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 Scans992
# of MS/MS Scans992
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 Matches24
Peptide Sequences21
Protein Groups7
Proteins8
Proteins (#Unique Peptides)1 (>2); 0 (=2); 7 (=1);
FDR (Peptide-Spectrum Matches)33.3%
FDR (Peptide Sequences)38.1%
FDR (Protein)12.5%
De Novo Only Spectra15
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 5201000

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: 5_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 124.48 24 6 6 Y 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
11 10470 tr|A0A1W7R9S0|A0A1W7R9S0_9SCOR 26.39 3 1 1 N 24154 Ribosomal protein L15 OS=Hadrurus spadix OX=141984 PE=3 SV=1
11 10471 tr|A0A2I9LPK3|A0A2I9LPK3_9SCOR 26.39 3 1 1 N 24183 Ribosomal protein L15 OS=Centruroides hentzi OX=88313 PE=3 SV=1
12 10472 tr|A0A8H6QEA9|A0A8H6QEA9_9EURO 22.82 9 1 1 N 9170 Invertebrate defensins family profile domain-containing protein OS=Aspergillus hiratsukae OX=1194566 GN=CNMCM6106_005558 PE=3 SV=1
4 4984 tr|A0A1W7RAQ1|A0A1W7RAQ1_9SCOR 22.18 0 1 1 N 419079 Dystrophin OS=Hadrurus spadix OX=141984 PE=4 SV=1
13 10473 tr|A0A8K1NA23|A0A8K1NA23_HEMLE 20.93 2 1 1 N 59934 succinate dehydrogenase (Fragment) OS=Hemiscorpius lepturus OX=520031 PE=2 SV=1
14 7678 tr|A0A1W7RB60|A0A1W7RB60_9SCOR 20.67 1 1 1 N 101271 Alpha-catenin OS=Hadrurus spadix OX=141984 PE=3 SV=1
3 10474 tr|A0A1W7RAL1|A0A1W7RAL1_9SCOR 20.01 1 1 1 Y 116351 Endonuclease-reverse transcriptase OS=Hadrurus spadix OX=141984 PE=4 SV=1
total 8 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 64.94 2162.0491 16.9 1082.0500 2 30.29 942 3 73 92
K.SIVHPSYNSN.T Y 56.61 1116.5200 900.5 559.7700 2 16.06 412 2 93 102
K.DSC(+57.02)QGDSGGPVVC(+57.02)SGK.L Y 46.18 1608.6508 -28.2 805.3100 2 14.91 370 1 194 209 Carbamidomethylation
D.NINVVEGN.E Y 36.26 857.4243 1176.1 859.4400 1 18.03 484 1 77 84
K.LQGIVSW.G Y 21.16 801.4385 1253.1 803.4500 1 30.00 930 1 210 216
K.NKPGVY.T Y 15.20 676.3544 -2.5 677.3600 1 9.64 176 1 224 229
total 6 peptides
Best Unique PSM (Scan 942, m/z=1082.0500, z=2, RT=30.29, ppm=16.9):
tr|A0A1W7R9S0|A0A1W7R9S0_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
G.LTSAGR.K Y 26.39 603.3340 -1676.1 603.3300 1 45.83 1522 1 164 169
total 1 peptides
Best Unique PSM (Scan 1522, m/z=603.3300, z=1, RT=45.83, ppm=-1676.1):
tr|A0A2I9LPK3|A0A2I9LPK3_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
G.LTSAGR.K Y 26.39 603.3340 -1676.1 603.3300 1 45.83 1522 1 164 169
total 1 peptides
Best Unique PSM (Scan 1522, m/z=603.3300, z=1, RT=45.83, ppm=-1676.1):
tr|A0A8H6QEA9|A0A8H6QEA9_9EURO
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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
G.VTAAPAAE.A Y 22.82 728.3704 -51.7 729.3400 1 11.52 246 1 18 25
total 1 peptides
Best Unique PSM (Scan 246, m/z=729.3400, z=1, RT=11.52, ppm=-51.7):
tr|A0A1W7RAQ1|A0A1W7RAQ1_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
V.VIEVQR.S Y 22.18 742.4337 -109.1 743.3600 1 11.63 250 1 1724 1729
total 1 peptides
Best Unique PSM (Scan 250, m/z=743.3600, z=1, RT=11.63, ppm=-109.1):
tr|A0A8K1NA23|A0A8K1NA23_HEMLE
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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
I.VVGAGGAGLR.A Y 20.93 855.4926 939.6 429.1555 2 19.44 536 1 60 69
total 1 peptides
Best Unique PSM (Scan 536, m/z=429.1555, z=2, RT=19.44, ppm=939.6):
tr|A0A1W7RB60|A0A1W7RB60_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
R.ILTEAVDDIT.T Y 20.67 1088.5601 -13.4 545.2800 2 48.60 1626 1 498 507
total 1 peptides
Best Unique PSM (Scan 1626, m/z=545.2800, z=2, RT=48.60, ppm=-13.4):
tr|A0A1W7RAL1|A0A1W7RAL1_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
E.VNSRIAM(+15.99)AK.Q Y 20.01 1004.5437 -18.2 503.2700 2 6.82 70 1 818 826 Oxidation (M)
total 1 peptides
Best Unique PSM (Scan 70, m/z=503.2700, z=2, RT=6.82, ppm=-18.2):
 


Prepared with PEAKS ™ (bioinfor.com)