From 908eba05f65b50507400cb695cb4c6d6c2699f29 Mon Sep 17 00:00:00 2001 From: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com> Date: Wed, 11 Feb 2026 12:18:24 -0800 Subject: [PATCH 1/3] Formatting updates for GL-DPPD-[LFQ-MBR].md --- .../GL-DPPD-[LFQ-MBR].md | 166 +++++++++--------- 1 file changed, 84 insertions(+), 82 deletions(-) diff --git a/Proteomics/Pipeline_GL-DPPD-[LFQ-MBR]_Versions/GL-DPPD-[LFQ-MBR].md b/Proteomics/Pipeline_GL-DPPD-[LFQ-MBR]_Versions/GL-DPPD-[LFQ-MBR].md index 5879d0c60..667745935 100644 --- a/Proteomics/Pipeline_GL-DPPD-[LFQ-MBR]_Versions/GL-DPPD-[LFQ-MBR].md +++ b/Proteomics/Pipeline_GL-DPPD-[LFQ-MBR]_Versions/GL-DPPD-[LFQ-MBR].md @@ -100,7 +100,7 @@ cd .. **Input Data:** -- `*.mzML` (input mass spectrometry raw data in mzML format) +- *.mzML (input mass spectrometry raw data in mzML format) **Output Data:** @@ -129,7 +129,7 @@ zip -r All_GLProteomics_qc-report.zip qc-report.html resources/ **Input Data:** -- `*.mzML` (input mass spectrometry raw data in mzML format) +- *.mzML (input mass spectrometry raw data in mzML format) **Output Data:** @@ -188,25 +188,25 @@ fragpipe \ **Input Data:** -- `LFQ-MBR.workflow` (FragPipe LFQ-MBR workflow configuration file) -- `manifest.tsv` (manifest file with sample information and file paths) -- `tools_folder/` (directory containing FragPipe tools not included in the Docker image) -- `*.mzML` (input mass spectrometry raw data in mzML format) -- `*-decoys-reviewed-contam-*.fas` (proteome FASTA database with decoys and contaminants, output from [Step 2](#2-create-proteome-fasta-database)) +- LFQ-MBR.workflow (FragPipe LFQ-MBR workflow configuration file) +- manifest.tsv (manifest file with sample information and file paths) +- tools_folder/ (directory containing FragPipe tools not included in the Docker image) +- *.mzML (input mass spectrometry raw data in mzML format) +- *-decoys-reviewed-contam-*.fas (proteome FASTA database with decoys and contaminants, output from [Step 2](#2-create-proteome-fasta-database)) **Output Data:** -- `fragger.params` (MSFragger parameter configuration file) -- `msbooster_params.txt` (MSBooster parameter configuration file) -- `filelist_proteinprophet.txt` (list of interact.pep.xml files to be passed to ProteinProphet) -- `filelist_ionquant.txt` (file list for IonQuant) -- `modmasses_ionquant.txt` (modification masses file for IonQuant) -- **`experiment_annotation.tsv`** (experiment annotation file) -- `fragpipe.workflow` (updated FragPipe workflow configuration file) -- `fragpipe-files.fp-manifest` (FragPipe files manifest) -- `fragpipe.job` (FragPipe job configuration file) -- `log_*.txt` (FragPipe execution log file with timestamp) -- `sdrf.tsv` (Sample and Data Relationship Format file) +- fragger.params (MSFragger parameter configuration file) +- msbooster_params.txt (MSBooster parameter configuration file) +- filelist_proteinprophet.txt (list of interact.pep.xml files to be passed to ProteinProphet) +- filelist_ionquant.txt (file list for IonQuant) +- modmasses_ionquant.txt (modification masses file for IonQuant) +- **experiment_annotation.tsv** (experiment annotation file) +- fragpipe.workflow (updated FragPipe workflow configuration file) +- fragpipe-files.fp-manifest (FragPipe files manifest) +- fragpipe.job (FragPipe job configuration file) +- log_*.txt (FragPipe execution log file with timestamp) +- sdrf.tsv (Sample and Data Relationship Format file) @@ -229,7 +229,7 @@ java -Xmx55G -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar **Input Data:** -- `*.mzML` (input mass spectrometry raw data in mzML format) +- *.mzML (input mass spectrometry raw data in mzML format) **Output Data:** @@ -280,9 +280,9 @@ java -jar -Dfile.encoding=UTF-8 -Xmx55G MSFragger-4.3.jar fragger.params sample1 **Input Data:** -- `fragger.params` (MSFragger parameter configuration file, output from [Step 3a](#3a-launch-fragpipe)) -- `*.mzML` (input mass spectrometry raw data in mzML format) -- `*-decoys-reviewed-contam-*.fas` (proteome FASTA database with decoys and contaminants, output from [Step 2](#2-create-proteome-fasta-database)) +- fragger.params (MSFragger parameter configuration file, output from [Step 3a](#3a-launch-fragpipe)) +- *.mzML (input mass spectrometry raw data in mzML format) +- *-decoys-reviewed-contam-*.fas (proteome FASTA database with decoys and contaminants, output from [Step 2](#2-create-proteome-fasta-database)) **Output Data:** @@ -317,9 +317,9 @@ java -Xmx55G -cp MSBooster-1.3.17.jar:batmass-io-1.35.4.jar mainsteps.MainClass **Input Data:** -- `msbooster_params.txt` (MSBooster parameter configuration file, output from [Step 3a](#3a-launch-fragpipe)) -- `*.pin` (Percolator