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 Scans994
# of MS/MS Scans994
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 Matches34
Peptide Sequences26
Protein Groups6
Proteins21
Proteins (#Unique Peptides)2 (>2); 11 (=2); 8 (=1);
FDR (Peptide-Spectrum Matches)64.7%
FDR (Peptide Sequences)80.8%
FDR (Protein)38.1%
De Novo Only Spectra21
Table 4. PTM profile.
Name ∆Mass #PSM Position
Carbamidomethyl57.027C

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 7.1231200

4. Other Information

Table 6. Search parameters.
Search Engine Name: PEAKS 7.0
Parent Mass Error Tolerance: 0.1 Da
Fragment Mass Error Tolerance: 0.1 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: 7.1_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 6157 sp|P00760|TRY1_BOVIN 97.64 14 4 4 Y 25785 Serine protease 1 OS=Bos taurus OX=9913 GN=PRSS1 PE=1 SV=3
1 15044 tr|A0A1E1WVX0|A0A1E1WVX0_TITOB 74.09 16 4 4 N 8616 Putative bradykinin-potentiating peptide OS=Tityus obscurus OX=1221240 PE=4 SV=1
6 17373 tr|A0A1E1WVU5|A0A1E1WVU5_TITOB 48.94 16 1 1 Y 6863 Putative potassium channel toxin OS=Tityus obscurus OX=1221240 PE=4 SV=1
3 16346 tr|A0A4U6TKV4|A0A4U6TKV4_SETVI 27.81 14 2 2 N 10320 Knottin scorpion toxin-like domain-containing protein OS=Setaria viridis OX=4556 GN=SEVIR_8G241500v2 PE=4 SV=1
3 47061 tr|A0A368SB02|A0A368SB02_SETIT 27.81 14 2 2 N 10263 Knottin scorpion toxin-like domain-containing protein OS=Setaria italica OX=4555 GN=SETIT_8G231300v2 PE=4 SV=1
3 20754 tr|A0A368SCG1|A0A368SCG1_SETIT 27.81 14 2 2 N 10607 Knottin scorpion toxin-like domain-containing protein OS=Setaria italica OX=4555 GN=SETIT_8G230900v2 PE=4 SV=1
3 85972 tr|A0A4U6TIZ7|A0A4U6TIZ7_SETVI 27.81 14 2 2 N 10761 Knottin scorpion toxin-like domain-containing protein OS=Setaria viridis OX=4556 GN=SEVIR_8G242100v2 PE=4 SV=1
3 85971 tr|A0A368SAY7|A0A368SAY7_SETIT 27.81 14 2 2 N 10775 Knottin scorpion toxin-like domain-containing protein OS=Setaria italica OX=4555 GN=SETIT_8G231700v2 PE=4 SV=1
3 66106 tr|A0A4U6TGE2|A0A4U6TGE2_SETVI 27.81 14 2 2 N 10655 Knottin scorpion toxin-like domain-containing protein OS=Setaria viridis OX=4556 GN=SEVIR_8G173300v2 PE=4 SV=1
3 47064 tr|A0A368SAQ8|A0A368SAQ8_SETIT 27.81 14 2 2 N 10672 Knottin scorpion toxin-like domain-containing protein OS=Setaria italica OX=4555 GN=SETIT_8G231600v2 PE=4 SV=1
3 83633 tr|A0A4U6TX98|A0A4U6TX98_SETVI 27.81 14 2 2 N 10672 Knottin scorpion toxin-like domain-containing protein OS=Setaria viridis OX=4556 GN=SEVIR_8G242000v2 PE=4 SV=1
3 66107 tr|A0A368S8C9|A0A368S8C9_SETIT 27.81 14 2 2 N 10754 Knottin scorpion toxin-like domain-containing protein OS=Setaria italica OX=4555 GN=SETIT_8G162900v2 PE=4 SV=1
3 16349 tr|A0A368SA39|A0A368SA39_SETIT 27.81 13 2 2 N 10890 Knottin scorpion toxin-like domain-containing protein OS=Setaria italica OX=4555 GN=SETIT_8G163000v2 PE=4 SV=1
3 108417 tr|A0A4U6TJ21|A0A4U6TJ21_SETVI 27.81 13 2 2 N 10895 Knottin scorpion toxin-like domain-containing protein OS=Setaria viridis OX=4556 GN=SEVIR_8G241300v2 PE=4 SV=1
5 9265 tr|A0A7X9IXF7|A0A7X9IXF7_UNCMY 21.68 1 1 1 N 99020 Disintegrin domain-containing protein OS=Myxococcales bacterium OX=2026763 GN=GYA57_13210 PE=4 SV=1
5 4934 sp|F1LMY4|RYR1_RAT 21.68 0 1 1 N 565491 Ryanodine receptor 1 OS=Rattus norvegicus OX=10116 GN=Ryr1 PE=1 SV=1
5 4931 sp|E9PZQ0|RYR1_MOUSE 21.68 0 1 1 N 565047 Ryanodine receptor 1 OS=Mus musculus OX=10090 GN=Ryr1 PE=1 SV=1
5 4951 sp|P11716|RYR1_RABIT 21.68 0 1 1 N 565261 Ryanodine receptor 1 OS=Oryctolagus cuniculus OX=9986 GN=RYR1 PE=1 SV=1
5 4936 sp|P16960|RYR1_PIG 21.68 0 1 1 N 565340 Ryanodine receptor 1 OS=Sus scrofa OX=9823 GN=RYR1 PE=2 SV=2
5 4929 sp|P21817|RYR1_HUMAN 21.68 0 1 1 N 565184 Ryanodine receptor 1 OS=Homo sapiens OX=9606 GN=RYR1 PE=1 SV=3
20 26762 tr|A0A1W7RAT0|A0A1W7RAT0_9SCOR 21.16 1 1 1 N 63343 Multifunctional fusion protein OS=Hadrurus spadix OX=141984 PE=3 SV=1
total 21 proteins

