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 Scans998
# of MS/MS Scans998
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 Matches19
Peptide Sequences15
Protein Groups5
Proteins5
Proteins (#Unique Peptides)0 (>2); 1 (=2); 4 (=1);
FDR (Peptide-Spectrum Matches)78.9%
FDR (Peptide Sequences)80.0%
FDR (Protein)0.0%
De Novo Only Spectra19
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.026C
Acetylation42.012N-term
Deamidation.982N
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 8132000

4. Other Information

Table 6. Search parameters.
Search Engine Name: PEAKS 7.0
Parent Mass Error Tolerance: 0.07 Da
Fragment Mass Error Tolerance: 0.07 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
  Acetylation (N-term): 42.01
  Deamidation (NQ): 0.98
Max variable PTM per peptide: 3
Database: Scopion2023
Taxon: All
Searched Entry: 15746
FDR Estimation: Enabled
Merge Options: 0.1 min. 0.1 Da
Precursor Options: corrected
Charge Options: no correction
Filter Options: no filter
Process: true
Table 7. Instrument parameters.
Fractions: 8_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 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 49.54 16 2 2 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
5 16621 tr|A0A2I9LPF0|A0A2I9LPF0_9SCOR 37.47 2 2 1 N 56566 Protein disulfide-isomerase OS=Centruroides hentzi OX=88313 PE=3 SV=1
3 6157 sp|P00760|TRY1_BOVIN 35.20 8 1 1 Y 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
6 5040 tr|A0A1W7RAM6|A0A1W7RAM6_9SCOR 31.98 1 2 1 N 126852 Dynactin subunit 1 OS=Hadrurus spadix OX=141984 PE=4 SV=1
10 5291 tr|A0A1W7R9J9|A0A1W7R9J9_9SCOR 21.26 0 1 1 N 279093 Spectrin alpha chain OS=Hadrurus spadix OX=141984 PE=3 SV=1
total 5 proteins

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 38.51 1250.5271 -1.3 626.2700 2 13.54 334 4 32 41 Carbamidomethylation
S.DC(+57.02)KPDLC(+57.02)EK.A Y 22.06 1163.4951 -8.3 582.7500 2 13.91 348 1 33 41 Carbamidomethylation
total 2 peptides
Best Unique PSM (Scan 334, m/z=626.2700, z=2, RT=13.54, ppm=-1.3):
tr|A0A2I9LPF0|A0A2I9LPF0_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.KLGEK.Y Y 26.62 573.3486 24.7 574.3700 1 5.32 14 1 407 411
L.EGLSK.F N 21.69 532.2856 32.1 533.3100 1 9.85 188 1 461 465
total 2 peptides
Best Unique PSM (Scan 14, m/z=574.3700, z=1, RT=5.32, ppm=24.7):
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 35.20 2162.0491 -6.3 1082.0250 2 30.31 958 2 73 92
R.LGEDNIN(+.98)VVEGNEQFISASK.S Y 21.20 2163.0332 -77.6 1082.4399 2 30.44 962 2 73 92 Deamidation (NQ)
total 2 peptides
Best Unique PSM (Scan 958, m/z=1082.0250, z=2, RT=30.31, ppm=-6.3):
tr|A0A1W7RAM6|A0A1W7RAM6_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
I.EGLSK.P N 21.69 532.2856 32.1 533.3100 1 9.85 188 1 875 879
K.DQLAK.L Y 20.56 573.3122 53.2 574.3500 1 49.57 1676 1 939 943
total 2 peptides
Best Unique PSM (Scan 1676, m/z=574.3500, z=1, RT=49.57, ppm=53.2):
tr|A0A1W7R9J9|A0A1W7R9J9_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.SVQTLQR.K Y 21.26 830.4610 14.1 831.4800 1 14.59 374 1 291 297
total 1 peptides
Best Unique PSM (Scan 374, m/z=831.4800, z=1, RT=14.59, ppm=14.1):
 


Prepared with PEAKS ™ (bioinfor.com)