Files

parameters.py (py)

LICENSE (LICENSE)

coremsHDF5.py (py)

parameter_to_dict.py (py)

ESI_NEG_SRFA_COREMS_withdupes.csv (csv)

molecularSQL.html (html)

.bumpversion.cfg (cfg)

masslist_ref.py (py)

GC_Calc.html (html)

andiNetCDF.html (html)

brukerSolarix.html (html)

corems_hdf5.html (html)

parserbase.html (html)

AutoRecalibration.html (html)

masslist_ref.html (html)

classification.html (html)

spectrum_search_results.html (html)

molecular_id.html (html)

test_classification.py (py)

submethods.xml (xml)

MANIFEST.in (in)

.dockerignore (dockerignore)

DockerfileDevEnv (DockerfileDevEnv)

.env (env)

pypi_publish.yml (yml)

Makefile (Makefile)

GC_Calc.py (py)

boosterHDF5.py (py)

MassErrorPrediction.py (py)

GC_RI_Calibration.py (py)

MassSpectrumCalc.py (py)

rawFileReader.py (py)

NoiseCalc.py (py)

neg_calibrants_PIP_NTwHMC.ref (ref)

disclaimer.txt (txt)

nistMSI.py (py)

Molecular Formula Data Aggreation.py (py)

pytest.ini (ini)

s3_test.py (py)

test_input.py (py)

test_gcms.py (py)

test_lcms_metabolomics.py (py)

test_mass_spectrum.py (py)

test_molecular_formula_search.py (py)

ATTRIBUTION.md (markdown)

test_molecular_formula_db_factory.py (py)

test_db.msp (msp)

corems-k8s-debug.yaml (yaml)

GC_Class.py (py)

input.html (html)

nom_grow_workflow.py (py)

NEG_ESI_SRFA_CoreMS_scan0.csv (csv)

desktop.ini (ini)

priorityAssignment.py (py)

chroma_peak.html (html)

ThermoFisher.CommonCore.MassPrecisionEstimator.xml (xml)

factory.html (html)

test_setting_settings.py (py)

Hawkes_neg.ref (ref)

ExciteSweep (ExciteSweep)

MolecularFormulaCalc.py (py)

SignalProcessing.html (html)

ClusterFilter.py (py)

boosterHDF5.html (html)

input.html (html)

mass_spectra.html (html)

calc.html (html)

factory.html (html)

coremsHDF5.html (html)

massList.html (html)

Hawkes_neg.ref (ref)

MolecularFilter.html (html)

lipid_molecular_metadata.html (html)

andiNetCDF.py (py)

boosterHDF5.py (py)

brukerSolarix.py (py)

compoundSearch.html (html)

molecularFormulaSearch.html (html)

TransientCalc.html (html)

ms_peak.html (html)

brukerSolarix.html (html)

README.md (md)

System.IO.FileSystem.AccessControl.xml (xml)

OpenMcdf.xml (xml)

ThermoFisher.CommonCore.MassPrecisionEstimator.xml (xml)

version (version)

System.Security.AccessControl.xml (xml)

Analysis.mzXML (mzXML)

Installing CoreMS.md (md)

.gitattributes (gitattributes)

CONTRIBUTING.md (md)

Dockerfile (Dockerfile)

lc_calc.py (py)

massList.py (py)

GC_Deconvolution.py (py)

README.md (md)

.gitlab-ci.yml (yml)

massList.py (py)

MassSpectrumClasses.py (py)

corems_hdf5.py (py)

parserbase.py (py)

MeanResolvingPowerFilter.py (py)

mzml.py (py)

MZSearch.py (py)

KendrickGroup.py (py)

SpectralSimilarity.py (py)

SignalProcessing.py (py)

PeakPicking.py (py)

molecularSQL.py (py)

classification.py (py)

compoundSearch.py (py)

SRFA.ref (ref)

spectrum_search_results.py (py)

lcms_spectral_search.py (py)

database_interfaces.py (py)

molecularFormulaSearch.py (py)

findOxygenPeaks.py (py)

LC-ICPMS_metal_peaks.py (py)

HR-MS Thermo Raw 21T.py (py)

docker-compose-jupyter.yml (yml)

LCMS_isotopes.py (py)

LCMS-Thermo.py (py)

ChromaPeakCalc.html (html)

GCMS_Tutorial.ipynb (ipynb)

GC-MS MetabRef.py (py)

GC-MS NetCDF.py (py)

DI HR-MS MassList.py (py)

README.md (md)

MSParams_example.py (py)

docker-compose.yml (yml)

AtomicWeightsAndIsotopicCompNIST2019.txt (txt)

gcms_workflow.py (py)

requirements-dev.txt (txt)

AtomsDescription.py (py)

filefinder.py (py)

lipidomics_workflow.py (py)

