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Test dev version #30

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50af305
:art: add fixed modifications to SDRF
enryH Jun 1, 2026
d0f4f6e
:art: re-order parameters
enryH Jun 2, 2026
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23 changes: 14 additions & 9 deletions PXD040621_w_contaminants-params.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,20 @@ skip_post_msstats: true
custom_config_base: https://raw.githubusercontent.com/nf-core/configs/master
# minimum length of peptides
min_peptide_length: 6
# search engines
search_engines: comet # comet,msgf,sage
# protein quantification and aggregation settings
protein_quant: unique_peptides
min_peptides_per_protein: 1
targeted_only: true
alignment_order: star
fdr_level: psm_level_fdrs
lfq_seeding_algorithm: multiplex
# pmultiqc settings
enable_pmultiqc: true
pmultiqc_idxml_skip: true
skip_table_plots: false
#
msstatslfq_removeFewMeasurements: true
plaintext_email: false
luciphor_debug: 0
Expand All @@ -40,24 +52,20 @@ min_reporter_intensity: 0
normalize: false
skip_preliminary_analysis: false
description_correct_features: 0
decoy_string: DECOY_
decoy_string: DECOY_
variable_mods: Oxidation (M)
fragment_mass_tolerance: 0.03
msstatslfq_quant_summary_method: TMP
skip_factor_validation: true
psm_level_fdr_cutoff: 0.01
skip_table_plots: false
scan_window_automatic: true
corr_diff: 1
pmultiqc_idxml_skip: true
version: false
openms_peakpicking: false
feature_without_id_min_score: 0.75
msstatsiso_remove_norm_channel: true
min_precursor_charge: 2
consensusid_algorithm: best
protein_quant: unique_peptides
min_peptides_per_protein: 1
validationSchemaIgnoreParams: genomes,igenomes_base
precursor_isotope_deviation: 10
num_hits: 1
Expand Down Expand Up @@ -90,7 +98,6 @@ run_fdr_cutoff: 0.1
lfq_intensity_threshold: 1000
protein_inference_debug: 0
quantification_method: feature_intensity
enable_pmultiqc: true
use_shared_peptides: true
sage_processes: 1
help: false
Expand All @@ -100,7 +107,6 @@ train_FDR: 0.05
skip_ms_validation: false
export_mztab: true
klammer: false
search_engines: comet
idfilter_debug: 0
msstats_threshold: 0.05
monochrome_logs: false
Expand All @@ -113,7 +119,6 @@ protocol: automatic
skip_experimental_design_validation: false
posterior_probabilities: percolator
add_triqler_output: false
targeted_only: true
max_multiqc_email_size: 25.MB
msstatsiso_useunique_peptide: true
max_time: 10d
Expand Down Expand Up @@ -153,7 +158,7 @@ rescore_range: independent_run
random_preanalysis_seed: 42
calibration_set_size: 0.15
quantify_decoys: false
reference_channel: '126'
reference_channel: "126"
contrasts: pairwise
idmapper_debug: 0
ratios: false
Expand Down
18 changes: 9 additions & 9 deletions data/PXD040621/PXD040621.sdrf.tsv
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
source name characteristics[biological replicate] characteristics[cell type] characteristics[disease] characteristics[organism part] characteristics[organism] characteristics[strain/breed] characteristics[treatment] characteristics[medium supplements] characteristics[temperature] characteristics[aeration] assay name technology type comment[alkylation reagent] comment[cleavage agent details] comment[collision energy] comment[data file] comment[dissociation method] comment[file uri] comment[fraction identifier] comment[fragment mass tolerance] comment[instrument] comment[label] comment[modification parameters] comment[precursor mass tolerance] comment[reduction reagent] comment[technical replicate] comment[tool metadata] factor value[phenotype]
sample 1 1 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Control Not applicable 37°C Anaerobiosis run 1 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_DMSO_rep1_EG-1.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_DMSO_rep1_EG-1.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" 10 ppm TCEP 1 lesSDRF v0.1.0 Control
sample 2 2 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Control Not applicable 37°C Anaerobiosis run 2 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_DMSO_rep2_EG-2.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_DMSO_rep2_EG-2.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" 10 ppm TCEP 1 lesSDRF v0.1.0 Control
sample 3 3 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Control Not applicable 37°C Anaerobiosis run 3 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_DMSO_rep3_EG-3.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_DMSO_rep3_EG-3.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" 10 ppm TCEP 1 lesSDRF v0.1.0 Control
sample 4 4 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Control Not applicable 37°C Anaerobiosis run 4 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_DMSO_rep4_EG-4.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_DMSO_rep4_EG-4.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" 10 ppm TCEP 1 lesSDRF v0.1.0 Control
sample 5 1 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Sulforaphane Sulforaphane 37°C Anaerobiosis run 5 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_Suf_rep1_EG-5.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_Suf_rep1_EG-5.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" 10 ppm TCEP 1 lesSDRF v0.1.0 Sulforaphane
