├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── test_coverage.yml └── workflows │ ├── codeql.yml │ └── pylint.yml ├── .gitignore ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING ├── LICENSE ├── MANIFEST.in ├── README.md ├── SECURITY.md ├── VERSION_LOG.md ├── docs ├── .readthedocs.yaml ├── make.bat ├── requirements.txt └── source │ ├── README.md │ ├── conf.py │ ├── index.rst │ ├── modules.rst │ ├── pcpfm_acquisition.rst │ ├── pcpfm_empcpds.rst │ ├── pcpfm_experiment.rst │ ├── pcpfm_featuretable.rst │ ├── pcpfm_main.rst │ └── pcpfm_report.rst ├── examples ├── auth_std_libraries │ ├── README.md │ ├── auth_std_HILIC_pos_12_01_2024_JM_wMS2.csv │ └── auth_std_RP_neg_12_01_2024_JM_wMS2.csv ├── configurations │ └── khipu_isotopes. │ │ └── up_to_three_groups.json ├── filters │ ├── README.md │ ├── drop_dda.json │ ├── hilicneg.json │ ├── hilicpos.json │ ├── qaqc_drop.json │ ├── rpneg.json │ └── rppos.json ├── report_templates │ ├── README.md │ ├── default_batch_corrected.json │ ├── default_w_tics.json │ └── minimal.json └── workflows │ ├── .DS_Store │ ├── README.md │ ├── bash_workflows │ ├── .DS_Store │ ├── README.md │ ├── generic │ │ ├── basic_processing_no_AcquireX.sh │ │ ├── basic_processing_no_AcquireX_noFilter.sh │ │ ├── basic_processing_w_AcquireX.sh │ │ ├── minimal_processing.sh │ │ └── two_chromatography_modes_using_filters.sh │ └── manuscript │ │ ├── .DS_Store │ │ ├── Ansone_2021.sh │ │ ├── Bowen_2023_cell.sh │ │ ├── Checkmate.sh │ │ ├── Checkmate_subset.sh │ │ ├── HZV029_HILIC_subset.sh │ │ ├── HZV029_QC.sh │ │ ├── HZV029_RP_subset.sh │ │ ├── HZV029_plasma_HILIC.sh │ │ ├── HZV029_plasma_RP.sh │ │ ├── HZV029_plasma_RP_batch_correct.sh │ │ ├── HZV029_two_phase_HILIC.sh │ │ ├── README.md │ │ ├── bowen_2023_media.sh │ │ ├── khipu.log │ │ ├── sequence_files │ │ ├── .DS_Store │ │ ├── HZV029_Plasma_w_reruns.csv │ │ ├── HZV029_QC_sequence.csv │ │ ├── HZV029_TwoPhase.csv │ │ ├── README.md │ │ ├── ansone_sequence.csv │ │ ├── bowen_cell_wo_QC.csv │ │ ├── bowen_media_wo_QC.csv │ │ └── checkmate_orbi_full.csv │ │ └── subset_sequence_files │ │ ├── HILIC_pos_subset_sequence.csv │ │ ├── RP_neg_subset_sequence.csv │ │ └── checkmate_orbi_subset_sequence.csv │ └── nextflow │ ├── README.md │ ├── compatible_workflows │ ├── basic_process_w_filter_w_acquireX.sh │ ├── example_filter_acquirex_jobs.csv │ ├── example_input_minimal_jobs.csv │ └── minimal_processing.sh │ ├── minimal_nextflow.nf │ ├── nextflow │ └── process_w_filter_w_acquireX.nf ├── helper_scripts ├── block_designer.py ├── example2_for_block_designer.xlsx ├── example_for_block_designer.csv └── randomizer.py ├── notebooks └── manuscript │ ├── .DS_Store │ └── figures │ ├── .DS_Store │ ├── Figure 1 │ ├── README.md │ └── example_empcpd.json │ ├── Figure 2 │ ├── MetaboAnalystProcessing.R │ ├── README.md │ ├── annotation_counting.ipynb │ └── figure2.ipynb │ ├── Figure 3 │ ├── CD_MoNA_HILIC_pos.csv │ ├── CD_MoNA_RP_neg.csv │ ├── Customized Untargeted Metabolomics using Online Databases, MoNA+nopredictioncomp, noRTtol, RPneg.cdProcessingWF │ ├── Customized Untargeted Metabolomics using Online Databases, MoNA, nopredictcomp, noRTtol, HILICpos.cdProcessingWF │ ├── Figure3.ipynb │ └── README.md │ ├── Figure 4 │ ├── Figure4.ipynb │ ├── README.md │ ├── batch5_MT_20210730_001.mzML │ └── batch5_MT_20210730_003.mzML │ ├── Figure 5 │ ├── .DS_Store │ ├── Figure5.txt │ ├── ansone │ │ ├── ansone_2021_analysis.ipynb │ │ └── s_MTBLS3852.csv │ ├── bowen │ │ ├── bowen_2023_analysis.ipynb │ │ └── s_MTBLS2746.txt │ └── checkmate_comparison │ │ ├── MetaboAnalystProcessing.R │ │ └── compare_pcpfm_metaboanalystR.ipynb │ └── README.md ├── pcpfm ├── Acquisition.py ├── EmpCpds.py ├── Experiment.py ├── FeatureTable.py ├── MSnSpectrum.py ├── Report.py ├── Report2.py ├── __init__.py ├── __main__.py ├── annotation_sources │ └── README.md ├── default_configs │ ├── README.md │ ├── __init__.py │ ├── default_adducts_neg_feature.json │ ├── default_adducts_neg_khipu.json │ ├── 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