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
K.LQGIVSWGSGC(+57.02)AQK.N Y 50.82 1489.7347 7.2 745.8800 2 24.91 748 1 210 223 Carbamidomethylation
D.NINVVEGNEQFISASK.S Y 47.91 1747.8740 -16.4 874.9300 2 26.53 808 1 77 92
R.LGEDNINVVEGNEQFISASK.S Y 42.83 2162.0491 -29.4 1082.0000 2 30.73 964 2 73 92
K.LQGIVSW.G Y 34.36 801.4385 -7.2 802.4400 1 30.08 940 1 210 216
total 4 peptides
Best Unique PSM (Scan 748, m/z=745.8800, z=2, RT=24.91, ppm=7.2):
tr|A0A1E1WVX0|A0A1E1WVX0_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
E.EAPAEAPAAAE.R Y 38.85 1025.4666 25.5 1026.5000 1 16.24 426 3 62 72
A.EEAPAEAP.A Y 33.80 812.3552 -3.0 813.3600 1 15.32 392 1 61 68
E.EAPAEAPAA.A Y 31.62 825.3868 -4.9 826.3900 1 15.05 382 2 62 70
E.EAPAEAPAAA.E Y 31.13 896.4239 32.2 897.4600 1 15.81 410 3 62 71
total 4 peptides
Best Unique PSM (Scan 426, m/z=1026.5000, z=1, RT=16.24, ppm=25.5):
tr|A0A1E1WVU5|A0A1E1WVU5_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.SDC(+57.02)KPDLC(+57.02)EK.A Y 48.94 1250.5271 -1.3 626.2700 2 13.50 324 2 32 41 Carbamidomethylation
total 1 peptides
Best Unique PSM (Scan 324, m/z=626.2700, z=2, RT=13.50, ppm=-1.3):
tr|A0A4U6TKV4|A0A4U6TKV4_SETVI
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
MAHSAGK.S Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 93 99
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A368SB02|A0A368SB02_SETIT
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
MAHSAGK.S Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 93 99
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A368SCG1|A0A368SCG1_SETIT
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
MAHSAGK.N Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 97 103
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A4U6TIZ7|A0A4U6TIZ7_SETVI
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
MAHSAGK.T Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 97 103
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A368SAY7|A0A368SAY7_SETIT
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
MAHSAGK.T Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 97 103
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A4U6TGE2|A0A4U6TGE2_SETVI
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
MAHSAGK.N Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 97 103
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A368SAQ8|A0A368SAQ8_SETIT
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
MAHSAGK.N Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 97 103
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A4U6TX98|A0A4U6TX98_SETVI
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
MAHSAGK.N Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 97 103
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A368S8C9|A0A368S8C9_SETIT
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
MAHSAGK.N Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 97 103
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A368SA39|A0A368SA39_SETIT
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
MAHSAGK.N Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 99 105
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A4U6TJ21|A0A4U6TJ21_SETVI
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
MAHSAGK.N Y 19.39 700.3326 57.2 701.3800 1 8.41 132 2 1 7
A.ASAPIPA Y 16.84 625.3435 78.7 626.4000 1 12.13 272 1 99 105
total 2 peptides
Best Unique PSM (Scan 132, m/z=701.3800, z=1, RT=8.41, ppm=57.2):
tr|A0A7X9IXF7|A0A7X9IXF7_UNCMY
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
C.DPVGG.C Y 21.68 443.2016 160.5 444.2800 1 13.29 316 2 283 287
total 1 peptides
Best Unique PSM (Scan 316, m/z=444.2800, z=1, RT=13.29, ppm=160.5):
sp|F1LMY4|RYR1_RAT
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.DPVGG.S Y 21.68 443.2016 160.5 444.2800 1 13.29 316 2 1828 1832
total 1 peptides
Best Unique PSM (Scan 316, m/z=444.2800, z=1, RT=13.29, ppm=160.5):
sp|E9PZQ0|RYR1_MOUSE
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.DPVGG.S Y 21.68 443.2016 160.5 444.2800 1 13.29 316 2 1830 1834
total 1 peptides
Best Unique PSM (Scan 316, m/z=444.2800, z=1, RT=13.29, ppm=160.5):
sp|P11716|RYR1_RABIT
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.DPVGG.S Y 21.68 443.2016 160.5 444.2800 1 13.29 316 2 1828 1832
total 1 peptides
Best Unique PSM (Scan 316, m/z=444.2800, z=1, RT=13.29, ppm=160.5):
sp|P16960|RYR1_PIG
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.DPVGG.S Y 21.68 443.2016 160.5 444.2800 1 13.29 316 2 1829 1833
total 1 peptides
Best Unique PSM (Scan 316, m/z=444.2800, z=1, RT=13.29, ppm=160.5):
sp|P21817|RYR1_HUMAN
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.DPVGG.S Y 21.68 443.2016 160.5 444.2800 1 13.29 316 2 1828 1832
total 1 peptides
Best Unique PSM (Scan 316, m/z=444.2800, z=1, RT=13.29, ppm=160.5):
tr|A0A1W7RAT0|A0A1W7RAT0_9SCOR
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.DTDEAL.G Y 21.16 662.2759 221.7 663.4300 1 7.22 86 1 468 473
total 1 peptides
Best Unique PSM (Scan 86, m/z=663.4300, z=1, RT=7.22, ppm=221.7):
 


Prepared with PEAKS ™ (bioinfor.com)