Result Files
CoMPaseD generates four result files:
ProteinAbundance.tsv - Generated during execution of the export module.
Column Name |
Description |
|---|---|
Identifier |
Protein identifier from the input FASTA file. |
Sequence_Len[aa] |
Length of the protein in amino acids. |
Group |
Group that the protein is assigned to during protease score calculation. |
Random_Sampling_x |
Protein abundance in replicate x of the Monte Carlo Simulation. A value of zero indicates that the protein is not expressed in the corresponding sampling replicate. One column for each replicate. |
RandomSampling.tsv - A file listing all peptides identified during a CoMPaseD analysis. Since this file can become quite large, its output can be suppressed by setting the parameter
Sampling_outputto false in the parameter file.
Column Name |
Description |
|---|---|
index |
Internal peptide index. |
peptide |
Peptide sequence. |
protein |
Protein identifier from the input FASTA file. |
location |
Position of the peptides first amino acid in the protein sequence. |
MC |
Number of missed cleavage sites in peptide. |
Enzyme |
Protease that generated this peptide. Identical peptides produced by different proteases are listed as separate entries. |
Sequence_Len[aa] |
Length of the protein in amino acids. |
Group |
Group that the protein is assigned to during protease score calculation. |
Random_Sampling_x |
Protein abundance in replicate x of the Monte Carlo Simulation. One column for each replicate. |
DeepMSPep_prediction |
Predicted detectability by DeepMSPeptide. |
subset |
String that combines enzyme and MC information. |
ID |
Internal peptide index. |
sampling_x |
Presence (1) or absence (0) of the peptide in replicate x of the Monte Carlo simulation. One column for each replicate. |
CoMPaseD_results.tsv - This file contains detailed data necessary for calculating protease scores across Monte Carlo simulations. Filtered columns include values calculated with a requirement of at least two unique peptides per protein, whereas unfiltered columns also include proteins identified by a single unique peptide. The file can be visualised in the
Resultstab of the GUI.
Column Number |
Column Name |
Description |
|---|---|---|
1 |
Protease combination |
Protease combination used in this iteration. |
2 |
Protein group |
Group for that the score was calculated. |
3 |
Random sampling |
Sampling replicate for that the score was calulated. |
4 |
Protease score (unfiltered) |
Prediceted protease score for current protease combination and sampling replicate considering all identified peptides. |
5 |
Protease score (filtered) |
Prediceted protease score for current protease combination and sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
6 |
Total proteins identified (unfiltered) |
Number of identified proteins in the current protease combination and sampling replicate considering all identified peptides. |
7 |
Total number of peptides identified (unfiltered) |
Total number of identified peptides in the current protease combination and sampling replicate considering all identified peptides. |
8 |
Mean number of peptides per protein identified (unfiltered) |
Average number of identified peptides per proteins in the current protease combination and sampling replicate considering all peptides. |
9 |
Median number of peptides per protein identified (unfiltered) |
Median number of identified peptides per proteins in the current protease combination and sampling replicate considering all peptides. |
10 |
Mean protein coverage (unfiltered) |
Average protein sequence coverage in the current protease combination and sampling replicate considering all peptides. |
11 |
Median protein coverage (unfiltered) |
Median protein sequence coverage in the current protease combination and sampling replicate considering all peptides. |
12 |
Min peptides per protein for filtering |
Number of peptides required for a protein to be identified under filtered criteria. Fixed to two currently. |
13 |
Total proteins identified (filtered) |
Number of identified proteins in the current protease combination and sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
