# Result Files CoMPaseD generates four result files: - [ProteinAbundance.tsv](result-protein_abundance) - Generated during execution of the export module. ```{table} :class: result-table 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](result-random_sampling) - 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_output`](sampling_output) to false in the parameter file. ```{table} :class: result-table 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](CoMPaseD_results) - 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 `Results` tab of the GUI. ```{table} :class: result-table 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](CoMPaseD_results_summary) - 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). ```{table} :class: result-table 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. | ``` --- (result-protein_abundance)= ## ProteinAbundance.tsv ```{table} :class: result-table | 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 | ... | ... | ...| ... | ... | ... | ... ``` --- (result-random_sampling)= ## RandomSampling.tsv ```{table} :class: result-table | 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)= ## CoMPaseD_results.tsv ```{table} :class: result-table 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)= ## CoMPaseD_results_summary.tsv ```{table} :class: result-table 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 ... | ... | ... | ... | ... | ... ```