LC-MS

NOTE: Several versions of this metadata schema have been created over time. The (Latest) version contains most attributes, but there may be some deprecated attributes in the older versions for which data has been collected. HuBMAP is in the process of creating a reference which combines all of these versions into a single view. That reference will be available here once completed.

Version 4 (Latest)

Attribute	Type	Description	Allowable Values	Required
dataset_type	Allowable Value	The specific type of dataset being produced.	`10X Multiome` `2D Imaging Mass Cytometry` `ATACseq` `Auto-fluorescence` `Cell DIVE` `CODEX` `Confocal` `CosMx` `CyCIF` `DBiT` `DESI` `Enhanced Stimulated Raman Spectroscopy (SRS)` `GeoMx (nCounter)` `GeoMx (NGS)` `HiFi-Slide` `Histology` `LC-MS` `Light Sheet` `MALDI` `MERFISH` `MIBI` `Molecular Cartography` `MUSIC` `nanoSPLITS` `PhenoCycler` `Resolve` `RNAseq` `RNAseq (with probes)` `Second Harmonic Generation (SHG)` `SIMS` `SNARE-seq2` `Stereo-seq` `Thick section Multiphoton MxIF` `Visium (no probes)` `Visium (with probes)` `Xenium`	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	`Chromatin` `DNA` `DNA + RNA` `Endogenous fluorophores` `Fluorochrome` `Lipid` `Metabolite` `Nucleic acid and protein` `Peptide` `Polysaccharide` `Protein` `RNA`	True
acquisition_instrument_vendor	Allowable Value	An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass.	`Akoya Biosciences` `Andor` `BGI Genomics` `Bruker` `Cytiva` `Evident Scientific (Olympus)` `GE Healthcare` `Hamamatsu` `Huron Digital Pathology` `Illumina` `In-House` `Ionpath` `Keyence` `Leica Biosystems` `Leica Microsystems` `Motic` `NanoString` `Resolve Biosciences` `Sciex` `Standard BioTools (Fluidigm)` `Thermo Fisher Scientific` `Zeiss Microscopy`	True
acquisition_instrument_model	Allowable Value	Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data.	`Aperio AT2` `Aperio CS2` `Axio Observer 3` `Axio Observer 5` `Axio Observer 7` `Axio Scan.Z1` `BZ-X710` `BZ-X800` `BZ-X810` `CosMx Spatial Molecular Imager` `Custom: Multiphoton` `Digital Spatial Profiler` `DM6 B` `DNBSEQ-T7` `EVOS M7000` `HiSeq 2500` `HiSeq 4000` `Hyperion Imaging System` `IN Cell Analyzer 2200` `Lightsheet 7` `MALDI timsTOF Flex Prototype` `MIBIscope` `MoticEasyScan One` `NanoZoomer 2.0-HT` `NanoZoomer S210` `NanoZoomer S360` `NanoZoomer S60` `NanoZoomer-SQ` `NextSeq 2000` `NextSeq 500` `NextSeq 550` `NovaSeq 6000` `NovaSeq X` `NovaSeq X Plus` `Orbitrap Eclipse Tribrid` `Orbitrap Fusion Lumos Tribrid` `Phenocycler-Fusion 1.0` `Phenocycler-Fusion 2.0` `PhenoImager Fusion` `Q Exactive` `Q Exactive HF` `Q Exactive UHMR` `QTRAP 5500` `Resolve Biosciences Molecular Cartography` `SCN400` `STELLARIS 5` `TissueScope LE Slide Scanner` `Unknown` `VS200 Slide Scanner` `Xenium Analyzer` `Zyla 4.2 sCMOS`	True
source_storage_duration_value	Numeric	How long was the source material (parent) stored, prior to this sample being processed.		True
source_storage_duration_unit	Allowable Value	The time duration unit of measurement	`hour` `month` `day` `minute` `year`	True
time_since_acquisition_instrument_calibration_value	Numeric	The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture.		False
time_since_acquisition_instrument_calibration_unit	Allowable Value	The time unit of measurement	`Column-by-column` `Not applicable` `Row-by-row` `Snake-by-columns` `Snake-by-rows`	False
preparation_protocol_doi	Textfield	DOI for the protocols.io page that describes the assay or sample procurment and preparation. For example for an imaging assay, the protocol might include staining of a section through the creation of an OME-TIFF file. In this case the protocol would include any image processing steps required to create the OME-TIFF file. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1		True
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay (“Yes” or “No”). The CODEX analyte is protein.	`Yes` `No`	True
contributors_path	Textfield	The path to the file with the ORCID IDs for all contributors of this dataset (e.g., “./extras/contributors.tsv” or “./contributors.tsv”). This is an internal metadata field that is just used for ingest.		True
data_path	Textfield	The top level directory containing the raw and/or processed data. For a single dataset upload this might be “.” where as for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For instance, if the data is within a directory called “TEST001-RK” use syntax “./TEST001-RK” for this field. If there are multiple directory levels, use the format “./TEST001-RK/Run1/Pass2” in which “Pass2” is the subdirectory where the single dataset’s data is stored. This is an internal metadata field that is just used for ingest.		True