input files from MSFragger, output from [Step 3d](#3d-msfragger-database-search)) -- `*.mzML` (original mass spectrometry raw data in mzML format) +- msbooster_params.txt (MSBooster parameter configuration file, output from [Step 3a](#3a-launch-fragpipe)) +- *.pin (Percolator input files from MSFragger, output from [Step 3d](#3d-msfragger-database-search)) +- *.mzML (original mass spectrometry raw data in mzML format) **Output Data:** @@ -372,7 +372,7 @@ percolator \ **Input Data:** -- `*_edited.pin` (Percolator input files with MSBooster features, output from [Step 3e](#3e-msbooster-deep-learning-feature-addition)) +- *_edited.pin (Percolator input files with MSBooster features, output from [Step 3e](#3e-msbooster-deep-learning-feature-addition)) **Output Data:** @@ -414,10 +414,10 @@ java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/* \ **Input Data:** -- `*.pin` (original Percolator input files from MSFragger, output from [Step 3d](#3d-msfragger-database-search)) -- `*_percolator_target_psms.tsv` (Percolator target PSM results, output from [Step 3f](#3f-percolator-psm-rescoring-and-statistical-validation)) -- `*_percolator_decoy_psms.tsv` (Percolator decoy PSM results, output from [Step 3f](#3f-percolator-psm-rescoring-and-statistical-validation)) -- `*.mzML` (original mass spectrometry raw data in mzML format) +- *.pin (original Percolator input files from MSFragger, output from [Step 3d](#3d-msfragger-database-search)) +- *_percolator_target_psms.tsv (Percolator target PSM results, output from [Step 3f](#3f-percolator-psm-rescoring-and-statistical-validation)) +- *_percolator_decoy_psms.tsv (Percolator decoy PSM results, output from [Step 3f](#3f-percolator-psm-rescoring-and-statistical-validation)) +- *.mzML (original mass spectrometry raw data in mzML format) **Output Data:** @@ -446,8 +446,8 @@ philosopher proteinprophet --maxppmdiff 2000000 --output combined filelist_prote **Input Data:** -- `filelist_proteinprophet.txt` (list of interact.pep.xml files to be passed to ProteinProphet, output from [Step 3a](#3a-launch-fragpipe)) -- `interact-*.pep.xml` (pepXML files listed in filelist_proteinprophet.txt, output from [Step 3f.1](#3f1-add-percolator-validation-information-to-pepxml)) +- filelist_proteinprophet.txt (list of interact.pep.xml files to be passed to ProteinProphet, output from [Step 3a](#3a-launch-fragpipe)) +- interact-*.pep.xml (pepXML files listed in filelist_proteinprophet.txt, output from [Step 3f.1](#3f1-add-percolator-validation-information-to-pepxml)) **Output Data:** @@ -475,7 +475,7 @@ philosopher database --annotate *.fas --prefix rev_ **Input Data:** -- `*-decoys-reviewed-contam-*.fas` (proteome FASTA database with decoys and contaminants, output from [Step 2](#2-create-proteome-fasta-database)) +- *-decoys-reviewed-contam-*.fas (proteome FASTA database with decoys and contaminants, output from [Step 2](#2-create-proteome-fasta-database)) **Output Data:** @@ -548,8 +548,8 @@ philosopher filter \ **Input Data:** -- `interact-*.pep.xml` (peptide-spectrum matches with validation information generated by Percolator, output from [Step 3f.1](#3f1-add-percolator-validation-information-to-pepxml)) -- `combined.prot.xml` (protein identifications with validation information generated by ProteinProphet via Philosopher, output from [Step 3g](#3g-proteinprophet-protein-inference-and-statistical-validation)) +- interact-*.pep.xml (peptide-spectrum matches with validation information generated by Percolator, output from [Step 3f.1](#3f1-add-percolator-validation-information-to-pepxml)) +- combined.prot.xml (protein identifications with validation information generated by ProteinProphet via Philosopher, output from [Step 3g](#3g-proteinprophet-protein-inference-and-statistical-validation)) - .meta/ (Philosopher workspace metadata, output from [Step 3h](#3h-database-annotation)) **Output Data:** @@ -695,13 +695,13 @@ java -Xmx55G \ **Input Data:** -- `filelist_ionquant.txt` (file list for IonQuant, output from [Step 3a](#3a-launch-fragpipe)) -- `modmasses_ionquant.txt` (modification masses file for IonQuant, output from [Step 3a](#3a-launch-fragpipe)) -- `protein.tsv` (sample-specific protein report, output from [Step 3j](#3j-generate-reports)) -- `peptide.tsv` (sample-specific peptide report, output from [Step 3j](#3j-generate-reports)) -- `psm.tsv` (sample-specific PSM report, output from [Step 3j](#3j-generate-reports)) -- `ion.tsv` (sample-specific ion report, output from [Step 3j](#3j-generate-reports)) -- `*.mzML` (original mass spectrometry raw data in mzML format; accessed via `--specdir` parameter specified in `filelist_ionquant.txt` to extract intensity data for MS1 quantification and match-between-runs feature matching) +- filelist_ionquant.txt (file list for IonQuant, output from [Step 3a](#3a-launch-fragpipe)) +- modmasses_ionquant.txt (modification masses file for IonQuant, output from [Step 3a](#3a-launch-fragpipe)) +- protein.tsv (sample-specific protein report, output from [Step 3j](#3j-generate-reports)) +- peptide.tsv (sample-specific peptide report, output from [Step 3j](#3j-generate-reports)) +- psm.tsv (sample-specific PSM report, output from [Step 3j](#3j-generate-reports)) +- ion.tsv (sample-specific ion report, output from [Step 3j](#3j-generate-reports)) +- *.mzML (original mass spectrometry raw data in mzML format; accessed via `--specdir` parameter specified in `filelist_ionquant.txt` to extract intensity data for MS1 quantification and match-between-runs feature matching) **Output Data:** @@ -712,13 +712,13 @@ java -Xmx55G \ - *_model.png (sample-specific IonQuant model visualization plot showing quantification model fits) - combined_protein.tsv (combined protein report with MS1 quantification data across all samples) - combined_peptide.tsv (combined peptide report with MS1 quantification data and additional data across all samples) -- combined_modified_peptide.tsv (combined modified peptide report with MS1 quantification data and additional data across all samples) -- combined_ion.tsv (combined ion report with MS1 quantification data and additional data across all samples) -- **combined_site_*.tsv** (site-specific modification reports, e.g., `combined_site_C_57.0215.tsv` for carbamidomethylation, `combined_site_M_15.9949.tsv` for oxidation) +- **combined_modified_peptide.tsv** (combined modified peptide report with MS1 quantification data and additional data across all samples) +- **combined_ion.tsv** (combined ion report with MS1 quantification data and additional data across all samples) +- **combined_site_*.tsv** (site-specific modification reports, e.g., "combined_site_C_57.0215.tsv" for carbamidomethylation, "combined_site_M_15.9949.tsv" for oxidation) - reprint.int.tsv (input file for the Resource for Evaluation of Protein Interaction Networks (REPRINT) containing protein intensities, generated by Philosopher) - reprint.spc.tsv (input file for the Resource for Evaluation of Protein Interaction Networks (REPRINT) containing protein spectral counts, generated by Philosopher) -- **msstats.csv** (formatted input file for the MSstats R package for downstream differential analysis; contains columns: `ProteinName`, `PeptideSequence`, `PrecursorCharge`, `FragmentIon`, `Condition`, `BioReplicate`, `Run`, `Intensity`; main input for downstream statistical analysis) -- msstats_ptm.csv (MSstats input file for PTM (post-translational modification) analysis; includes PTM site columns) +- **msstats.csv** (formatted input file for the MSstats R package for downstream differential analysis; contains columns: "ProteinName", "PeptideSequence", "PrecursorCharge", "FragmentIon", "Condition", "BioReplicate", "Run", "Intensity"; main input for downstream statistical analysis) +- **msstats_ptm.csv** (MSstats input file for PTM (post-translational modification) analysis; includes PTM site columns) @@ -749,13 +749,13 @@ clean_multiqc_paths.py multiqc_GLProteomics_data /path/to/pmultiqc/output/direct **Input Data:** -- `psm.tsv` (sample-specific PSM reports, output from [Step 3k](#3k-ionquant-label-free-quantification)) -- `ion.tsv` (sample-specific ion reports, output from [Step 3k](#3k-ionquant-label-free-quantification)) -- `combined_protein.tsv` (combined protein report, output from [Step 3k](#3k-ionquant-label-free-quantification)) -- `combined_peptide.tsv` (combined peptide report, output from [Step 3k](#3k-ionquant-label-free-quantification)) -- `combined_ion.tsv` (combined ion report, output from [Step 3k](#3k-ionquant-label-free-quantification)) -- `*.workflow` (FragPipe workflow file, output from [Step 3a](#3a-launch-fragpipe)) -- `fragger.params` (MSFragger parameters file, output from [Step 3a](#3a-launch-fragpipe)) +- psm.tsv (sample-specific PSM reports, output from [Step 3k](#3k-ionquant-label-free-quantification)) +- ion.tsv (sample-specific ion reports, output from [Step 3k](#3k-ionquant-label-free-quantification)) +- combined_protein.tsv (combined protein report, output from [Step 3k](#3k-ionquant-label-free-quantification)) +- combined_peptide.tsv (combined peptide report, output from [Step 3k](#3k-ionquant-label-free-quantification)) +- combined_ion.tsv (combined ion report, output from [Step 3k](#3k-ionquant-label-free-quantification)) +- *.workflow (FragPipe