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MALDI

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.

Maldi Version 2 (latest)

Maldi Version 2 (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_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)   True
mass-to-charge_resolving_power Numeric The peak (m/z) used to calculate the resolving power.   True
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
matrix_deposition_method Allowable Value Common methods of depositing matrix for assisting in desorption and ionization in imaging mass spectrometry include robotic spotting, electrospray deposition, and sublimation. Electrospray deposition Not applicable Robotic spotting Robotic spraying Sublimation True
preparation_instrument_vendor Allowable Value The manufacturer of the instrument used to prepare (staining/processing) the sample for the assay. If an automatic slide staining method was indicated this field should list the manufacturer of the instrument. 10x Genomics Hamamatsu HTX Technologies In-House Leica Biosystems Not applicable Roche Diagnostics SunChrom Thermo Fisher Scientific False
preparation_instrument_model Allowable Value Manufacturers of a staining system instrument may offer various versions (models) of that instrument with different features. Differences in features or sensitivities may be relevant to processing or interpretation of the data. AutoStainer XL Chromium Connect Chromium Controller Chromium iX Chromium X Discovery Ultra EVOS M7000 M3+ Sprayer M5 Sprayer NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 Not applicable ST5020 Multistainer Sublimator SunCollect Sprayer TM-Sprayer Visium CytAssist False
preparation_matrix Allowable Value The matrix is a compound of crystallized molecules that acts like a buffer between the sample and the ionizing probe. It also helps ionize the sample, carrying it along the flight tube so it can be detected. 2,5-DHA (2,5-dihydroxyacetophenone) 2,5-DHB (2,5-Dihydroxybenzoic acid) 9-AA (9-aminoacridine) CHCA (alpha-cyano-4-hydroxy-cinnamic acid) DAN (1,5-diaminonapthalene) DMACA (4-(dimethylamino)cinnamic acid) NEDC (N-(1-naphthyl) ethylenediamine dihydrochloride) SA (sinapic acid) 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
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
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
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
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
IMS Version 2

IMS 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 folder generated 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 the hour 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 of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. [‘mass_spectrometry_imaging’] True
assay_type Allowable Value The specific type of assay being executed. [‘MALDI-IMS’, ‘SIMS-IMS’, ‘NanoDESI’, ‘DESI’] True
analyte_class Allowable Value Analytes are the target molecules being measured with the assay. [‘protein’, ‘metabolites’, ‘lipids’, ‘peptides’, ‘phosphopeptides’, ‘glycans’] True
is_targeted Allowable Value Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. [‘Yes’,’No’] True
acquisition_instrument_vendor Textfield 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.   True
acquisition_instrument_model Textfield 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.   True
ms_source Allowable Value The ion source type used for surface sampling (MALDI, MALDI-2, DESI, nanoDESI or SIMS). [‘MALDI’, ‘MALDI-2’, ‘LDI’, ‘LA’, ‘SIMS-C60’, ‘SIMS-H2O’, ‘DESI’, ‘nanoDESI’] 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/∆m where ∆m is the FWHM for a given peak with a specified m/z (m). (unitless)   True
mz_resolving_power Numeric The peak (m/z) used to calculate the resolving power.   True
ion_mobility Allowable Value Specifies whether or not ion mobility spectrometry was performed and which technology was used. 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). [‘TIMS’, ‘TWIMS’, ‘FAIMS’, ‘DTIMS’, ‘SLIMS’] False
ms_scan_mode Allowable Value Scan mode refers to the number of steps in the separation of fragments. [‘MS’, ‘MS/MS’, ‘MS3’] True
resolution_x_value Numeric The width of a pixel.   True
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   True
resolution_y_unit Allowable Value The unit of measurement of the height of a pixel. [‘nm’, ‘um’] False
preparation_type Textfield Common methods of depositing matrix for MALDI imaging include robotic spotting, electrospray deposition, and spray-coating with an airbrush.   False
preparation_instrument_vendor Textfield The manufacturer of the instrument used to prepare the sample for the assay.   False
preparation_instrument_model Textfield The model number/name of the instrument used to prepare the sample for the assay   False
preparation_maldi_matrix Textfield The matrix is a compound of crystallized molecules that acts like a buffer between the sample and the laser. It also helps ionize the sample, carrying it along the flight tube so it can be detected.   False
desi_solvent Textfield Solvent composition for conducting nanospray desorption electrospray ionization (nanoDESI) or desorption electrospray ionization (DESI).   False
desi_solvent_flow_rate Numeric The rate of flow of the solvent into a spray.   False
desi_solvent_flow_rate_unit Allowable Value Units of the rate of solvent flow. [‘uL/minute’] False
section_prep_protocols_io_doi Textfield DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.   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.   True
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. Downstream processing will depend on filename extension conventions.   True
IMS Version 1