mass_analysis_polarity	Allowable Value	The polarity of the mass analysis (positive or negative ion modes).	`Negative and positive ion mode` `Negative ion mode` `Positive ion mode`	True
mass-to-charge_range_low_value	Numeric	The low value of the scanned mass-to-charge range, for MS1. (unitless)		False
mass-to-charge_range_high_value	Numeric	The high value of the scanned mass-to-charge range, for MS1. (unitless)		False
mass_resolving_power	Numeric	The mass resolving power m/∆m, where ∆m is defined as the full width at half-maximum (FWHM) for a given peak with a specified mass-to-charge (m/z). (unitless)		False
mass-to-charge_resolving_power	Numeric	The peak (m/z) used to calculate the resolving power.		False
ion_mobility	Allowable Value	Specifies which technology was used for ion mobility spectrometry. Technologies for measuring ion mobility: Traveling Wave Ion Mobility Spectrometry (TWIMS), Trapped Ion Mobility Spectrometry (TIMS), High Field Asymmetric waveform ion Mobility Spectrometry (FAIMS), Drift Tube Ion Mobility Spectrometry (DTIMS), Structures for Lossless Ion Manipulations (SLIM), and cyclic Ion Mobility Spectrometry (cIMS).	`cIMS` `DTIMS` `FAIMS` `SLIM` `TIMS` `TWIMS`	False
ms_ionization_technique	Allowable Value	The ionization approach (i.e., sample probing method) for performing imaging mass spectrometry.	`DESI` `ESI` `HESI` `LA` `LDI` `MALDI` `MALDI-2` `nanoDESI` `SIMS-C60` `SIMS-H20`	True
ms_scan_mode	Allowable Value	MS (mass spectrometry) scan mode refers to the number of steps in the separation of fragments.	`MS1` `MS2` `MS3`	True
label_name	Textfield	If the samples were labeled (e.g. TMT), provide the name/ID of the label on this sample. Leave blank if not applicable.		False
lc_instrument_vendor	Allowable Value	The manufacturer of the instrument used for liquid chromatography.	`Agilent Technologies` `Bruker` `Evosep` `In-House` `Sciex` `Thermo Fisher Scientific` `Waters`	False
lc_instrument_model	Textfield	The model number/name of the instrument used for liquid chromatography.		False
lc_column_model	Textfield	The model number/name of the liquid chromatography column. If it is a custom self-packed, pulled tip capillary is used enter “Pulled tip capilary”.		False
lc_resin	Textfield	Details of the resin used for liquid chromatography, including vendor, particle size, pore size.		False
lc_column_length_value	Numeric	Liquid chromatography column length.		False
lc_column_length_unit	Allowable Value	Units for liquid chromatography column length (typically cm).	`um` `mm` `cm`	False
lc_temperature_value	Numeric	Liquid chromatography temperature.		False
lc_inner_diameter_value	Numeric	Liquid chromatography column inner diameter.		False
lc_flow_rate_value	Numeric	Value of flow rate.		False
lc_gradient_value	Numeric	Liquid chromatography gradient.		False
lc_gradient_unit	Allowable Value	Unit for liquid chromatography gradient	`Minute`	False
lc_mobile_phase_a	Textfield	Composition of mobile phase A.		False
lc_mobile_phase_b	Textfield			False
spatial_sampling_technique	Allowable Value		`LCM` `LESA` `microLESA` `microPOTS` `nanoPOTS` `nanoSPLITS`	False
spatial_sampling_target	Textfield	Specifies the cell-type or functional tissue unit (FTU) that is targeted in the spatial profiling experiment. Leave blank if data are generated in imaging mode without a specific target structure.		False
analysis_protocol_doi	Textfield	A DOI to a protocols.io protocol describing the software and database(s) used to process the raw data. Example: https://dx.doi.org/10.17504/protocols.io.bsu5ney6		True
metadata_schema_id	Textfield	The string that serves as the definitive identifier for the metadata schema version and is readily interpretable by computers for data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9		True
data_collection_mode	Allowable Value	Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition), DIA (Data-independent acquisition), SRM (multiple reaction monitoring), or PRM (parallel reaction monitoring).	`DDA` `PRM` `DIA` `SRM`	False
lc_column_vendor	Allowable Value	The manufacturer of the liquid chromatography column unless self-packed, pulled tip capillary is used.	`Bruker` `Evosep` `In-House` `IonOpticks` `Thermo Fisher Scientific` `Waters`	False