workflow file, output from [Step 3a](#3a-launch-fragpipe)) +- fragger.params (MSFragger parameters file, output from [Step 3a](#3a-launch-fragpipe)) **Output Data:** @@ -782,14 +782,14 @@ msstats_analysis.R . assay_suffix runsheet.tsv msstats.csv **Input Data:** -- `msstats.csv` (MSstats input file, output from [Step 3k](#3k-ionquant-label-free-quantification)) -- `runsheet.tsv` (runsheet file with sample metadata and factor values) +- msstats.csv (MSstats input file, output from [Step 3k](#3k-ionquant-label-free-quantification)) +- runsheet.tsv (runsheet file with sample metadata and factor values) **Output Data:** -- msstats_comparison_*.csv (pairwise differential abundance comparison results) -- msstats_comparison_all.csv (all pairwise comparisons combined) -- msstats_contrasts.csv (contrast definitions) +- **msstats_comparison_*.csv** (pairwise differential abundance comparison results) +- **msstats_comparison_all.csv** (all pairwise comparisons combined) +- **msstats_contrasts.csv** (contrast definitions)
@@ -827,6 +827,8 @@ Rscript fp_analyst_analysis.R \ --output_dir "output/" ``` +**Peptide run:** + ```bash Rscript fp_analyst_analysis.R \ --experiment_annotation experiment_annotation.tsv \ @@ -880,31 +882,31 @@ Rscript fp_analyst_analysis.R \ **Input Data:** -- `experiment_annotation.tsv` (experiment annotation file, output from [Step 3a](#3a-launch-fragpipe)) -- `combined_protein.tsv` (combined protein report, output from [Step 3k](#3k-ionquant-label-free-quantification)) -- `combined_peptide.tsv` (combined peptide report, output from [Step 3k](#3k-ionquant-label-free-quantification)) +- experiment_annotation.tsv (experiment annotation file, output from [Step 3a](#3a-launch-fragpipe)) +- combined_protein.tsv (combined protein report, output from [Step 3k](#3k-ionquant-label-free-quantification)) +- combined_peptide.tsv (combined peptide report, output from [Step 3k](#3k-ionquant-label-free-quantification)) **Output Data:** -- `fp_analyst_parameters.txt` (run parameters) -- `pca.pdf`, `pca.png` (PCA plot) -- `correlation_heatmap.pdf`, `correlation_heatmap.png` (sample correlation heatmap) -- `missing_value_heatmap.pdf`, `missing_value_heatmap.png` (missing value pattern heatmap) -- `feature_numbers.pdf`, `feature_numbers.png` (feature count per sample) -- `sample_coverage.pdf`, `sample_coverage.png` (sample coverage) -- `density.pdf`, `density.png` (intensity distribution) -- `sample_cvs.pdf`, `sample_cvs.png` (sample coefficient of variation) -- `jaccard.pdf`, `jaccard.png` (Jaccard similarity plot) -- `upset.pdf`, `upset.png` (UpSet plot) -- `venndiagram/` (pairwise Venn diagrams) -- `feature/protein/boxplot/`, `feature/protein/violinplot/`, `feature/gene/boxplot/`, `feature/gene/violinplot/` (protein run: top 10 by protein ID and top 10 by gene; filenames `boxplot_feature_*.pdf`, `violinplot_feature_*.pdf`) -- `feature/peptide/boxplot/`, `feature/peptide/violinplot/` (peptide run: top 10 by peptide ID only) -- `unimputed_matrix.tsv` (filtered data, before imputation) -- `normalized_matrix.tsv` (after normalization; when normalization is "none", equals filtered) -- `imputed_matrix.tsv` (protein intensities after imputation) -- `de_results.tsv` (differential expression results) -- `de_heatmap.pdf`, `de_heatmap.png` (DE heatmap) -- `volcano/` (volcano plots per contrast) -- `enrichment/` (pathway and GO enrichment plots and TSV tables) +- fp_analyst_parameters.txt (run parameters) +- pca.pdf, pca.png (PCA plot) +- correlation_heatmap.pdf, correlation_heatmap.png (sample correlation heatmap) +- missing_value_heatmap.pdf, missing_value_heatmap.png (missing value pattern heatmap) +- feature_numbers.pdf, feature_numbers.png (feature count per sample) +- sample_coverage.pdf, sample_coverage.png (sample coverage) +- density.pdf, density.png (intensity distribution) +- sample_cvs.pdf, sample_cvs.png (sample coefficient of variation) +- jaccard.pdf, jaccard.png (Jaccard similarity plot) +- upset.pdf, upset.png (UpSet plot) +- venndiagram/ (pairwise Venn diagrams) +- feature/protein/boxplot/, feature/protein/violinplot/, feature/gene/boxplot/, feature/gene/violinplot/ (protein run: top 10 by protein ID and top 10 by gene; filenames boxplot_feature_\*.pdf, violinplot_feature_\*.pdf) +- feature/peptide/boxplot/, feature/peptide/violinplot/ (peptide run: top 10 by peptide ID only) +- unimputed_matrix.tsv (filtered data, before imputation) +- normalized_matrix.tsv (after normalization; when normalization is "none", equals filtered) +- imputed_matrix.tsv (protein intensities after imputation) +- de_results.tsv (differential expression results) +- de_heatmap.pdf, de_heatmap.png (DE heatmap) +- volcano/ (volcano plots per contrast) +- enrichment/ (pathway and GO enrichment plots and TSV tables)
