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 Scans1025
# of MS/MS Scans1025
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 Matches41
Peptide Sequences31
Protein Groups8
Proteins10
Proteins (#Unique Peptides)2 (>2); 0 (=2); 8 (=1);
FDR (Peptide-Spectrum Matches)34.1%
FDR (Peptide Sequences)45.2%
FDR (Protein)20.0%
De Novo Only Spectra9
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.027C
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 46256000

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: 46_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
3 16451 tr|A0A1E1WVY9|A0A1E1WVY9_TITOB 71.48 4 1 1 N 44304 Putative cysteine-rich protein OS=Tityus obscurus OX=1221240 PE=4 SV=1
1 6157 sp|P00760|TRY1_BOVIN 70.65 22 4 4 Y 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
23 32736 tr|A0A1E1WVV0|A0A1E1WVV0_TITOB 65.75 3 1 1 N 49029 Putative cysteine-rich protein OS=Tityus obscurus OX=1221240 PE=4 SV=1
2 74883 sp|P84693|SCX5_TITOB 64.98 30 5 5 Y 9310 Toxin To5 OS=Tityus obscurus OX=1221240 PE=1 SV=2
6 23721 tr|A0A1E1WVU0|A0A1E1WVU0_TITOB 41.24 13 1 1 N 9716 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
4 4987 tr|A0A077S8H7|A0A077S8H7_WHEAT 28.12 0 1 1 N 207714 Uncharacterized protein OS=Triticum aestivum OX=4565 GN=TRAES_3BF139100070CFD_c1 PE=3 SV=1
24 8954 tr|A0A933ZE42|A0A933ZE42_UNCDE 21.28 1 1 1 Y 107880 TNFR-Cys domain-containing protein OS=Deltaproteobacteria bacterium OX=2026735 GN=HY898_09650 PE=4 SV=1
35 13583 tr|A0A4S4E7H1|A0A4S4E7H1_CAMSI 20.75 1 1 1 N 72824 UBX domain-containing protein OS=Camellia sinensis var. sinensis OX=542762 GN=TEA_023691 PE=4 SV=1
35 9168 tr|A0A498HG22|A0A498HG22_MALDO 20.75 1 1 1 N 77829 UBX domain-containing protein OS=Malus domestica OX=3750 GN=DVH24_007674 PE=4 SV=1
35 5303 tr|A0A498I886|A0A498I886_MALDO 20.75 0 1 1 N 150664 UBX domain-containing protein OS=Malus domestica OX=3750 GN=DVH24_040246 PE=4 SV=1
total 10 proteins

tr|A0A1E1WVY9|A0A1E1WVY9_TITOB
back to list

| 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.VSDSDIQIILAAHNELR.N Y 71.48 1892.9956 6.7 632.0100 3 33.44 1118 5 48 64
total 1 peptides
Best Unique PSM (Scan 1118, m/z=632.0100, z=3, RT=33.44, ppm=6.7):
sp|P00760|TRY1_BOVIN
back to list

| 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 47.84 2162.0491 -29.4 1082.0000 2 30.80 1018 3 73 92
K.SIVHPSYNSNTLNNDIM(+15.99)LIK.L Y 24.20 2288.1470 -3.9 763.7200 3 29.35 964 1 93 112 Oxidation (M)
K.NKPGVY.T Y 19.40 676.3544 -2.5 677.3600 1 9.38 178 3 224 229
K.LQGIVSW.G Y 16.96 801.4385 -7.2 802.4400 1 30.43 1004 1 210 216
total 4 peptides
Best Unique PSM (Scan 1018, m/z=1082.0000, z=2, RT=30.80, ppm=-29.4):
tr|A0A1E1WVV0|A0A1E1WVV0_TITOB
back to list

| 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.DIILQWADELR.S Y 65.75 1370.7194 4.4 686.3700 2 39.93 1364 1 138 148
total 1 peptides
Best Unique PSM (Scan 1364, m/z=686.3700, z=2, RT=39.93, ppm=4.4):
sp|P84693|SCX5_TITOB
back to list

| 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
W.C(+57.02)YSLPDNR.N Y 37.76 1023.4443 -18.5 512.7200 2 18.05 524 1 64 71 Carbamidomethylation
Y.SLPDNR.N Y 25.02 700.3504 -64.2 351.1600 2 9.78 194 1 66 71
R.NIWGSYPNNC(+57.02).G Y 23.35 1223.5029 2.1 612.7600 2 26.67 860 2 72 81 Carbamidomethylation
Y.C(+57.02)AWPSC(+57.02)W.C Y 15.50 965.3524 -20.4 966.3400 1 29.69 976 1 57 63 Carbamidomethylation
Y.C(+57.02)AWPSC(+57.02)WC(+57.02)Y.S Y 15.24 1288.4464 -0.8 645.2300 2 32.33 1076 1 57 65 Carbamidomethylation
total 5 peptides
Best Unique PSM (Scan 524, m/z=512.7200, z=2, RT=18.05, ppm=-18.5):
tr|A0A1E1WVU0|A0A1E1WVU0_TITOB
back to list

| 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
S.LVSLIPDETLR.N Y 41.24 1254.7183 -10.2 628.3600 2 31.42 1042 2 29 39
total 1 peptides
Best Unique PSM (Scan 1042, m/z=628.3600, z=2, RT=31.42, ppm=-10.2):
tr|A0A077S8H7|A0A077S8H7_WHEAT
back to list

| 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.ITSSQR.F Y 28.12 690.3660 -1366.4 690.4300 1 43.04 1482 2 1187 1192
total 1 peptides
Best Unique PSM (Scan 1482, m/z=690.4300, z=1, RT=43.04, ppm=-1366.4):
tr|A0A933ZE42|A0A933ZE42_UNCDE
back to list

| 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.ADGDYC(+57.02)DA.N Y 21.28 885.2811 -1373.1 443.0400 2 20.99 638 1 889 896 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 638, m/z=443.0400, z=2, RT=20.99, ppm=-1373.1):
tr|A0A4S4E7H1|A0A4S4E7H1_CAMSI
back to list

| 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
A.IPGASK.F Y 20.75 571.3329 -0.3 572.3400 1 12.38 300 1 573 578
total 1 peptides
Best Unique PSM (Scan 300, m/z=572.3400, z=1, RT=12.38, ppm=-0.3):
tr|A0A498HG22|A0A498HG22_MALDO
back to list

| 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
A.IPGASK.N Y 20.75 571.3329 -0.3 572.3400 1 12.38 300 1 427 432
total 1 peptides
Best Unique PSM (Scan 300, m/z=572.3400, z=1, RT=12.38, ppm=-0.3):
tr|A0A498I886|A0A498I886_MALDO
back to list

| 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
A.IPGASK.N Y 20.75 571.3329 -0.3 572.3400 1 12.38 300 1 432 437
total 1 peptides
Best Unique PSM (Scan 300, m/z=572.3400, z=1, RT=12.38, ppm=-0.3):
 


Prepared with PEAKS ™ (bioinfor.com)