lc_temperature_unit	Allowable Value		`Celsius`	False
lc_inner_diameter_unit	Allowable Value		`um` `mm` `cm`	False
lc_flow_rate_unit	Allowable Value	Units of flow rate.	`mL/min` `nL/min`	False
spatial_sampling_type	Allowable Value	Specifies whether or not the analysis was performed in a spatially targeted manner. Spatial profiling experiments target specific tissue foci but do not necessarily generate images. Spatial imaging expriments collect data from a regular array (pixels) that can be visualized as heat maps of ion intensity at each location (molecular images). Leave blank if data are derived from bulk analysis.	`Imaging` `Profiling`	False
parent_sample_id	Textfield	Unique HuBMAP or SenNet identifier of the sample (i.e., block, section or suspension) used to perform this assay. For example, for a RNAseq assay, the parent would be the suspension, whereas, for one of the imaging assays, the parent would be the tissue section. If an assay comes from multiple parent samples then this should be a comma separated list. Example: HBM386.ZGKG.235, HBM672.MKPK.442 or SNT232.UBHJ.322, SNT329.ALSK.102		True

Version 3

Attribute	Type	Description	Allowable Values	Required
version	Allowable Value	Version of the schema to use when validating this metadata.	[‘3’]	True
description	Textfield	Free-text description of this assay.		True
donor_id	Textfield	HuBMAP Display ID of the donor of the assayed tissue.		True
tissue_id	Textfield	HuBMAP Display ID of the assayed tissue.		True
execution_datetime	Datetime	Start date and time of assay, typically a date-time stamped foldergenerated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year,MM is the month with leading 0s, and DD is the day with leading 0s, hh is thehour with leading zeros, mm are the minutes with leading zeros.		True
protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for this assay.		True
operator	Textfield	Name of the person responsible for executing the assay.		True
operator_email	Textfield	Email address for the operator.		True
pi	Textfield	Name of the principal investigator responsible for the data.		True
pi_email	Textfield	Email address for the principal investigator.		True
assay_category	Allowable Value	Each assay is placed into one of the following 4 general categories:generation of images of microscopic entities, identification & quantitation ofmolecules by mass spectrometry, imaging mass spectrometry, and determination ofnucleotide sequence.	[‘mass_spectrometry’]	True
assay_type	Allowable Value	Bottom-up refers to analyzing proteins in a sample by digesting themto peptides. Top-down refers to analyzing whole proteins without digestion. LC-MSand MS are for lipids/metabolites. LC-MS Bottom-Up and MS Bottom-Up are for peptides.LC-MS Top-Down and MS Top-Down are for proteins.	[‘LC-MS’, ‘MS’, ‘LC-MS Bottom-Up’, ‘MS Bottom-Up’, ‘LC-MS Top-Down’, ‘MS Top-Down’]	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	[‘protein’, ‘metabolites’, ‘lipids’, ‘peptides’, ‘phosphopeptides’, ‘glycans’]	False
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted fordetection/measurement by the assay.	[‘Yes’,’No’]	True
acquisition_instrument_vendor	Textfield	An acquisition instrument is the device that contains the signal detectionhardware and signal processing software. Assays generate signals such as lightof various intensities or color or signals representing the molecular mass.		True
acquisition_instrument_model	Textfield	Manufacturers of an acquisition instrument may offer various versions(models) of that instrument with different features or sensitivities. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data.		True
dms	Allowable Value	Was differential mobility spectrometry used in this assay?	[‘Yes’,’No’]	True
ms_source	Allowable Value	The ion source type used for surface sampling.	[‘ESI’]	True
polarity	Allowable Value	The polarity of the mass analysis (positive or negative ion modes)	[‘negative ion mode’, ‘positive ion mode’, ‘negative and positive ion mode’]	True
mz_range_low_value	Numeric	The low value of the scanned mass range for MS1. (unitless)		True
mz_range_high_value	Numeric	The high value of the scanned mass range for MS1. (unitless)		True
mass_resolving_power	Numeric	The MS1 resolving power defined as m/âm where âm is the FWHM for a given peak with a specified m/z (m). (unitless)		False