Mass_Recalibration_Tutorial.ipynb (ipynb)

metabref_lipid_metadata.json (json)

nmdc_metadata_gen.py (py)

test_output.py (py)

FAMES_REF.MSL (MSL)

test_calibration.py (py)

test_assembly_identification.py (py)

requirements-support.txt (txt)

xtest_mz_search.py (py)

parameter_to_json.py (py)

configuration.hss (hss)

test_mass_spectrum_export_import.py (py)

.gitignore (gitignore)

factory (factory)

DI HR-MS Halogens Bruker.py (py)

calc (calc)

factory (factory)

setup.py (py)

__init__.py (py)

transient (transient)

calc (calc)

CreateAtomsDescription.py (py)

input (input)

__init__.py (py)

output (output)

__init__.py (py)

factory (factory)

__init__.py (py)

input (input)

__init__.py (py)

molecular_id (molecular_id)

__init__.py (py)

calc (calc)

factory (factory)

input (input)

factory (factory)

input (input)

molecular_formula (molecular_formula)

calc (calc)

db (db)

factory (factory)

input (input)

factory (factory)

search (search)

.zenodo.json (json)

ms_peak (ms_peak)

examples (examples)

archive (archive)

notebooks (notebooks)

scripts (scripts)

dotnet (dotnet)

metadata (metadata)

20190205_WK_SRFA_opt_000001.d (d)

ProjectCreationHelper (ProjectCreationHelper)

SyncHelper (SyncHelper)

calc (calc)

__init__.py (py)

factory (factory)

__init__.py (py)

encapsulation (encapsulation)

__init__.py (py)

mass_spectra (mass_spectra)

__init__.py (py)

calc (calc)

__init__.py (py)

factory (factory)

__init__.py (py)

input (input)

__init__.py (py)

output (output)

__init__.py (py)

calc (calc)

output (output)

__init__.py (py)

factory (factory)

__init__.py (py)

input (input)

__init__.py (py)

molecular_formula (molecular_formula)

__init__.py (py)

factory (factory)

__init__.py (py)

input (input)

__init__.py (py)

search (search)

__init__.py (py)

ms_peak (ms_peak)

__init__.py (py)

calc (calc)

__init__.py (py)

factory (factory)

__init__.py (py)

transient (transient)

__init__.py (py)

calc (calc)

__init__.py (py)

factory (factory)

__init__.py (py)

input (input)

__init__.py (py)

docs (docs)

corems (corems)

chroma_peak (chroma_peak)

calc (calc)

factory (factory)

encapsulation (encapsulation)

factory (factory)

input (input)

output (output)

notebooks (notebooks)

support_code (support_code)

atom_parsers (atom_parsers)

nmdc (nmdc)

lipidomics (lipidomics)

metabolomics (metabolomics)

nom (nom)

archived_scripts (archived_scripts)

windows_only_importers (windows_only_importers)

tests (tests)

archive_tests (archive_tests)

tests_data (tests_data)

ftms (ftms)

ESI_NEG_SRFA.d (d)

1901_Neg_CompMix_1.4s_150-1000.m (m)

ProjectCreationHelper (ProjectCreationHelper)

SyncHelper (SyncHelper)

gcms (gcms)

icpms (icpms)

lcms (lcms)

test_molecular_formula.py (py)

conftest.py (py)

lipid_molecular_metadata.py (py)

ESI_NEG_SRFA_UnCal_Unassign.csv (csv)

CoreMS_tutorial.py (py)

Single Mz Search.py (py)

metabref_spec_lib.json (json)

calc.html (html)

factory.html (html)

input (input)

transient.html (html)

midasDatFile.html (html)

input.html (html)

__init__.py (py)

calc (calc)

mass_spectra (mass_spectra)

calc (calc)

factory.html (html)

MSPeakCalc.html (html)

processingSetting.py (py)

parameter_from_json.py (py)

MolecularFormulaFactory.py (py)

calc.html (html)

GC_RI_Calibration.html (html)

GC_Class.html (html)

GC_Deconvolution.html (html)

factory.html (html)

chromat_data.html (html)

massList.html (html)

output (output)

mass_spectrum (mass_spectrum)

output.html (html)

calc (calc)

CalibrationCalc.html (html)

Calibration.html (html)

NoiseCalc.html (html)

NoiseCalc_Bayes.html (html)

MassSpectrumCalc.html (html)

MassErrorPrediction.html (html)

baseClass.html (html)

output (output)

output.html (html)

numpyArray.html (html)

input.html (html)

export.html (html)

mass_spectrum.html (html)

molecular_formula.html (html)

MolecularFormulaCalc.html (html)

input.html (html)

calc.html (html)

MolecularFormulaFactory.html (html)

molecular_id (molecular_id)

calc (calc)

SpectralSimilarity.html (html)

math_distance.html (html)