14 |
Total number of peptides identified (filtered) |
Total number of identified peptides in the current protease combination and sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
15 |
Mean number of peptides per protein identified (filtered) |
Average number of identified peptides per proteins in the current protease combination and sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
16 |
Median number of peptides per protein identified (filtered) |
Median number of identified peptides per proteins in the current protease combination and sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
17 |
Mean protein coverage (filtered) |
Average protein sequence coverage in the current protease combination and sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
18 |
Median protein coverage (filtered) |
Median protein sequence coverage in the current protease combination and sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
19 |
Protease combination trypsin |
Helper column stating that the following columns refer to the values observed for trypsin as protease (control condition). |
20 |
Total proteins identified (unfiltered) trypsin |
Number of identified proteins in the tryptic digestion and the current sampling replicate considering all identified peptides. |
21 |
Total number of peptides identified (unfiltered) trypsin |
Total number of identified peptides in the tryptic digestion and the current sampling replicate considering all identified peptides. |
22 |
Mean number of peptides per protein identified (unfiltered) trypsin |
Average number of identified peptides per proteins in the tryptic digestion and the current sampling replicate considering all peptides. |
23 |
Median number of peptides per protein identified (unfiltered) trypsin |
Median number of identified peptides per proteins in the tryptic digestion and the current sampling replicate considering all peptides. |
24 |
Mean protein coverage (unfiltered) trypsin |
Average protein sequence coverage in the tryptic digestion and the current sampling replicate considering all peptides. |
25 |
Median protein coverage (unfiltered) trypsin |
Median protein sequence coverage in the tryptic digestion and the current sampling replicate considering all peptides. |
26 |
Min peptides per protein for filtering trypsin |
Number of peptides required for a protein to be identified under filtered criteria in the tryptic digestion. Fixed to two currently. |
27 |
Total proteins identified (filtered) trypsin |
Number of identified proteins in the tryptic digestion and the current sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
28 |
Total number of peptides identified (filtered) trypsin |
Total number of identified peptides in the tryptic digestion and the current sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
29 |
Mean number of peptides per protein identified (filtered) trypsin |
Average number of identified peptides per proteins in the tryptic digestion and the current sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
30 |
Median number of peptides per protein identified (filtered) trypsin |
Median number of identified peptides per proteins in the tryptic digestion and the current sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
31 |
Mean protein coverage (filtered) trypsin |
Average protein sequence coverage in the tryptic digestion and the current sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
32 |
Median protein coverage (filtered) trypsin |
Median protein sequence coverage in the tryptic digestion and the current sampling replicate considering all peptides that belong to proteins identified by at least two peptides. |
33 |
Protein ID ratio (unfiltered) |
Ratio between columns 6 and 20 |
34 |
Protein ID ratio (filtered) |
Ratio between columns 13 and 27 |
35 |
Protein ID weight |
Weighting factor of the number of identified proteins during protease score calculation. |
36 |
Peptide ID ratio (unfiltered) |
Ratio between columns 7 and 21 |
37 |
Peptide ID ratio (filtered) |
Ratio between columns 14 and 28 |
38 |
Peptide ID weight |
Weighting factor of the number of identified peptides during protease score calculation. |
