppm=764.7):
 


Prepared with PEAKS ™ (bioinfor.com)