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 Scans987
# of MS/MS Scans987
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 Matches26
Peptide Sequences19
Protein Groups3
Proteins7
Proteins (#Unique Peptides)2 (>2); 0 (=2); 5 (=1);
FDR (Peptide-Spectrum Matches)80.8%
FDR (Peptide Sequences)89.5%
FDR (Protein)214.3%
De Novo Only Spectra18
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0214C
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 23126100

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: 23_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 32607 sp|P0DQU5|KA212_TITME 141.08 83 6 6 Y 4010 Potassium channel toxin OS=Tityus metuendus OX=2203750 PE=1 SV=1
1 32608 tr|A0A1E1WVP6|A0A1E1WVP6_TITOB 141.08 45 6 6 Y 7302 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
12 7789 tr|A0A2E5JHX1|A0A2E5JHX1_9BACT 26.66 1 1 1 N 131824 Uncharacterized protein OS=Halobacteriovorax sp OX=2020862 GN=CME71_04850 PE=4 SV=1
11 16584 tr|A0A2I9LNW9|A0A2I9LNW9_9SCOR 20.47 1 1 1 N 57810 Cytochrome P450 OS=Centruroides hentzi OX=88313 PE=3 SV=1
11 6371 tr|A0A1W7R9L3|A0A1W7R9L3_9SCOR 20.47 1 1 1 N 102045 Solute carrier family 12 member 9 OS=Hadrurus spadix OX=141984 PE=4 SV=1
11 4937 tr|A0A1W7R9J6|A0A1W7R9J6_9SCOR 20.47 1 1 1 N 100959 Solute carrier family 12 member 9 OS=Hadrurus spadix OX=141984 PE=4 SV=1
11 5085 tr|A0A8T2AQ62|A0A8T2AQ62_ARASU 20.47 0 1 1 N 158839 Endonuclease/exonuclease/phosphatase superfamily OS=Arabidopsis suecica OX=45249 GN=ISN44_As09g029250 PE=4 SV=1
total 7 proteins

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
TAIGNC(+57.02)NPFTC(+57.02)DK.E Y 66.89 1496.6388 4.5 749.3300 2 23.00 678 4 1 13 Carbamidomethylation
R.GYC(+57.02)ENYNC(+57.02)EC(+57.02)SK.W Y 64.94 1582.5487 -65.3 792.2300 2 14.90 374 3 23 34 Carbamidomethylation
TAIGNC(+57.02)NPFTC(+57.02)DKEC(+57.02)K.T Y 64.51 1913.8070 -4.6 638.9400 3 20.61 586 2 1 16 Carbamidomethylation
K.RGYC(+57.02)ENYNC(+57.02)EC(+57.02)SK.W Y 45.41 1738.6498 -2.5 870.3300 2 13.82 334 1 22 34 Carbamidomethylation
N.PFTC(+57.02)DKEC(+57.02)K.T Y 31.30 1183.5001 -12.4 592.7500 2 11.21 236 1 8 16 Carbamidomethylation
TAIGNC(+57.02)NPF.T Y 15.53 992.4385 -13.2 497.2200 2 23.66 702 2 1 9 Carbamidomethylation
total 6 peptides
Best Unique PSM (Scan 678, m/z=749.3300, z=2, RT=23.00, ppm=4.5):
tr|A0A1E1WVP6|A0A1E1WVP6_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
A.TAIGNC(+57.02)NPFTC(+57.02)DK.E Y 66.89 1496.6388 4.5 749.3300 2 23.00 678 4 28 40 Carbamidomethylation
R.GYC(+57.02)ENYNC(+57.02)EC(+57.02)SK.W Y 64.94 1582.5487 -65.3 792.2300 2 14.90 374 3 50 61 Carbamidomethylation
A.TAIGNC(+57.02)NPFTC(+57.02)DKEC(+57.02)K.T Y 64.51 1913.8070 -4.6 638.9400 3 20.61 586 2 28 43 Carbamidomethylation
K.RGYC(+57.02)ENYNC(+57.02)EC(+57.02)SK.W Y 45.41 1738.6498 -2.5 870.3300 2 13.82 334 1 49 61 Carbamidomethylation
N.PFTC(+57.02)DKEC(+57.02)K.T Y 31.30 1183.5001 -12.4 592.7500 2 11.21 236 1 35 43 Carbamidomethylation
A.TAIGNC(+57.02)NPF.T Y 15.53 992.4385 -13.2 497.2200 2 23.66 702 2 28 36 Carbamidomethylation
total 6 peptides
Best Unique PSM (Scan 678, m/z=749.3300, z=2, RT=23.00, ppm=4.5):
tr|A0A2E5JHX1|A0A2E5JHX1_9BACT
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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.TGIDGGDGNRVR.I Y 26.66 1215.5956 -913.2 608.2500 2 12.91 300 1 942 953
total 1 peptides
Best Unique PSM (Scan 300, m/z=608.2500, z=2, RT=12.91, ppm=-913.2):
tr|A0A2I9LNW9|A0A2I9LNW9_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.IIDSR.K Y 20.47 602.3387 -259.0 603.1900 1 5.16 8 1 261 265
total 1 peptides
Best Unique PSM (Scan 8, m/z=603.1900, z=1, RT=5.16, ppm=-259.0):
tr|A0A1W7R9L3|A0A1W7R9L3_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
L.LLDSR.K Y 20.47 602.3387 -259.0 603.1900 1 5.16 8 1 554 558
total 1 peptides
Best Unique PSM (Scan 8, m/z=603.1900, z=1, RT=5.16, ppm=-259.0):
tr|A0A1W7R9J6|A0A1W7R9J6_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
L.LLDSR.K Y 20.47 602.3387 -259.0 603.1900 1 5.16 8 1 544 548
total 1 peptides
Best Unique PSM (Scan 8, m/z=603.1900, z=1, RT=5.16, ppm=-259.0):
tr|A0A8T2AQ62|A0A8T2AQ62_ARASU
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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.LIDSR.S Y 20.47 602.3387 -259.0 603.1900 1 5.16 8 1 931 935
total 1 peptides
Best Unique PSM (Scan 8, m/z=603.1900, z=1, RT=5.16, ppm=-259.0):
 


Prepared with PEAKS ™ (bioinfor.com)