39 |
Protein coverage ratio (unfiltered) |
Ratio between columns 10 and 24 |
40 |
Protein coverage ratio (filtered) |
Ratio between columns 17 and 31 |
41 |
Protein coverage weight |
Weighting factor of the protein coverage during protease score calculation. |
CoMPaseD_results_summary.tsv - This file summarises the predicted protease scores, including the average and standard deviation, for all protease combinations and protein groups. The values are provided unfiltered (i.e. considering all identified unique peptides) and filtered (i.e. considering only peptides for proteins that are identified by at leat two unique peptides).
Column Name |
Description |
|---|---|
Protease combination |
Individual protease or combination of proteases for this row. |
Protein group |
Group for that the score was calculated. |
Mean_score_unfiltered |
Average protease score based on unfiltered data. |
Protease SD_score_unfiltered |
Standard deviation of the protease score between sampling replicates calculated from unfiltered data. |
Mean_score_filtered |
Average protease score based on filtered data. |
Protease SD_score_filtered |
Standard deviation of the protease score between sampling replicates calculated from filtered data. |
ProteinAbundance.tsv
Identifier |
Sequence_Len[aa] |
Group |
Random_sampling_1 |
Random_sampling_2 |
… |
|---|---|---|---|---|---|
AL009126.3_prot_CAB11777.1_1 |
446 |
large_proteins |
0.000497626 |
3.51E-05 |
… |
AL009126.3_prot_CAB11777.1_2 |
378 |
large_proteins |
0 |
0.002066499 |
… |
AL009126.3_prot_CAB11777.1_3 |
71 |
medium_proteins |
0 |
0.000109971 |
… |
AL009126.3_prot_CAB11777.1_4 |
370 |
large_proteins |
5.68E-06 |
0 |
… |
AL009126.3_prot_CAB11777.1_5 |
81 |
medium_proteins |
3.36E-05 |
0.000395656 |
… |
… |
… |
… |
… |
… |
… |
RandomSampling.tsv
index |
peptide |
protein |
location |
MC |
Enzyme |
Identifier |
Sequence_Len[aa] |
Group |
Random_sampling_1 |
Random_sampling_2 |
… |
DeepMSPep_prediction |
subset |
ID |
sampling_1 |
sampling_2 |
… |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
397 |
AALELLQVEYKELEVMDSPE |
AL009126.3_prot_CAB15238.1_3421 |
111 |
5 |
glu-c |
AL009126.3_prot_CAB15238.1_3421 |
745 |
large_proteins |
1.17683e-05 |
2.80666e-05 |
… |
0.546137 |
glu-c__5 |
397 |
0 |
1 |
… |
1459 |
AEGKTVMLVSLDGEAAGLVAVADTLKDTSRKAVARLKE |
AL009126.3_prot_CAB15355.2_3532 |
605 |
5 |
glu-c |
AL009126.3_prot_CAB15355.2_3532 |
802 |
large_proteins |
0.0002083 |
0.0 |
… |
0.484481 |
glu-c__5 |
1459 |
0 |
0 |
… |
2494 |
AGKALADYLLSKNLYFEVYTDDHLLSPFDGE |
AL009126.3_prot_CAB15602.1_3775 |
84 |
5 |
glu-c |
AL009126.3_prot_CAB15602.1_3775 |
286 |
large_proteins |
0.000523 |
0.000129 |
… |
0.815637 |
glu-c__5 |
2494 |
1 |
0 |
… |
2751 |
AGYTPMLQQYLKLKAEHQDAFLFFRLGDFYEMFFED |
AL009126.3_prot_CAB13577.2_1779 |
2 |
5 |
glu-c |
AL009126.3_prot_CAB13577.2_1779 |
858 |
large_proteins |
0.0001213 |
0.0 |
… |
0.617249 |
glu-c__5 |
2751 |
0 |
0 |
… |
2836 |
AHNVKTRNFHTQEALYVLEKEFGSELPYMLTENAE |
AL009126.3_prot_CAB15641.1_3816 |
195 |
5 |
glu-c |
AL009126.3_prot_CAB15641.1_3816 |
254 |
large_proteins |
0.00051 |
0.004293 |
… |
0.827224 |
glu-c__5 |
2836 |
0 |
1 |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
CoMPaseD_results.tsv
Protease combination |
Protein group |
Random sampling |
Protease score (unfiltered) |
Protease score (filtered) |
Total proteins identified (unfiltered) |
Total number of peptides identified (unfiltered) |
Mean number of peptides per protein identified (unfiltered) |
Median number of peptides per protein identified (unfiltered) |
Mean protein coverage (unfiltered) |
Median protein coverage (unfiltered) |
Min peptides per protein for filtering |
Total proteins identified (filtered) |
Total number of peptides identified (filtered) |
Mean number of peptides per protein identified (filtered) |
Median number of peptides per protein identified (filtered) |
Mean protein coverage (filtered) |
Median protein coverage (filtered) |
Protease combination trypsin |
Total proteins identified (unfiltered) trypsin |
Total number of peptides identified (unfiltered) trypsin |
Mean number of peptides per protein identified (unfiltered) trypsin |