mz_resolving_power	Numeric	The peak (m/z) used to calculate the resolving power.		False
ion_mobility	Allowable Value	Specifies whether or not ion mobility spectrometry was performed andwhich technology was used. Technologies for measuring ion mobility: TravelingWave Ion Mobility Spectrometry (TWIMS), Trapped Ion Mobility Spectrometry (TIMS),High Field Asymmetric waveform ion Mobility Spectrometry (FAIMS), Drift Tube IonMobility Spectrometry (DTIMS, Structures for Lossless Ion Manipulations (SLIM).	[‘TIMS’, ‘TWIMS’, ‘FAIMS’, ‘DTIMS’, ‘SLIMS’]	False
data_collection_mode	Allowable Value	Mode of data collection in tandem MS assays. Either DDA (Data-dependentacquisition), DIA (Data-independent acquisition), MRM (multiple reaction monitoring),or PRM (parallel reaction monitoring).	[‘DDA’, ‘DIA’, ‘MRM’, ‘PRM’]	True
ms_scan_mode	Textfield	Indicates whether experiment is MS, MS/MS, or other (possibly MS3 forTMT)		True
labeling	Textfield	Indicates whether samples were labeled prior to MS analysis (e.g.,TMT)		True
label_name	Textfield	If the samples were labeled (e.g. TMT), provide the name/ID of thelabel on this sample.		False
section_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing tissuesections for the assay.		True
lc_instrument_vendor	Textfield	The manufacturer of the instrument used for LC		False
lc_instrument_model	Textfield	The model number/name of the instrument used for LC		False
lc_column_vendor	Textfield	OPTIONAL: The manufacturer of the LC Column unless self-packed, pulledtip capilary is used		False
lc_column_model	Textfield	The model number/name of the LC Column - IF custom self-packed, pulledtip calillary is used enter “Pulled tip capilary”		False
lc_resin	Textfield	Details of the resin used for lc, including vendor, particle size,pore size		False
lc_length_value	Numeric	LC column length		False
lc_length_unit	Allowable Value	units for LC column length (typically cm)	[‘um’, ‘mm’, ‘cm’]	False
lc_temp_value	Numeric	LC temperature		False
lc_temp_unit	Allowable Value	units for LC temperature	[‘C’]	False
lc_id_value	Numeric	LC column inner diameter (microns)		False
lc_id_unit	Allowable Value	units of LC column inner diameter (typically microns)	[‘um’, ‘mm’, ‘cm’]	False
lc_flow_rate_value	Numeric	Value of flow rate.		False
lc_flow_rate_unit	Allowable Value	Units of flow rate.	[‘nL/min’, ‘mL/min’]	False
lc_gradient	Textfield	LC gradient		False
lc_mobile_phase_a	Textfield	Composition of mobile phase A		False
lc_mobile_phase_b	Textfield	Composition of mobile phase B		False
spatial_type	Allowable Value	Specifies whether or not the analysis was performed in a spatialy targetedmanner and the technique used for spatial sampling. For example, Laser-capturemicrodissection (LCM), Liquid Extraction Surface Analysis (LESA), NanodropletProcessing in One pot for Trace Samples (nanoPOTS).	[‘LCM’, ‘LESA’, ‘nanoPOTS’, ‘microLESA’]	False
spatial_sampling_type	Allowable Value	Specifies whether or not the analysis was performed in a spatiallytargeted manner. Spatial profiling experiments target specific tissue foci butdo not necessarily generate images. Spatial imaging expriments collect data froma regular array (pixels) that can be visualized as heat maps of ion intensityat each location (molecular images). Leave blank if data are derived from bulkanalysis.	[‘profiling’, ‘imaging’]	False
spatial_target	Textfield	Specifies the cell-type or functional tissue unit (FTU) that is targetedin the spatial profiling experiment. Leave blank if data are generated in imagingmode without a specific target structure.		False
resolution_x_value	Numeric	The width of a pixel.		False
resolution_x_unit	Allowable Value	The unit of measurement of the width of a pixel.	[‘nm’, ‘um’]	False
resolution_y_value	Numeric	The height of a pixel		False
resolution_y_unit	Allowable Value	The unit of measurement of the height of a pixel.	[‘nm’, ‘um’]	False
processing_search	Textfield	Software for analyzing and searching LC-MS/MS omics data		True
processing_protocols_io_doi	Textfield	DOI for analysis protocols.io for this assay.		False
overall_protocols_io_doi	Textfield	DOI for protocols.io for the overall process for this assay.		False
contributors_path	Textfield	Relative path to file with ORCID IDs for contributors for this dataset.		True
data_path	Textfield	Relative path to file or directory with instrument data. Downstreamprocessing will depend on filename extension conventions.		True

Version 2

