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 Matches31
Peptide Sequences20
Protein Groups4
Proteins4
Proteins (#Unique Peptides)2 (>2); 0 (=2); 2 (=1);
FDR (Peptide-Spectrum Matches)22.6%
FDR (Peptide Sequences)35.0%
FDR (Protein)50.0%
De Novo Only Spectra18
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.0215C
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 13172100

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: 13_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 87.12 37 6 6 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
2 6157 sp|P00760|TRY1_BOVIN 77.62 14 4 4 Y 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
9 10550 tr|A0A1W7RAF8|A0A1W7RAF8_9SCOR 24.81 1 1 1 N 107991 Hypoxia up-regulated protein 1 OS=Hadrurus spadix OX=141984 PE=3 SV=1
5 5187 tr|A0A2I9LP29|A0A2I9LP29_9SCOR 20.19 1 1 1 N 159702 Homeobox protein cut-like OS=Centruroides hentzi OX=88313 PE=3 SV=1
total 4 proteins

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 49.83 1250.5271 398.5 626.5200 2 13.40 320 7 32 41 Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)KGDTC(+57.02)K.C Y 29.63 1558.6578 0.2 520.5600 3 12.02 266 1 48 60 Oxidation (M); Carbamidomethylation
K.GKPM(+15.99)DFC(+57.02)K.G Y 27.24 997.4361 -10.7 499.7200 2 11.22 236 3 48 55 Oxidation (M); Carbamidomethylation
S.DC(+57.02)KPDLC(+57.02)EK.A Y 26.02 1163.4951 -8.3 582.7500 2 13.32 316 1 33 41 Carbamidomethylation
K.PDLC(+57.02)EK.A Y 20.08 760.3425 -12.9 761.3400 1 13.27 314 1 36 41 Carbamidomethylation
M.DFC(+57.02)KGDTC(+57.02)K.C Y 17.22 1129.4532 10.8 565.7400 2 7.55 98 1 52 60 Carbamidomethylation
total 6 peptides
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
R.LGEDNINVVEGNEQFISASK.S Y 44.80 2162.0491 -1.8 1082.0299 2 30.70 970 5 73 92
K.LQGIVSWGSGC(+57.02)AQK.N Y 33.75 1489.7347 7.2 745.8800 2 25.29 766 1 210 223 Carbamidomethylation
K.LQGIVSW.G Y 28.84 801.4385 -7.2 802.4400 1 30.27 952 2 210 216
R.LGEDNINVVEGNEQF.I Y 25.34 1675.7689 582.7 839.3800 2 31.40 994 1 73 87
total 4 peptides
tr|A0A1W7RAF8|A0A1W7RAF8_9SCOR
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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
Q.VILAGAATR.T Y 24.81 870.5287 1338.0 436.8540 2 13.68 330 1 372 380
total 1 peptides
tr|A0A2I9LP29|A0A2I9LP29_9SCOR
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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.YANETLNTL.N Y 20.19 1037.5029 -942.1 519.2700 2 39.83 1310 1 404 412
total 1 peptides
 


Prepared with PEAKS ™ (bioinfor.com)