Median number of peptides per protein identified (unfiltered) trypsin |
Mean protein coverage (unfiltered) trypsin |
Median protein coverage (unfiltered) trypsin |
Min peptides per protein for filtering trypsin |
Total proteins identified (filtered) trypsin |
Total number of peptides identified (filtered) trypsin |
Mean number of peptides per protein identified (filtered) trypsin |
Median number of peptides per protein identified (filtered) trypsin |
Mean protein coverage (filtered) trypsin |
Median protein coverage (filtered) trypsin |
Protein ID ratio (unfiltered) |
Protein ID ratio (filtered) |
Protein ID weight |
Peptide ID ratio (unfiltered) |
Peptide ID ratio (filtered) |
Peptide ID weight |
Protein coverage ratio (unfiltered) |
Protein coverage ratio (filtered) |
Protein coverage weight |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
lysarginase |
large_proteins |
sampling_1 |
0.991033528 |
0.988085663 |
1741 |
9586 |
5.506031017 |
3 |
0.229539862 |
0.142857143 |
2 |
1157 |
9002 |
7.780466724 |
4 |
0.3100638 |
0.23566879 |
trypsin |
1822 |
9584 |
5.260153677 |
2 |
0.225389713 |
0.141463415 |
2 |
1261 |
9023 |
7.155432197 |
4 |
0.294220951 |
0.224264706 |
0.955543359 |
0.917525773 |
1 |
1.000208681 |
0.997672614 |
1 |
1.01841321 |
1.053846772 |
1 |
lysarginase |
large_proteins |
sampling_2 |
0.991713591 |
0.988836114 |
1726 |
9650 |
5.590961761 |
3 |
0.230335557 |
0.147518687 |
2 |
1188 |
9112 |
7.67003367 |
4 |
0.301459803 |
0.223596148 |
trypsin |
1767 |
9629 |
5.449349179 |
3 |
0.231181224 |
0.144615385 |
2 |
1218 |
9080 |
7.454844007 |
4 |
0.305178172 |
0.230672836 |
0.976796831 |
0.975369458 |
1 |
1.002180912 |
1.003524229 |
1 |
0.996341974 |
0.987815742 |
1 |
lysarginase |
large_proteins |
sampling_3 |
0.989773687 |
0.992397163 |
1739 |
9650 |
5.549166187 |
2 |
0.22425363 |
0.139534884 |
2 |
1165 |
9076 |
7.79055794 |
4 |
0.300496672 |
0.219298246 |
trypsin |
1809 |
9627 |
5.32172471 |
2 |
0.222858461 |
0.134110787 |
2 |
1193 |
9011 |
7.553227158 |
4 |
0.302405791 |
0.227722772 |
0.961304588 |
0.976529757 |
1 |
1.002389114 |
1.007213406 |
1 |
1.006260337 |
0.993686897 |
1 |
lysarginase |
large_proteins |
sampling_4 |
0.998754169 |
0.994863905 |
1729 |
9620 |
5.563909774 |
3 |
0.229890039 |
0.144781145 |
2 |
1150 |
9041 |
7.86173913 |
4 |
0.309665507 |
0.235915328 |
trypsin |
1755 |
9594 |
5.466666667 |
3 |
0.227948936 |
0.145922747 |
2 |
1193 |
9032 |
7.570829841 |
5 |
0.303453218 |
0.231343284 |
0.985185185 |
0.963956412 |
1 |
1.002710027 |
1.000996457 |
1 |
1.008515518 |
1.020471985 |
1 |
lysarginase |
large_proteins |
sampling_5 |
0.985180868 |
0.980941375 |
1745 |
9725 |
5.573065903 |
2 |
0.223660864 |
0.137870855 |
2 |
1160 |
9140 |
7.879310345 |
4 |
0.301024102 |
0.232362468 |
trypsin |
1746 |
9699 |
5.554982818 |
3 |
0.234399096 |
0.145454545 |
2 |
1183 |
9136 |
7.7227388 |
4 |
0.312849496 |
0.232323232 |
0.999427262 |
0.980557904 |
1 |
1.002680689 |
1.000437828 |
1 |
0.954188252 |
0.962201012 |
1 |
lysarginase |
large_proteins |
sampling_6 |
0.986787078 |
0.990287818 |
1652 |
9647 |
5.839588378 |
3 |
0.227821016 |
0.150684932 |
2 |
1125 |
9120 |
8.106666667 |
4 |
0.301925487 |
0.232727273 |
trypsin |
1750 |
9631 |
5.503428571 |
2.5 |
0.224190039 |
0.140801179 |
2 |
1171 |
9052 |
7.730145175 |
4 |
0.30092716 |
0.238095238 |
0.944 |
0.960717336 |
1 |
1.001661302 |
1.007512152 |
1 |
1.016195977 |
1.003317503 |
1 |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
… |
CoMPaseD_results_summary.tsv
Protease combination |
Protein group |
Mean_score_unfiltered |
SD_score_unfiltered |
Mean_score_filtered |
SD_score_filtered |
|---|---|---|---|---|---|
trypsin - lysarginase - glu-c - chymotrypsin - lys-c |
large_proteins |
2.354363188 |
0.008808405 |
2.458483168 |
0.012681445 |
trypsin - lysarginase - glu-c - lys-c |
large_proteins |
2.123887564 |
0.008527206 |
2.211297635 |
0.012756247 |
trypsin - lysarginase - chymotrypsin - lys-c |
large_proteins |
2.116116367 |
0.006825438 |
2.203260086 |
0.009988885 |
trypsin - glu-c - chymotrypsin - lys-c |
large_proteins |
2.111351133 |
0.007827643 |
2.198311019 |
0.010794093 |
… |
… |
… |
… |
… |
… |