Attribute	Type	Description	Allowable Values	Required
version	Allowable Value	Version of the schema to use when validating this metadata.	[‘2’]	True
description	Textfield	Free-text description of this assay.		True
donor_id	Textfield	HuBMAP Display ID of the donor of the assayed tissue.		True
tissue_id	Textfield	HuBMAP Display ID of the assayed tissue.		True
execution_datetime	Datetime	Start date and time of assay, typically a date-time stamped foldergenerated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year,MM is the month with leading 0s, and DD is the day with leading 0s, hh is thehour with leading zeros, mm are the minutes with leading zeros.		True
protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for this assay.		True
operator	Textfield	Name of the person responsible for executing the assay.		True
operator_email	Textfield	Email address for the operator.		True
pi	Textfield	Name of the principal investigator responsible for the data.		True
pi_email	Textfield	Email address for the principal investigator.		True
assay_category	Allowable Value	Each assay is placed into one of the following 4 general categories:generation of images of microscopic entities, identification & quantitation ofmolecules by mass spectrometry, imaging mass spectrometry, and determination ofnucleotide sequence.	[‘mass_spectrometry’]	True
assay_type	Allowable Value	Bottom-up refers to analyzing proteins in a sample by digesting themto peptides. Top-down refers to analyzing whole proteins without digestion. LC-MSand MS are for lipids/metabolites. LC-MS Bottom-Up and MS Bottom-Up are for peptides.LC-MS Top-Down and MS Top-Down are for proteins.	[‘LC-MS’, ‘MS’, ‘LC-MS Bottom-Up’, ‘MS Bottom-Up’, ‘LC-MS Top-Down’, ‘MS Top-Down’]	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	[‘protein’, ‘metabolites’, ‘lipids’, ‘peptides’, ‘phosphopeptides’, ‘glycans’]	False
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted fordetection/measurement by the assay.	[‘Yes’,’No’]	True
acquisition_instrument_vendor	Textfield	An acquisition instrument is the device that contains the signal detectionhardware and signal processing software. Assays generate signals such as lightof various intensities or color or signals representing the molecular mass.		True
acquisition_instrument_model	Textfield	Manufacturers of an acquisition instrument may offer various versions(models) of that instrument with different features or sensitivities. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data.		True
ms_source	Allowable Value	The ion source type used for surface sampling.	[‘ESI’]	True
polarity	Allowable Value	The polarity of the mass analysis (positive or negative ion modes)	[‘negative ion mode’, ‘positive ion mode’, ‘negative and positive ion mode’]	True
mz_range_low_value	Numeric	The low value of the scanned mass range for MS1. (unitless)		True
mz_range_high_value	Numeric	The high value of the scanned mass range for MS1. (unitless)		True
mass_resolving_power	Numeric	The MS1 resolving power defined as m/âm where âm is the FWHM for a given peak with a specified m/z (m). (unitless)		False
mz_resolving_power	Numeric	The peak (m/z) used to calculate the resolving power.		False
ion_mobility	Allowable Value	Specifies whether or not ion mobility spectrometry was performed andwhich technology was used. Technologies for measuring ion mobility: TravelingWave Ion Mobility Spectrometry (TWIMS), Trapped Ion Mobility Spectrometry (TIMS),High Field Asymmetric waveform ion Mobility Spectrometry (FAIMS), Drift Tube IonMobility Spectrometry (DTIMS, Structures for Lossless Ion Manipulations (SLIM).	[‘TIMS’, ‘TWIMS’, ‘FAIMS’, ‘DTIMS’, ‘SLIMS’]	False
data_collection_mode	Allowable Value	Mode of data collection in tandem MS assays. Either DDA (Data-dependentacquisition), DIA (Data-independent acquisition), MRM (multiple reaction monitoring),or PRM (parallel reaction monitoring).	[‘DDA’, ‘DIA’, ‘MRM’, ‘PRM’]	True
ms_scan_mode	Textfield	Indicates whether experiment is MS, MS/MS, or other (possibly MS3 forTMT)		True
labeling	Textfield	Indicates whether samples were labeled prior to MS analysis (e.g.,TMT)		True
section_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing tissuesections for the assay.		True
lc_instrument_vendor	Textfield	The manufacturer of the instrument used for LC		False
lc_instrument_model	Textfield	The model number/name of the instrument used for LC		False
