Completed at 20240919, 11:54
Experiment set | Proteins ID and quant. (1%FDR) | Proteins ID and quant. (gene centric, 1%FDR) | Peptides (unique, 1%FDR) | Peptides/protein (unique, median) | Peptides/protein (genecentric, unique, median) | PSMs (total) | PSMs/protein for quant (median) | PSMs/protein for quant (genecentric, median) |
---|---|---|---|---|---|---|---|---|
0set.A | 222 | 211 | 248 | 1 | 1 | 320 | 1 | 1 |
ID in # sets | Amount peptides |
---|---|
1 | 248 |
ID in # sets | Amount proteins |
---|---|
1 | 222 |
ID in # sets | Amount genes |
---|---|
1 | 211 |
Experiment set | Channel | Norm. factor |
---|---|---|
0set-A | tmt16plex_126 | -0.3812506907666733 |
0set-A | tmt16plex_127N | -0.4011267803010927 |
0set-A | tmt16plex_127C | -0.3547112924044207 |
0set-A | tmt16plex_128N | -0.2669261591935985 |
0set-A | tmt16plex_128C | 0.26047016422005953 |
0set-A | tmt16plex_129N | 0.37160990273899763 |
0set-A | tmt16plex_129C | 0.08846498738009956 |
0set-A | tmt16plex_130N | 0.27067254897136195 |
0set-A | tmt16plex_130C | 0.13814126982141417 |
0set-A | tmt16plex_131N | 0.3823908661598434 |
0set-A | tmt16plex_131C | 0.4980175659594499 |
0set-A | tmt16plex_132N | 0.3748644880634959 |
0set-A | tmt16plex_132C | 1.2041017452439537 |
0set-A | tmt16plex_133N | 1.0981915784122291 |
0set-A | tmt16plex_133C | 1.7086654834168744 |
0set-A | tmt16plex_134N | 1.8767710235687378 |
Experiment set | Channel | Norm. factor |
---|---|---|
0set-A | tmt16plex_126 | -0.3792997724856786 |
0set-A | tmt16plex_127N | -0.40706423038385875 |
0set-A | tmt16plex_127C | -0.3480516226837693 |
0set-A | tmt16plex_128N | -0.2608539967570165 |
0set-A | tmt16plex_128C | 0.2547556200296608 |
0set-A | tmt16plex_129N | 0.3740302570353098 |
0set-A | tmt16plex_129C | 0.08726388180043854 |
0set-A | tmt16plex_130N | 0.2688540737791776 |
0set-A | tmt16plex_130C | 0.137313195917109 |
0set-A | tmt16plex_131N | 0.3801105153735058 |
0set-A | tmt16plex_131C | 0.49962367130928254 |
0set-A | tmt16plex_132N | 0.3748644880634959 |
0set-A | tmt16plex_132C | 1.2071837599900648 |
0set-A | tmt16plex_133N | 1.1276934303003197 |
0set-A | tmt16plex_133C | 1.719477751875088 |
0set-A | tmt16plex_134N | 1.8731164699632172 |
Experiment set | Channel | Norm. factor |
---|---|---|
0set-A | tmt16plex_126 | -0.38011051537350404 |
0set-A | tmt16plex_127N | -0.4120933450102102 |
0set-A | tmt16plex_127C | -0.34943292533801795 |
0set-A | tmt16plex_128N | -0.2608539967570165 |
0set-A | tmt16plex_128C | 0.25399634843590135 |
0set-A | tmt16plex_129N | 0.37177403362153427 |
0set-A | tmt16plex_129C | 0.08836398508510968 |
0set-A | tmt16plex_130N | 0.26826770426831636 |
0set-A | tmt16plex_130C | 0.13485246539688767 |
0set-A | tmt16plex_131N | 0.38190347103521916 |
0set-A | tmt16plex_131C | 0.500756819072544 |
0set-A | tmt16plex_132N | 0.3768240801003251 |
0set-A | tmt16plex_132C | 1.2016533965111194 |
0set-A | tmt16plex_133N | 1.1162654616075098 |
0set-A | tmt16plex_133C | 1.702628562698326 |
0set-A | tmt16plex_134N | 1.8517048010662904 |
Software | Version | Container |
---|---|---|
python | 3.12 | python:3.12 |
msstitch | 3.16 | quay.io/biocontainers/msstitch:3.16--pyhdfd78af_0 |
proteowizard | 3.0.24172 | proteowizard/pwiz-skyline-i-agree-to-the-vendor-licenses:3.0.24172-63d00b1 |
hardklor | 2.3.2 | quay.io/biocontainers/hardklor:2.3.2--he1b5a44_0 |
kronik | 2.20 | quay.io/biocontainers/kronik:2.20--h4ac6f70_6 |
openms | 3.1.0 | quay.io/biocontainers/openms:3.1.0--h191ead1_4 |
msgfplus | 2023.01.1202 | quay.io/biocontainers/msgf_plus:2023.01.1202--hdfd78af_0 |
percolator | 3.5 | quay.io/biocontainers/percolator:3.5--hfd1433f_1 |
ddamsproteomics | 3.0 | ghcr.io/lehtiolab/ddamsproteomics:master |
deqms | 1.18.0 | ghcr.io/lehtiolab/ddamsproteomics:master |
Parameter | Value |
---|---|
--tracedir | test_output/tmt16denomdeq/pipeline_info |
--name | tmt16denomdeq |
--tdb | /home/jorrit/tests/dda/static-resources/test-data/ddamsproteomics/tmt16_fa.fa |
--mods | carbamidomethyl;oxidation;43.005814,*,opt,N-term,Unknown |
--isobaric | 0set-A:tmtpro:126:131N |
--genes | true |
--hardklor | true |
--keepnapsmsquant | true |
--sampletable | /home/jorrit/repos/ddamsproteomics/tests//tmt16_samples.txt |
--deqms | true |
--strips | {3-10={intercept=3.5478, fr_width=0.0676, tolerance=0.11, fr_amount=72, reverse=false}, 3.7-4.9={intercept=3.5959, fr_width=0.0174, tolerance=0.08, fr_amount=72, reverse=false}, 11-6={intercept=10.3936, fr_width=-0.0762, tolerance=0.11, fr_amount=60, reverse=true}, 6-9={intercept=6.1159, fr_width=0.0336, pi_tolerance=0.11, fr_amount=72, reverse=false}, 3.4-4.8={1-21={intercept=3.4395, fr_width=0.0221, tolerance=0.08, fr_amount=21, reverse=false}, 22-64={intercept=3.6374, fr_width=0.0128, tolerance=0.08, fr_amount=43, reverse=false}, 65-72={intercept=1.7364, fr_width=0.0424, tolerance=0.08, fr_amount=8, reverse=false}}} |
filename | instrument | setname | plate | fraction |
---|---|---|---|---|
tmt16_fr07>_1000@.mzML | qe | 0set-A | 3-10 | 07 |
tmt16_fr08_1000.mzML | qe | 0set-A | 3-10 | A2 |
Overlap for all sets: 248
Total uniques: 248
Overlap for all sets: 222
Total identified: 222
Overlap for all sets: 211
Total identified: 211
Overlap with values in all 16 channels: 246
Overlap with values in all 16 channels: 221
Overlap with values in all 16 channels: 209