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 Scans985
# of MS/MS Scans985
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 Matches14
Peptide Sequences14
Protein Groups2
Proteins5
Proteins (#Unique Peptides)0 (>2); 0 (=2); 5 (=1);
FDR (Peptide-Spectrum Matches)121.4%
FDR (Peptide Sequences)107.1%
FDR (Protein)60.0%
De Novo Only Spectra21
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.024C
Oxidation15.991M

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 21113000

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: 21_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
9 7719 tr|A0A2I9LNS7|A0A2I9LNS7_9SCOR 28.32 2 1 1 N 56580 ATP synthase subunit beta OS=Centruroides hentzi OX=88313 PE=3 SV=1
9 7720 tr|A0A1W7RAW4|A0A1W7RAW4_9SCOR 28.32 2 1 1 N 56628 ATP synthase subunit beta OS=Hadrurus spadix OX=141984 PE=3 SV=1
16 18648 tr|F6MEN6|F6MEN6_MAIZE 25.51 15 1 1 Y 8663 Defensin OS=Zea mays subsp. mays OX=381124 GN=DEF1 PE=2 SV=1
16 18651 tr|B6SJI6|B6SJI6_MAIZE 25.51 15 1 1 Y 8661 Low-molecular-weight cysteine-rich protein LCR69 OS=Zea mays OX=4577 PE=2 SV=1
16 18653 tr|W5S0Y8|W5S0Y8_MAIZE 25.51 15 1 1 Y 8663 Defensin 1 OS=Zea mays OX=4577 GN=DEF1 PE=2 SV=1
total 5 proteins

tr|A0A2I9LNS7|A0A2I9LNS7_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
Q.MNEPPGAR.A Y 28.32 870.4017 -151.3 436.1423 2 30.31 934 1 268 275
total 1 peptides
Best Unique PSM (Scan 934, m/z=436.1423, z=2, RT=30.31, ppm=-151.3):
tr|A0A1W7RAW4|A0A1W7RAW4_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
Q.MNEPPGAR.A Y 28.32 870.4017 -151.3 436.1423 2 30.31 934 1 268 275
total 1 peptides
Best Unique PSM (Scan 934, m/z=436.1423, z=2, RT=30.31, ppm=-151.3):
tr|F6MEN6|F6MEN6_MAIZE
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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.GLC(+57.02)MSSNNC(+57.02)ANV.C Y 25.51 1325.5162 -656.9 663.3300 2 46.99 1552 1 43 54 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1552, m/z=663.3300, z=2, RT=46.99, ppm=-656.9):
tr|B6SJI6|B6SJI6_MAIZE
back to list

| 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.GLC(+57.02)MSSNNC(+57.02)ANV.C Y 25.51 1325.5162 -656.9 663.3300 2 46.99 1552 1 43 54 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1552, m/z=663.3300, z=2, RT=46.99, ppm=-656.9):
tr|W5S0Y8|W5S0Y8_MAIZE
back to list

| 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.GLC(+57.02)MSSNNC(+57.02)ANV.C Y 25.51 1325.5162 -656.9 663.3300 2 46.99 1552 1 43 54 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 1552, m/z=663.3300, z=2, RT=46.99, ppm=-656.9):
 


Prepared with PEAKS ™ (bioinfor.com)