From 684531b894b4af083cd5329dddba3ca443302e9d Mon Sep 17 00:00:00 2001 From: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com> Date: Wed, 11 Feb 2026 12:42:13 -0800 Subject: [PATCH 2/3] Formatting updates for GL-DPPD-[TMT10].md --- .../GL-DPPD-[TMT10].md | 130 +++++++++--------- 1 file changed, 66 insertions(+), 64 deletions(-) diff --git a/Proteomics/Pipeline_GL-DPPD-[TMT10]_Versions/GL-DPPD-[TMT10].md b/Proteomics/Pipeline_GL-DPPD-[TMT10]_Versions/GL-DPPD-[TMT10].md index acbb95e9d..79222b218 100644 --- a/Proteomics/Pipeline_GL-DPPD-[TMT10]_Versions/GL-DPPD-[TMT10].md +++ b/Proteomics/Pipeline_GL-DPPD-[TMT10]_Versions/GL-DPPD-[TMT10].md @@ -99,12 +99,13 @@ cd .. **Input Data:** -- `*.mzML` (input mass spectrometry raw data in mzML format) +- *.mzML (input mass spectrometry raw data in mzML format) **Output Data:** -- `qc-report.html` (interactive HTML QC report with metrics and visualizations) -- `resources/` (directory containing QC report assets: CSS, JavaScript, and data files) +- qc-report.html (interactive HTML QC report with metrics and visualizations) +- resources/ (directory containing QC report assets: CSS, JavaScript, and data files) +- **\*_qc-report.zip** (zip archive containing qc-report.html and resources/ folder)
@@ -127,12 +128,13 @@ zip -r *-report.zip qc-report.html resources/ **Input Data:** -- `*.mzML` (all input mass spectrometry raw data files in mzML format) +- *.mzML (all input mass spectrometry raw data files in mzML format) **Output Data:** -- `qc-report.html` (interactive HTML QC report with metrics and visualizations across all samples) -- `resources/` (directory containing QC report assets: CSS, JavaScript, and data files) +- qc-report.html (interactive HTML QC report with metrics and visualizations across all samples) +- resources/ (directory containing QC report assets: CSS, JavaScript, and data files) +- **All_GLProteomics_qc-report.zip** (zip archive containing qc-report.html and resources/ folder for all samples combined)
@@ -160,7 +162,7 @@ philosopher-v5.1.2 database --custom UP000005640 --reviewed --isoforms --contam **Output Data:** -- `*-reviewed-isoforms-contam-*.fas` (proteome FASTA file with reviewed entries, isoforms, and contaminants) +- *-reviewed-isoforms-contam-*.fas (proteome FASTA file with reviewed entries, isoforms, and contaminants)
@@ -180,11 +182,11 @@ philosopher-v5.1.2 database --annotate --custom UP000005640 --reviewed --isoform **Input Data:** -- `*-reviewed-isoforms-contam-*.fas` (proteome FASTA file, output from [Step 2a](#2a-download-proteome-from-uniprot)) +- *-reviewed-isoforms-contam-*.fas (proteome FASTA file, output from [Step 2a](#2a-download-proteome-from-uniprot)) **Output Data:** -- `*-decoys-reviewed-isoforms-contam-*.fas` (proteome FASTA database with decoy sequences (prefixed with `rev_`), reviewed entries, isoforms, and contaminants) +- *-decoys-reviewed-isoforms-contam-*.fas (proteome FASTA database with decoy sequences (prefixed with `rev_`), reviewed entries, isoforms, and contaminants)
@@ -213,26 +215,26 @@ philosopher-v5.1.2 database --annotate --custom UP000005640 --reviewed --isoform **Input Data:** -- `TMT10.workflow` (FragPipe workflow configuration file for TMT-10 workflow) -- `manifest_GLProteomics.tsv` (FragPipe manifest TSV file with columns: input_file, joined_factor_values, bioreplicate, data_type) -- `*-decoys-reviewed-isoforms-contam-*.fas` (proteome FASTA database, output from [Step 2b](#2b-add-decoys-and-contaminants-to-fasta)) -- `*.mzML` (input mass spectrometry raw data in mzML format) +- TMT10.workflow (FragPipe workflow configuration file for TMT-10 workflow) +- manifest_GLProteomics.tsv (FragPipe manifest TSV file with columns: input_file, joined_factor_values, bioreplicate, data_type) +- *-decoys-reviewed-isoforms-contam-*.fas (proteome FASTA database, output from [Step 2b](#2b-add-decoys-and-contaminants-to-fasta)) +- *.mzML (input mass spectrometry raw data in mzML format) **Output Data:** -- `fragger.params` (MSFragger parameter configuration file) -- `msbooster_params.txt` (MSBooster parameter configuration file) -- `tmt-integrator-conf.yml` (TMTIntegrator configuration file) -- `filelist_proteinprophet.txt` (list of interact.pep.xml files to be passed to ProteinProphet) -- `filelist_ionquant.txt` (file list for IonQuant) -- `modmasses_ionquant.txt` (modification masses file for IonQuant) -- **`experiment_annotation.tsv`** (experiment annotation file mapping TMT channels to samples) -- `*_annotation.txt` (plex-specific annotation files