sample 6 2 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Sulforaphane Sulforaphane 37°C Anaerobiosis run 6 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_Suf_rep2_EG-6.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_Suf_rep2_EG-6.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" 10 ppm TCEP 1 lesSDRF v0.1.0 Sulforaphane
sample 7 3 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Sulforaphane Sulforaphane 37°C Anaerobiosis run 7 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_Suf_rep3_EG-7.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_Suf_rep3_EG-7.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" 10 ppm TCEP 1 lesSDRF v0.1.0 Sulforaphane
sample 8 4 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Sulforaphane Sulforaphane 37°C Anaerobiosis run 8 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_Suf_rep4_EG-8.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_Suf_rep4_EG-8.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" 10 ppm TCEP 1 lesSDRF v0.1.0 Sulforaphane
source name characteristics[biological replicate] characteristics[cell type] characteristics[disease] characteristics[organism part] characteristics[organism] characteristics[strain/breed] characteristics[treatment] characteristics[medium supplements] characteristics[temperature] characteristics[aeration] assay name technology type comment[alkylation reagent] comment[cleavage agent details] comment[collision energy] comment[data file] comment[dissociation method] comment[file uri] comment[fraction identifier] comment[fragment mass tolerance] comment[instrument] comment[label] comment[modification parameters] comment[modification parameters] comment[precursor mass tolerance] comment[reduction reagent] comment[technical replicate] comment[tool metadata] factor value[phenotype]
sample 1 1 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Control Not applicable 37°C Anaerobiosis run 1 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_DMSO_rep1_EG-1.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_DMSO_rep1_EG-1.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" NT=Carbamidomethyl;TA=C;MT=Fixed;AC=UNIMOD:4;PP=Anywhere;CF=H3C2NO;MM=57.021464 10 ppm TCEP 1 lesSDRF v0.1.0 Control
sample 2 2 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Control Not applicable 37°C Anaerobiosis run 2 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_DMSO_rep2_EG-2.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_DMSO_rep2_EG-2.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" NT=Carbamidomethyl;TA=C;MT=Fixed;AC=UNIMOD:4;PP=Anywhere;CF=H3C2NO;MM=57.021464 10 ppm TCEP 1 lesSDRF v0.1.0 Control
sample 3 3 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Control Not applicable 37°C Anaerobiosis run 3 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_DMSO_rep3_EG-3.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_DMSO_rep3_EG-3.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" NT=Carbamidomethyl;TA=C;MT=Fixed;AC=UNIMOD:4;PP=Anywhere;CF=H3C2NO;MM=57.021464 10 ppm TCEP 1 lesSDRF v0.1.0 Control
sample 4 4 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Control Not applicable 37°C Anaerobiosis run 4 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_DMSO_rep4_EG-4.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_DMSO_rep4_EG-4.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" NT=Carbamidomethyl;TA=C;MT=Fixed;AC=UNIMOD:4;PP=Anywhere;CF=H3C2NO;MM=57.021464 10 ppm TCEP 1 lesSDRF v0.1.0 Control
sample 5 1 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Sulforaphane Sulforaphane 37°C Anaerobiosis run 5 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_Suf_rep1_EG-5.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_Suf_rep1_EG-5.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" NT=Carbamidomethyl;TA=C;MT=Fixed;AC=UNIMOD:4;PP=Anywhere;CF=H3C2NO;MM=57.021464 10 ppm TCEP 1 lesSDRF v0.1.0 Sulforaphane
sample 6 2 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Sulforaphane Sulforaphane 37°C Anaerobiosis run 6 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_Suf_rep2_EG-6.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_Suf_rep2_EG-6.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" NT=Carbamidomethyl;TA=C;MT=Fixed;AC=UNIMOD:4;PP=Anywhere;CF=H3C2NO;MM=57.021464 10 ppm TCEP 1 lesSDRF v0.1.0 Sulforaphane
sample 7 3 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Sulforaphane Sulforaphane 37°C Anaerobiosis run 7 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_Suf_rep3_EG-7.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_Suf_rep3_EG-7.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" NT=Carbamidomethyl;TA=C;MT=Fixed;AC=UNIMOD:4;PP=Anywhere;CF=H3C2NO;MM=57.021464 10 ppm TCEP 1 lesSDRF v0.1.0 Sulforaphane
sample 8 4 Prokaryotic cell Not applicable Cell lysate Escherichia coli Escherichia coli O127:H6 strain E2348/69 Sulforaphane Sulforaphane 37°C Anaerobiosis run 8 Proteomic profiling by mass spectrometry IAA "NT=Trypsin; AC=1001251; CS=(?⇐[KR])(?!P)" "28;32;38%" 20220830_JL-4884_Forster_Ecoli_Suf_rep4_EG-8.raw "NT=HCD; AC=MS:1002481" https://ftp.pride.ebi.ac.uk/pride/data/archive/2023/07/PXD040621/20220830_JL-4884_Forster_Ecoli_Suf_rep4_EG-8.raw 1 20 ppm Q Exactive Plus label free sample "AC=UNIMOD:4;NT=Carbamidomethyl;TA=C" NT=Carbamidomethyl;TA=C;MT=Fixed;AC=UNIMOD:4;PP=Anywhere;CF=H3C2NO;MM=57.021464 10 ppm TCEP 1 lesSDRF v0.1.0 Sulforaphane
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