ClusterFilter.html (html)

MolecularLookupTable.html (html)

input (input)

nistMSI.html (html)

findOxygenPeaks.html (html)

priorityAssignment.html (html)

search.html (html)

input.html (html)

factory.html (html)

database_interfaces.html (html)

corems.html (html)

uml (uml)

index.html (html)

CoreMS_devel_lcms_isotopes.ipynb (ipynb)

ThermoFisher.CommonCore.BackgroundSubtraction.xml (xml)

lock.file (file)

LockInfo (LockInfo)

ESI_NEG_SRFA_COREMS.csv (csv)

NEG_ESI_SRFA_CoreMS.corems (corems)

NEG_ESI_SRFA_CoreMS_scan0.json (json)

.github (github)

workflows (workflows)

factory (factory)

corems (corems)

chroma_peak (chroma_peak)

__init__.py (py)

Calibration.py (py)

constant.py (py)

numpyArray.py (py)

AutoRecalibration.py (py)

chroma_peak_classes.py (py)

export.py (py)

chromat_data.py (py)

CalibrationCalc.py (py)

lc_class.py (py)

__init__.py (py)

mass_spectrum (mass_spectrum)

encapsulation.html (html)

midasDatFile.py (py)

TransientCalc.py (py)

MSPeakClasses.py (py)

MSPeakCalc.py (py)

brukerSolarix.py (py)

TransientClasses.py (py)

parameter_to_json.html (html)

Setting_MSParameters.ipynb (ipynb)

test_notebooks.py (py)

output.html (html)

parameter_from_json.html (html)

constant.html (html)

ResolvingPowerFilter_ICR.ipynb (ipynb)

factory.html (html)

parameter_to_dict.html (html)

processingSetting.html (html)

parameters.html (html)

calc.html (html)

ext_lib (ext_lib)

__init__.py (py)

bck (bck)

requirements.txt (txt)

BrukerCompassXtract.py (py)

test_wf_lipidomics.py (py)

ThermoMSFileReader.py (py)

ChemstationMSFileReader.xml (xml)

nom_workflow.py (py)

ESFA_15T_3sFID_calibrated.txt (txt)

desktop.ini (ini)

Noise_Thresholding_Methods.ipynb (ipynb)

ESI_NEG_ESFA.ascii (ascii)

ThermoFisher.CommonCore.BackgroundSubtraction.xml (xml)

NEG_ESI_SRFA_Auto.d (d)

20190709_WK_CADY_Auto_SRFA_QC_O1_1_01_32.d (d)

2019_Cady_SRFA_32.m (m)

LockInfo (LockInfo)

apexAcquisition.method (method)

submethods.xml (xml)

PULPROG__basic.compiled (compiled)

apexAcquisition.method (method)

PULPROG__basic.compiled (compiled)

ThermoFisher.CommonCore.BackgroundSubtraction.xml (xml)

Neg ESI Manual assignment with Cl adducts.ipynb (ipynb)

ChromaPeakCalc.py (py)

calc.html (html)

brukerSolarix_utils.py (py)

test_search_mass_list.py (py)

Dockerfile_py310_dotnet_base (Dockerfile_py310_dotnet_base)

lcms_spectral_search.html (html)

test_mspeak.py (py)

export.py (py)

KendrickGroup.html (html)

Dockerfile_py310_dotnet_base_clean (Dockerfile_py310_dotnet_base_clean)

scan.xml (xml)

.bumpversion.toml (toml)

mzml.html (html)

requirements.txt (txt)

PeakPicking.html (html)

boosterHDF5.html (html)

factory.html (html)

calc.html (html)

MS_Peak_Fitting.ipynb (ipynb)

System.Security.Principal.Windows.xml (xml)

ThermoFisher.CommonCore.MassPrecisionEstimator.xml (xml)

lcms_metabolomics_workflow.py (py)

desktop.ini (ini)

PULPROG__basic.event_seq (event_seq)

ExciteSweep (ExciteSweep)

hystar.method (method)

desktop.ini (ini)

NoiseCalc_Bayes.py (py)

TransientClasses.html (html)

brukerSolarix_utils.html (html)

math_distance.py (py)

dms_api.py (py)

MolecularLookupTable.py (py)

lc_class.html (html)

MSPeakClasses.html (html)

EI_SQL.py (py)

MeanResolvingPowerFilter.html (html)

baseClass.py (py)

test_ImportMassSpectraCompassXtract.py (py)

MolecularFilter.py (py)

PULPROG__basic.event_seq (event_seq)

chroma_peak_classes.html (html)

MZSearch.html (html)

SRFA.ref (ref)

EI_SQL.html (html)

github-repos/CoreMS

CoreMS

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• Updated Mar 4, 2026

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CoreMS is a comprehensive mass spectrometry software framework

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Created Feb 10, 2026