mapping TMT channels to sample names) -- `fragpipe.workflow` (updated FragPipe workflow configuration file) -- `fragpipe-files.fp-manifest` (FragPipe files manifest) -- `fragpipe.job` (FragPipe job configuration file) -- `log_*.txt` (FragPipe execution log file with timestamp) -- `sdrf.tsv` (Sample and Data Relationship Format file) +- fragger.params (MSFragger parameter configuration file) +- msbooster_params.txt (MSBooster parameter configuration file) +- tmt-integrator-conf.yml (TMTIntegrator configuration file) +- filelist_proteinprophet.txt (list of interact.pep.xml files to be passed to ProteinProphet) +- filelist_ionquant.txt (file list for IonQuant) +- modmasses_ionquant.txt (modification masses file for IonQuant) +- **experiment_annotation.tsv** (experiment annotation file mapping TMT channels to samples) +- *_annotation.txt (plex-specific annotation files mapping TMT channels to sample names) +- fragpipe.workflow (updated FragPipe workflow configuration file) +- fragpipe-files.fp-manifest (FragPipe files manifest) +- fragpipe.job (FragPipe job configuration file) +- log_*.txt (FragPipe execution log file with timestamp) +- sdrf.tsv (Sample and Data Relationship Format file)
@@ -253,7 +255,7 @@ java -Xmx55G -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/fragpipe-23.1.jar **Input Data:** -- `*.mzML` (input mass spectrometry raw data in mzML format) +- *.mzML (input mass spectrometry raw data in mzML format) **Output Data:** @@ -304,9 +306,9 @@ java -jar -Dfile.encoding=UTF-8 -Xmx55G MSFragger-4.3.jar fragger.params sample1 **Input Data:** -- `fragger.params` (MSFragger parameter configuration file, output from [Step 3a](#3a-launch-fragpipe)) -- `*.mzML` (input mass spectrometry raw data in mzML format) -- `*-decoys-reviewed-contam-*.fas` (proteome FASTA database with decoys and contaminants, output from [Step 2](#2-create-proteome-fasta-database)) +- fragger.params (MSFragger parameter configuration file, output from [Step 3a](#3a-launch-fragpipe)) +- *.mzML (input mass spectrometry raw data in mzML format) +- *-decoys-reviewed-contam-*.fas (proteome FASTA database with decoys and contaminants, output from [Step 2](#2-create-proteome-fasta-database)) **Output Data:** @@ -337,9 +339,9 @@ java -Xmx55G -cp MSBooster-1.3.17.jar:batmass-io-1.35.4.jar mainsteps.MainClass **Input Data:** -- `msbooster_params.txt` (MSBooster parameter configuration file, output from [Step 3a](#3a-launch-fragpipe)) -- `*.pin` (Percolator input files from MSFragger, output from [Step 3d](#3d-msfragger-database-search)) -- `*.mzML` (original mass spectrometry raw data in mzML format) +- msbooster_params.txt (MSBooster parameter configuration file, output from [Step 3a](#3a-launch-fragpipe)) +- *.pin (Percolator input files from MSFragger, output from [Step 3d](#3d-msfragger-database-search)) +- *.mzML (original mass spectrometry raw data in mzML format) **Output Data:** @@ -390,7 +392,7 @@ percolator \ **Input Data:** -- `*_edited.pin` (Percolator input files with MSBooster features, output from [Step 3e](#3e-msbooster-deep-learning-feature-addition)) +- *_edited.pin (Percolator input files with MSBooster features, output from [Step 3e](#3e-msbooster-deep-learning-feature-addition)) **Output Data:** @@ -430,10 +432,10 @@ java -cp /fragpipe_bin/fragpipe-23.1/fragpipe-23.1/lib/* \ **Input Data:** -- `*.pin` (original Percolator input files from MSFragger, output from [Step 3d](#3d-msfragger-database-search)) -- `*_percolator_target_psms.tsv` (Percolator target PSM results, output from [Step 3f](#3f-percolator-psm-rescoring-and-statistical-validation)) -- `*_percolator_decoy_psms.tsv` (Percolator decoy PSM results, output from [Step 3f](#3f-percolator-psm-rescoring-and-statistical-validation)) -- `*.mzML` (original mass spectrometry raw data in mzML format) +- *.pin (original Percolator input files from MSFragger, output from [Step 3d](#3d-msfragger-database-search)) +- *_percolator_target_psms.tsv (Percolator target PSM results, output from [Step 3f](#3f-percolator-psm-rescoring-and-statistical-validation)) +- *_percolator_decoy_psms.tsv (Percolator decoy PSM results, output from [Step 3f](#3f-percolator-psm-rescoring-and-statistical-validation)) +- *.mzML (original mass spectrometry raw data in mzML format) **Output Data:** @@ -461,8 +463,8 @@ philosopher proteinprophet --maxppmdiff 2000000 --minprob 0.5 --output combined **Input Data:** -- `filelist_proteinprophet.txt` (list of interact.pep.xml files to be passed to ProteinProphet, output from [Step 3a](#3a-launch-fragpipe)) -- `interact-*.pep.xml` (pepXML files listed in filelist_proteinprophet.txt, output from [Step 