IMS 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 folder generated 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 the hour 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 of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. [‘mass_spectrometry_imaging’] True
assay_type Allowable Value The specific type of assay being executed. [‘MALDI-IMS’] True
analyte_class Allowable Value Analytes are the target molecules being measured with the assay. [‘protein’, ‘metabolites’, ‘lipids’] True
is_targeted Allowable Value Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. [‘Yes’,’No’] True
acquisition_instrument_vendor Textfield 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.   True
acquisition_instrument_model Textfield 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.   True
ms_source Allowable Value The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI) [‘MALDI’, ‘MALDI-2’, ‘DESI’, ‘SIMS’, ‘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
resolution_x_value Numeric The width of a pixel.   True
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   True
resolution_y_unit Allowable Value The unit of measurement of the height of a pixel. [‘nm’, ‘um’] False
preparation_type Textfield Common methods of depositing matrix for MALDI imaging include robotic spotting, electrospray deposition, and spray-coating with an airbrush.   True
preparation_instrument_vendor Textfield The manufacturer of the instrument used to prepare the sample for the assay.   True
preparation_instrument_model Textfield The model number/name of the instrument used to prepare the sample for the assay   True
preparation_maldi_matrix Textfield The matrix is a compound of crystallized molecules that acts like a buffer between the sample and the laser. It also helps ionize the sample, carrying it along the flight tube so it can be detected.   True
section_prep_protocols_io_doi Textfield DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.   True
overall_protocols_io_doi Textfield DOI for protocols.io for the overall process.   True
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. Downstream processing will depend on filename extension conventions.   True
IMS Version 0

IMS 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 folder generated 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 the hour 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 of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. [‘mass_spectrometry_imaging’] True
assay_type Allowable Value The specific type of assay being executed. [‘MALDI-IMS’] True
analyte_class Allowable Value Analytes are the target molecules being measured with the assay. [‘protein’, ‘metabolites’, ‘lipids’] True
is_targeted Allowable Value Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. [‘Yes’,’No’] True
acquisition_instrument_vendor Textfield 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.   True
acquisition_instrument_model Textfield 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.   True
ms_source Allowable Value The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI) [‘MALDI’, ‘MALDI-2’, ‘DESI’, ‘SIMS’, ‘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
resolution_x_value Numeric The width of a pixel.   True
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   True
resolution_y_unit Allowable Value The unit of measurement of the height of a pixel. [‘nm’, ‘um’] False
preparation_type Textfield Common methods of depositing matrix for MALDI imaging include robotic spotting, electrospray deposition, and spray-coating with an airbrush.   True
preparation_instrument_vendor Textfield The manufacturer of the instrument used to prepare the sample for the assay.   True
preparation_instrument_model Textfield The model number/name of the instrument used to prepare the sample for the assay   True
preparation_maldi_matrix Textfield The matrix is a compound of crystallized molecules that acts like a buffer between the sample and the laser. It also helps ionize the sample, carrying it along the flight tube so it can be detected.   True
section_prep_protocols_io_doi Textfield DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.   True
overall_protocols_io_doi Textfield DOI for protocols.io for the overall process.   True
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. Downstream processing will depend on filename extension conventions.   True