DDA MS proteomics pipeline report

tmt16denomdeq

Completed at 20240919, 11:54

Pipeline version 3.0  DOI10.5281/zenodo.3548311

Identification summary

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

Overlap

Peptides
ID in # sets Amount peptides
1 248
Proteins
ID in # sets Amount proteins
1 222
Gene names
ID in # sets Amount genes
1 211
Median centered isobaric normalization factors
Peptides
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
Proteins
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
Gene names
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 versions

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

Non-default parameters

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}}}

Input files

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

# of PSMs and scans

# of missed cleavages

Isobaric missing values

Fraction yield

Plate: 0set-A_3-10

Precursor error

Plate: 0set-A_3-10

Search engine score

Plate: 0set-A_3-10

Retention time

Plate: 0set-A_3-10

Ion injection time

Plate: 0set-A_3-10

Precursor purity

Plate: 0set-A_3-10

Identifications

Peptides

Overlap for all sets: 248

Total uniques: 248

Proteins

Overlap for all sets: 222

Total identified: 222

Gene names

Overlap for all sets: 211

Total identified: 211

Isobaric intensities

Peptides

Overlap with values in all 16 channels: 246

Proteins

Overlap with values in all 16 channels: 221

Gene names

Overlap with values in all 16 channels: 209

Isobaric normalization factors

Peptides
Proteins
Gene names

Precursor area intensity

Peptides
Proteins
Gene names

# PSMs used for isobaric quantitation per identification

Peptides
Proteins
Gene names

# PSMs used for isobaric quantitation per identification for only complete overlapping set

Peptides
Proteins
Gene names

Percentage of identifications with >1 quantifying PSM in the complete overlapping set

Peptides
Proteins
Gene names

# peptides with MS1 quant per protein (top 3 used)

Proteins
Gene names

Overall protein coverage

Proteins

Principal component analysis

Peptides
Proteins
Gene names

DEqMS results

Peptides
Proteins
Gene names

DEqMS

Peptides
Proteins
Gene names