lc_column_vendor	Textfield	OPTIONAL: The manufacturer of the LC Column unless self-packed, pulledtip capilary is used		False
lc_column_model	Textfield	The model number/name of the LC Column - IF custom self-packed, pulledtip calillary is used enter “Pulled tip capilary”		False
lc_resin	Textfield	Details of the resin used for lc, including vendor, particle size,pore size		False
lc_length_value	Numeric	LC column length		False
lc_length_unit	Allowable Value	units for LC column length (typically cm)	[‘um’, ‘mm’, ‘cm’]	False
lc_temp_value	Numeric	LC temperature		False
lc_temp_unit	Allowable Value	units for LC temperature	[‘C’]	False
lc_id_value	Numeric	LC column inner diameter (microns)		False
lc_id_unit	Allowable Value	units of LC column inner diameter (typically microns)	[‘um’, ‘mm’, ‘cm’]	False
lc_flow_rate_value	Numeric	Value of flow rate.		False
lc_flow_rate_unit	Allowable Value	Units of flow rate.	[‘nL/min’, ‘mL/min’]	False
lc_gradient	Textfield	LC gradient		False
lc_mobile_phase_a	Textfield	Composition of mobile phase A		False
lc_mobile_phase_b	Textfield	Composition of mobile phase B		False
spatial_type	Allowable Value	Specifies whether or not the analysis was performed in a spatialy targetedmanner and the technique used for spatial sampling. For example, Laser-capturemicrodissection (LCM), Liquid Extraction Surface Analysis (LESA), NanodropletProcessing in One pot for Trace Samples (nanoPOTS).	[‘LCM’, ‘LESA’, ‘nanoPOTS’, ‘microLESA’]	False
spatial_sampling_type	Allowable Value	Specifies whether or not the analysis was performed in a spatiallytargeted manner. Spatial profiling experiments target specific tissue foci butdo not necessarily generate images. Spatial imaging expriments collect data froma regular array (pixels) that can be visualized as heat maps of ion intensityat each location (molecular images). Leave blank if data are derived from bulkanalysis.	[‘profiling’, ‘imaging’]	False
spatial_target	Textfield	Specifies the cell-type or functional tissue unit (FTU) that is targetedin the spatial profiling experiment. Leave blank if data are generated in imagingmode without a specific target structure.		False
resolution_x_value	Numeric	The width of a pixel.		False
resolution_x_unit	Allowable Value	The unit of measurement of the width of a pixel.	[‘nm’, ‘um’]	False
resolution_y_value	Numeric	The height of a pixel		False
resolution_y_unit	Allowable Value	The unit of measurement of the height of a pixel.	[‘nm’, ‘um’]	False
processing_search	Textfield	Software for analyzing and searching LC-MS/MS omics data		True
processing_protocols_io_doi	Textfield	DOI for analysis protocols.io for this assay.		False
overall_protocols_io_doi	Textfield	DOI for protocols.io for the overall process for this assay.		False
contributors_path	Textfield	Relative path to file with ORCID IDs for contributors for this dataset.		True
data_path	Textfield	Relative path to file or directory with instrument data. Downstreamprocessing will depend on filename extension conventions.		True

Version 1

Attribute	Type	Description	Allowable Values	Required
version	Allowable Value	Version of the schema to use when validating this metadata.	[‘1’]	True
description	Textfield	Free-text description of this assay.		True
donor_id	Textfield	HuBMAP Display ID of the donor of the assayed tissue.		True
tissue_id	Textfield	HuBMAP Display ID of the assayed tissue.		True
execution_datetime	Datetime	Start date and time of assay, typically a date-time stamped foldergenerated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year,MM is the month with leading 0s, and DD is the day with leading 0s, hh is thehour with leading zeros, mm are the minutes with leading zeros.		True
protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for this assay.		True
operator	Textfield	Name of the person responsible for executing the assay.		True
operator_email	Textfield	Email address for the operator.		True
pi	Textfield	Name of the principal investigator responsible for the data.		True
pi_email	Textfield	Email address for the principal investigator.		True
assay_category	Allowable Value	Each assay is placed into one of the following 4 general categories:generation of images of microscopic entities, identification & quantitation ofmolecules by mass spectrometry, imaging mass spectrometry, and determination ofnucleotide sequence.	[‘mass_spectrometry’]	True
