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 Matches33
Peptide Sequences25
Protein Groups4
Proteins4
Proteins (#Unique Peptides)2 (>2); 1 (=2); 1 (=1);
FDR (Peptide-Spectrum Matches)45.5%
FDR (Peptide Sequences)60.0%
FDR (Protein)75.0%
De Novo Only Spectra27
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0214C
Oxidation15.992M

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 16195100

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: 16_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 85.73 22 6 6 Y 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
2 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 81.43 37 4 4 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
4 20591 sp|P60211|KA181_TITOB 55.44 46 2 2 Y 6530 Potassium channel toxin alpha-KTx 18.1 OS=Tityus obscurus OX=1221240 PE=1 SV=2
16 20601 tr|A0A1E1WVW9|A0A1E1WVW9_TITOB 22.66 2 1 1 N 44401 Putative metalloproteinase OS=Tityus obscurus OX=1221240 PE=3 SV=1
total 4 proteins

sp|P00760|TRY1_BOVIN
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
N.MFC(+57.02)AGYLEGGK.D Y 40.01 1231.5365 7.3 616.7800 2 25.09 766 1 183 193 Carbamidomethylation
R.LGEDNINVVEGNEQFISASK.S Y 37.12 2162.0491 -38.7 1081.9900 2 30.84 982 3 73 92
R.LGEDNINVVEGNEQF.I Y 37.03 1675.7689 -2.1 838.8900 2 31.42 1004 2 73 87
K.VC(+57.02)NYVSWIK.Q Y 32.01 1167.5747 -8.0 584.7900 2 27.38 852 2 232 240 Carbamidomethylation
K.QTIASN Y 20.41 632.3129 -16.1 633.3100 1 6.18 48 1 241 246
K.LQGIVSW.G Y 16.33 801.4385 -7.2 802.4400 1 30.73 978 1 210 216
total 6 peptides
tr|A0A1E1WVU5|A0A1E1WVU5_TITOB
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| Protein Coverage | Supporting Peptides |
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 47.33 1250.5271 -1.3 626.2700 2 13.25 320 3 32 41 Carbamidomethylation
K.GKPMDFC(+57.02)KGDTC(+57.02)K.C Y 33.37 1542.6628 3.4 515.2300 3 14.63 374 3 48 60 Carbamidomethylation
K.GKPMDFC(+57.02)K.G Y 31.70 981.4412 -5.8 491.7250 2 14.42 366 1 48 55 Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)KGDTC(+57.02)K.C Y 28.48 1558.6578 0.2 520.5600 3 12.35 286 2 48 60 Oxidation (M); Carbamidomethylation
K.PDLC(+57.02)EK.A Y 27.38 760.3425 0.2 761.3500 1 13.46 328 1 36 41 Carbamidomethylation
total 5 peptides
sp|P60211|KA181_TITOB
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
K.SMESC(+57.02)QGDTC(+57.02)K.C Y 46.97 1301.4686 -2.5 651.7400 2 10.90 230 1 48 58 Carbamidomethylation
A.TGPQTTC(+57.02)QAAM(+15.99)C(+57.02)EAGC(+57.02)K.G Y 16.94 1885.7427 -19.8 943.8600 2 15.74 416 1 27 43 Carbamidomethylation; Oxidation (M)
total 2 peptides
tr|A0A1E1WVW9|A0A1E1WVW9_TITOB
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| Protein Coverage | Supporting Peptides |
Protein Coverage:
Supporting Peptides:
Peptide Uniq -10lgP Mass ppm m/z z RT Scan #Spec Start End PTM
L.KDGPGAK.S Y 22.66 671.3602 -130.3 672.2800 1 11.66 260 1 346 352
total 1 peptides
 


Prepared with PEAKS ™ (bioinfor.com)