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 Scans1006
# of MS/MS Scans1006
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 Matches17
Peptide Sequences14
Protein Groups3
Proteins3
Proteins (#Unique Peptides)2 (>2); 0 (=2); 1 (=1);
FDR (Peptide-Spectrum Matches)29.4%
FDR (Peptide Sequences)35.7%
FDR (Protein)66.7%
De Novo Only Spectra14
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.026C
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 12131000

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: 12_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
2 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 57.29 37 3 3 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
1 6157 sp|P00760|TRY1_BOVIN 50.73 13 3 3 N 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
4 19551 tr|A0A224XFJ9|A0A224XFJ9_9SCOR 29.04 3 2 1 N 45876 Putative Protease inhibitor OS=Megacormus gertschi OX=1843536 PE=3 SV=1
total 3 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 36.56 1250.5271 -1.3 626.2700 2 13.09 314 2 32 41 Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)K.G Y 31.04 997.4361 -10.7 499.7200 2 10.88 230 2 48 55 Oxidation (M); Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)KGDTC(+57.02)K.C Y 15.60 1558.6578 0.2 520.5600 3 11.79 264 2 48 60 Oxidation (M); Carbamidomethylation
total 3 peptides
Best Unique PSM (Scan 314, m/z=626.2700, z=2, RT=13.09, ppm=-1.3):
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 33.02 2162.0491 -75.7 1081.9500 2 30.93 992 3 73 92
K.LQGIVSW.G Y 23.38 801.4385 -32.2 802.4200 1 30.26 968 1 210 216
K.NKPGVY.T Y 18.05 676.3544 12.3 677.3700 1 9.07 160 1 224 229
total 3 peptides
Best Unique PSM (Scan 992, m/z=1081.9500, z=2, RT=30.93, ppm=-75.7):
tr|A0A224XFJ9|A0A224XFJ9_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
D.EIGVR.P N 20.74 572.3282 25.4 573.3500 1 49.73 1698 1 25 29
S.SLSSLL.S Y 16.60 618.3588 -9.9 619.3600 1 47.28 1606 1 59 64
total 2 peptides
Best Unique PSM (Scan 1606, m/z=619.3600, z=1, RT=47.28, ppm=-9.9):
 


Prepared with PEAKS ™ (bioinfor.com)