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 Scans1004
# of MS/MS Scans1004
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 Matches28
Peptide Sequences25
Protein Groups5
Proteins6
Proteins (#Unique Peptides)2 (>2); 0 (=2); 4 (=1);
FDR (Peptide-Spectrum Matches)10.7%
FDR (Peptide Sequences)12.0%
FDR (Protein)83.3%
De Novo Only Spectra12
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.025C
Oxidation15.994M

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 11204100

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: 11_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 87.44 14 4 4 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
2 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 66.12 37 3 3 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
6 17885 tr|A0A096ZQ90|A0A096ZQ90_9SCOR 28.47 2 1 1 N 39082 Cytochrome c oxidase subunit 1 (Fragment) OS=Kochius villosus OX=1532978 GN=COI PE=3 SV=1
23 16312 tr|A0A2I9LP26|A0A2I9LP26_9SCOR 22.34 1 1 1 N 97687 Alpha-1,4 glucan phosphorylase OS=Centruroides hentzi OX=88313 PE=3 SV=1
3 7833 tr|A0A510A7E6|A0A510A7E6_MESMA 21.59 0 1 1 N 169621 Dscam13 (Fragment) OS=Mesobuthus martensii OX=34649 PE=2 SV=1
3 12153 tr|A0A2I9LPH6|A0A2I9LPH6_9SCOR 21.59 1 1 1 N 42142 CLIP domain-containing serine protease OS=Centruroides hentzi OX=88313 PE=3 SV=1
total 6 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 51.82 2162.0491 -29.4 1082.0000 2 30.86 986 3 73 92
K.SIVHPSYN.S Y 40.27 915.4450 -21.4 458.7200 2 16.26 436 1 93 100
R.LGEDNINVVEGNEQF.I Y 28.76 1675.7689 -2.1 838.8900 2 31.35 1004 1 73 87
K.APILSD.S Y 23.57 614.3275 1489.8 616.2500 1 18.12 506 1 163 168
total 4 peptides
Best Unique PSM (Scan 986, m/z=1082.0000, z=2, RT=30.86, ppm=-29.4):
tr|A0A1E1WVU5|A0A1E1WVU5_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
K.SDC(+57.02)KPDLC(+57.02)EK.A Y 49.93 1250.5271 -1.3 626.2700 2 13.52 332 2 32 41 Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)KGDTC(+57.02)K.C Y 19.61 1558.6578 0.2 520.5600 3 11.89 268 2 48 60 Oxidation (M); Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)K.G Y 19.14 997.4361 -10.7 499.7200 2 10.98 232 2 48 55 Oxidation (M); Carbamidomethylation
total 3 peptides
Best Unique PSM (Scan 332, m/z=626.2700, z=2, RT=13.52, ppm=-1.3):
tr|A0A096ZQ90|A0A096ZQ90_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
A.IPTGIK.I Y 28.47 627.3955 1477.9 629.3300 1 10.20 202 1 298 303
total 1 peptides
Best Unique PSM (Scan 202, m/z=629.3300, z=1, RT=10.20, ppm=1477.9):
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.QISVK.G Y 22.34 573.3486 1768.8 575.3700 1 8.32 130 1 13 17
total 1 peptides
Best Unique PSM (Scan 130, m/z=575.3700, z=1, RT=8.32, ppm=1768.8):
tr|A0A510A7E6|A0A510A7E6_MESMA
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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.ELGAW.K Y 21.59 574.2751 -1588.7 574.3700 1 7.84 112 2 1142 1146
total 1 peptides
Best Unique PSM (Scan 112, m/z=574.3700, z=1, RT=7.84, ppm=-1588.7):
tr|A0A2I9LPH6|A0A2I9LPH6_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
S.ELGAW.P Y 21.59 574.2751 -1588.7 574.3700 1 7.84 112 2 133 137
total 1 peptides
Best Unique PSM (Scan 112, m/z=574.3700, z=1, RT=7.84, ppm=-1588.7):
 


Prepared with PEAKS ™ (bioinfor.com)