3f.1](#3f1-add-percolator-validation-information-to-pepxml)) +- filelist_proteinprophet.txt (list of interact.pep.xml files to be passed to ProteinProphet, output from [Step 3a](#3a-launch-fragpipe)) +- interact-*.pep.xml (pepXML files listed in filelist_proteinprophet.txt, output from [Step 3f.1](#3f1-add-percolator-validation-information-to-pepxml)) **Output Data:** @@ -488,7 +490,7 @@ philosopher database --annotate *.fas --prefix rev_ **Input Data:** -- `*-decoys-reviewed-contam-*.fas` (proteome FASTA database with decoys and contaminants, output from [Step 2](#2-create-proteome-fasta-database)) +- *-decoys-reviewed-contam-*.fas (proteome FASTA database with decoys and contaminants, output from [Step 2](#2-create-proteome-fasta-database)) **Output Data:** @@ -561,8 +563,8 @@ philosopher filter \ **Input Data:** -- `interact-*.pep.xml` (peptide-spectrum matches with validation information generated by Percolator, output from [Step 3f.1](#3f1-add-percolator-validation-information-to-pepxml)) -- `combined.prot.xml` (protein identifications with validation information generated by ProteinProphet via Philosopher, output from [Step 3g](#3g-proteinprophet-protein-inference-and-statistical-validation)) +- interact-*.pep.xml (peptide-spectrum matches with validation information generated by Percolator, output from [Step 3f.1](#3f1-add-percolator-validation-information-to-pepxml)) +- combined.prot.xml (protein identifications with validation information generated by ProteinProphet via Philosopher, output from [Step 3g](#3g-proteinprophet-protein-inference-and-statistical-validation)) - .meta/ (Philosopher workspace metadata, output from [Step 3h](#3h-database-annotation)) **Output Data:** @@ -712,14 +714,14 @@ java -Djava.awt.headless=true -Xmx55G \ **Input Data:** -- `filelist_ionquant.txt` (file list for IonQuant containing `--psm` entries pointing to `psm.tsv` files and `--specdir` entry pointing to mzML directory, output from [Step 3a](#3a-launch-fragpipe)) -- `modmasses_ionquant.txt` (modification masses file for IonQuant, output from [Step 3a](#3a-launch-fragpipe)) -- `protein.tsv` (protein report, output from [Step 3j](#3j-generate-reports)) -- `peptide.tsv` (peptide report, output from [Step 3j](#3j-generate-reports)) -- `psm.tsv` (PSM report, output from [Step 3j](#3j-generate-reports)) -- `ion.tsv` (ion report, output from [Step 3j](#3j-generate-reports)) -- `*_annotation.txt` (plex-specific annotation files mapping TMT channels to sample names, used in second pass only, output from [Step 3a](#3a-launch-fragpipe)) -- `*.mzML` (original mass spectrometry raw data in mzML format; accessed via `--specdir` parameter specified in `filelist_ionquant.txt` to extract TMT reporter ion intensities) +- filelist_ionquant.txt (file list for IonQuant containing `--psm` entries pointing to `psm.tsv` files and `--specdir` entry pointing to mzML directory, output from [Step 3a](#3a-launch-fragpipe)) +- modmasses_ionquant.txt (modification masses file for IonQuant, output from [Step 3a](#3a-launch-fragpipe)) +- protein.tsv (protein report, output from [Step 3j](#3j-generate-reports)) +- peptide.tsv (peptide report, output from [Step 3j](#3j-generate-reports)) +- psm.tsv (PSM report, output from [Step 3j](#3j-generate-reports)) +- ion.tsv (ion report, output from [Step 3j](#3j-generate-reports)) +- *_annotation.txt (plex-specific annotation files mapping TMT channels to sample names, used in second pass only, output from [Step 3a](#3a-launch-fragpipe)) +- *.mzML (original mass spectrometry raw data in mzML format; accessed via `--specdir` parameter specified in `filelist_ionquant.txt` to extract TMT reporter ion intensities) **Output Data:** @@ -727,10 +729,10 @@ java -Djava.awt.headless=true -Xmx55G \ - peptide.tsv (peptide report with TMT reporter ion intensities and additional data added from IonQuant) - ion.tsv (ion report with TMT reporter ion intensities and additional data added from IonQuant) - psm.tsv (PSM report with TMT reporter ion intensities (individual TMT channel columns) and additional data added from IonQuant) -- combined_protein.tsv (combined protein report with TMT reporter ion intensities across all samples) -- combined_peptide.tsv (combined peptide report with TMT reporter ion intensities and additional data across all samples) -- combined_ion.tsv (combined ion report with TMT reporter ion intensities and additional data across all samples) -- combined_modified_peptide.tsv (combined modified peptide report with TMT reporter ion intensities and additional data across all samples) +- **combined_protein.tsv** (combined protein report with TMT reporter ion intensities across all