assay_type	Allowable Value	The specific type of assay being executed.	[‘LC-MS (metabolomics)’, ‘LC-MS/MS (label-free proteomics)’, ‘MS (shotgun lipidomics)’]	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	[‘protein’, ‘metabolites’, ‘lipids’]	False
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted fordetection/measurement by the assay.	[‘Yes’,’No’]	True
acquisition_instrument_vendor	Textfield	An acquisition instrument is the device that contains the signal detectionhardware and signal processing software. Assays generate signals such as lightof various intensities or color or signals representing the molecular mass.		True
acquisition_instrument_model	Textfield	Manufacturers of an acquisition instrument may offer various versions(models) of that instrument with different features or sensitivities. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data.		True
ms_source	Textfield	The ion source type used for surface sampling (MALDI, MALDI-2, DESI,or SIMS) or LC-MS/MS data acquisition (nESI)		True
polarity	Allowable Value	The polarity of the mass analysis (positive or negative ion modes)	[‘negative ion mode’, ‘positive ion mode’, ‘negative and positive ion mode’]	True
mz_range_low_value	Numeric	The low value of the scanned mass range for MS1. (unitless)		True
mz_range_high_value	Numeric	The high value of the scanned mass range for MS1. (unitless)		True
data_collection_mode	Allowable Value	Mode of data collection in tandem MS assays. Either DDA (Data-dependentacquisition), DIA (Data-independent acquisition), MRM (multiple reaction monitoring),or PRM (parallel reaction monitoring).	[‘DDA’, ‘DIA’, ‘MRM’, ‘PRM’]	True
ms_scan_mode	Textfield	Indicates whether experiment is MS, MS/MS, or other (possibly MS3 forTMT)		True
labeling	Textfield	Indicates whether samples were labeled prior to MS analysis (e.g.,TMT)		True
section_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing tissuesections for the assay.		True
lc_instrument_vendor	Textfield	The manufacturer of the instrument used for LC		False
lc_instrument_model	Textfield	The model number/name of the instrument used for LC		False
lc_column_vendor	Textfield	OPTIONAL: The manufacturer of the LC Column unless self-packed, pulledtip capilary is used		False
lc_column_model	Textfield	The model number/name of the LC Column - IF custom self-packed, pulledtip calillary is used enter “Pulled tip capilary”		False
lc_resin	Textfield	Details of the resin used for lc, including vendor, particle size,pore size		False
lc_length_value	Numeric	LC column length		False
lc_length_unit	Allowable Value	units for LC column length (typically cm)	[‘um’, ‘mm’, ‘cm’]	False
lc_temp_value	Numeric	LC temperature		False
lc_temp_unit	Allowable Value	units for LC temperature	[‘C’]	False
lc_id_value	Numeric	LC column inner diameter (microns)		False
lc_id_unit	Allowable Value	units of LC column inner diameter (typically microns)	[‘um’, ‘mm’, ‘cm’]	False
lc_flow_rate_value	Numeric	Value of flow rate.		False
lc_flow_rate_unit	Allowable Value	Units of flow rate.	[‘nL/min’, ‘mL/min’]	False
lc_gradient	Textfield	LC gradient		False
lc_mobile_phase_a	Textfield	Composition of mobile phase A		False
lc_mobile_phase_b	Textfield	Composition of mobile phase B		False
processing_search	Textfield	Software for analyzing and searching LC-MS/MS omics data		True
processing_protocols_io_doi	Textfield	DOI for analysis protocols.io for this assay.		False
overall_protocols_io_doi	Textfield	DOI for protocols.io for the overall process for this assay.		False
contributors_path	Textfield	Relative path to file with ORCID IDs for contributors for this dataset.		True
data_path	Textfield	Relative path to file or directory with instrument data. Downstreamprocessing will depend on filename extension conventions.		True

Version 0

Attribute	Type	Description	Allowable Values	Required
donor_id	Textfield	HuBMAP Display ID of the donor of the assayed tissue.		True
tissue_id	Textfield	HuBMAP Display ID of the assayed tissue.		True
execution_datetime	Datetime	Start date and time of assay, typically a date-time stamped foldergenerated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year,MM is the month with leading 0s, and DD is the day with leading 0s, hh is thehour with leading zeros, mm are the minutes with leading zeros.		True
protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for this assay.		True
operator	Textfield	Name of the person responsible for executing the assay.		True
operator_email	Textfield	Email address for the operator.		True
pi	Textfield	Name of the principal investigator responsible for the data.		True
pi_email	Textfield	Email address for the principal investigator.		True
assay_category	Allowable Value	Each assay is placed into one of the following 4 general categories:generation of images of microscopic entities, identification & quantitation ofmolecules by mass spectrometry, imaging mass spectrometry, and determination ofnucleotide sequence.	[‘mass_spectrometry’]	True
assay_type	Allowable Value	The specific type of assay being executed.	[‘LC-MS (metabolomics)’, ‘LC-MS/MS (label-free proteomics)’, ‘MS (shotgun lipidomics)’]	True
analyte_class	Allowable Value	Analytes are the target molecules being measured with the assay.	[‘protein’, ‘metabolites’, ‘lipids’]	False
is_targeted	Allowable Value	Specifies whether or not a specific molecule(s) is/are targeted fordetection/measurement by the assay.	[‘Yes’,’No’]	True
acquisition_instrument_vendor	Textfield	An acquisition instrument is the device that contains the signal detectionhardware and signal processing software. Assays generate signals such as lightof various intensities or color or signals representing the molecular mass.		True
acquisition_instrument_model	Textfield	Manufacturers of an acquisition instrument may offer various versions(models) of that instrument with different features or sensitivities. Differencesin features or sensitivities may be relevant to processing or interpretation ofthe data.		True
ms_source	Textfield	The ion source type used for surface sampling (MALDI, MALDI-2, DESI,or SIMS) or LC-MS/MS data acquisition (nESI)		True
polarity	Allowable Value	The polarity of the mass analysis (positive or negative ion modes)	[‘negative ion mode’, ‘positive ion mode’, ‘negative and positive ion mode’]	True
mz_range_low_value	Numeric	The low value of the scanned mass range for MS1. (unitless)		True
mz_range_high_value	Numeric	The high value of the scanned mass range for MS1. (unitless)		True
data_collection_mode	Allowable Value	Mode of data collection in tandem MS assays. Either DDA (Data-dependentacquisition), DIA (Data-independent acquisition), MRM (multiple reaction monitoring),or PRM (parallel reaction monitoring).	[‘DDA’, ‘DIA’, ‘MRM’, ‘PRM’]	True
ms_scan_mode	Textfield	Indicates whether experiment is MS, MS/MS, or other (possibly MS3 forTMT)		True
labeling	Textfield	Indicates whether samples were labeled prior to MS analysis (e.g.,TMT)		True
section_prep_protocols_io_doi	Textfield	DOI for protocols.io referring to the protocol for preparing tissuesections for the assay.		True
lc_instrument_vendor	Textfield	The manufacturer of the instrument used for LC		False
lc_instrument_model	Textfield	The model number/name of the instrument used for LC		False
lc_column_vendor	Textfield	OPTIONAL: The manufacturer of the LC Column unless self-packed, pulledtip capilary is used		False
lc_column_model	Textfield	The model number/name of the LC Column - IF custom self-packed, pulledtip calillary is used enter “Pulled tip capilary”		False
lc_resin	Textfield	Details of the resin used for lc, including vendor, particle size,pore size		False
lc_length_value	Numeric	LC column length		False
lc_length_unit	Allowable Value	units for LC column length (typically cm)	[‘um’, ‘mm’, ‘cm’]	False
lc_temp_value	Numeric	LC temperature		False
lc_temp_unit	Allowable Value	units for LC temperature	[‘C’]	False
lc_id_value	Numeric	LC column inner diameter (microns)		False
lc_id_unit	Allowable Value	units of LC column inner diameter (typically microns)	[‘um’, ‘mm’, ‘cm’]	False
lc_flow_rate_value	Numeric	Value of flow rate.		False
lc_flow_rate_unit	Allowable Value	Units of flow rate.	[‘nL/min’, ‘mL/min’]	False
lc_gradient	Textfield	LC gradient		False
lc_mobile_phase_a	Textfield	Composition of mobile phase A		False
lc_mobile_phase_b	Textfield	Composition of mobile phase B		False
processing_search	Textfield	Software for analyzing and searching LC-MS/MS omics data		True
processing_protocols_io_doi	Textfield	DOI for analysis protocols.io for this assay.		False
overall_protocols_io_doi	Textfield	DOI for protocols.io for the overall process for this assay.		False
contributors_path	Textfield	Relative path to file with ORCID IDs for contributors for this dataset.		True
data_path	Textfield	Relative path to file or directory with instrument data. Downstreamprocessing will depend on filename extension conventions.		True