samples) +- **combined_peptide.tsv** (combined peptide report with TMT reporter ion intensities and additional data across all samples) +- **combined_ion.tsv** (combined ion report with TMT reporter ion intensities and additional data across all samples) +- **combined_modified_peptide.tsv** (combined modified peptide report with TMT reporter ion intensities and additional data across all samples) - reprint.int.tsv (input file for the Resource for Evaluation of Protein Interaction Networks (REPRINT) containing protein intensities, generated by Philosopher) - reprint.spc.tsv (input file for the Resource for Evaluation of Protein Interaction Networks (REPRINT) containing protein spectral counts, generated by Philosopher) @@ -755,8 +757,8 @@ java -Xmx55G -jar TMT-Integrator-6.1.1.jar \ **Input Data:** -- `tmt-integrator-conf.yml` (TMTIntegrator configuration file, output from [Step 3a](#3a-launch-fragpipe)) -- `psm.tsv` (PSM reports with TMT reporter ion intensities, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) +- tmt-integrator-conf.yml (TMTIntegrator configuration file, output from [Step 3a](#3a-launch-fragpipe)) +- psm.tsv (PSM reports with TMT reporter ion intensities, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) **Output Data:** @@ -794,13 +796,13 @@ clean_multiqc_paths.py multiqc_GLProteomics_data /path/to/pmultiqc/output/direct **Input Data:** -- `psm.tsv` (plex-specific PSM reports, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) -- `ion.tsv` (plex-specific ion reports, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) -- `combined_protein.tsv` (combined protein report, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) -- `combined_peptide.tsv` (combined peptide report, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) -- `combined_ion.tsv` (combined ion report, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) -- `*.workflow` (FragPipe workflow file, output from [Step 3a](#3a-launch-fragpipe)) -- `fragger.params` (MSFragger parameters file, output from [Step 3a](#3a-launch-fragpipe)) +- psm.tsv (plex-specific PSM reports, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) +- ion.tsv (plex-specific ion reports, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) +- combined_protein.tsv (combined protein report, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) +- combined_peptide.tsv (combined peptide report, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) +- combined_ion.tsv (combined ion report, output from [Step 3k](#3k-ionquant-tmt-reporter-ion-extraction)) +- *.workflow (FragPipe workflow file, output from [Step 3a](#3a-launch-fragpipe)) +- fragger.params (MSFragger parameters file, output from [Step 3a](#3a-launch-fragpipe)) **Output Data:** From 7df0a59aad03c9b974981410e42d4737983b33ca Mon Sep 17 00:00:00 2001 From: asaravia-butler <70983120+asaravia-butler@users.noreply.github.com> Date: Wed, 11 Feb 2026 12:43:39 -0800 Subject: [PATCH 3/3] bolding output files in GL-DPPD-[LFQ-MBR].md --- .../Pipeline_GL-DPPD-[LFQ-MBR]_Versions/GL-DPPD-[LFQ-MBR].md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Proteomics/Pipeline_GL-DPPD-[LFQ-MBR]_Versions/GL-DPPD-[LFQ-MBR].md b/Proteomics/Pipeline_GL-DPPD-[LFQ-MBR]_Versions/GL-DPPD-[LFQ-MBR].md index 667745935..346250a69 100644 --- a/Proteomics/Pipeline_GL-DPPD-[LFQ-MBR]_Versions/GL-DPPD-[LFQ-MBR].md +++ b/Proteomics/Pipeline_GL-DPPD-[LFQ-MBR]_Versions/GL-DPPD-[LFQ-MBR].md @@ -710,8 +710,8 @@ java -Xmx55G \ - ion.tsv (sample-specific ion report with MS1 quantification data and additional data added from IonQuant) - psm.tsv (sample-specific PSM report with MS1 quantification data and additional data added from IonQuant) - *_model.png (sample-specific IonQuant model visualization plot showing quantification model fits) -- combined_protein.tsv (combined protein report with MS1 quantification data across all samples) -- combined_peptide.tsv (combined peptide report with MS1 quantification data and additional data across all samples) +- **combined_protein.tsv** (combined protein report with MS1 quantification data across all samples) +- **combined_peptide.tsv** (combined peptide report with MS1 quantification data and additional data across all samples) - **combined_modified_peptide.tsv** (combined modified peptide report with MS1 quantification data and additional data across all samples) - **combined_ion.tsv** (combined ion report with MS1 quantification data and additional data across all samples) - **combined_site_*.tsv** (site-specific modification reports, e.g., "combined_site_C_57.0215.tsv" for carbamidomethylation, "combined_site_M_15.9949.tsv" for oxidation)