MPLeX Metadata Attributes
These metadata fields have been collected for MPLeX data.
These fields are available from the HuBMAP Search and Entity APIs at Dataset.metadata.<attribute>.
See the latest version of the MPLeX Ingest Metadata Specifications for the schema and directory structure needed when uploading data.
* indicates a required field
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| parent_sample_id * | The unique identifier from HuBMAP or SenNet for the sample (such as a block, section, or suspension) used to perform the assay. For instance, in an RNAseq assay, the parent sample would be the suspension, while in imaging assays, it would be the tissue section. If the assay is derived from multiple parent samples, this field should contain a comma-separated list of identifiers. Example: HBM386.ZGKG.235, HBM672.MKPK.442 | ||
| lab_id | An identifier assigned by the data provider to reference an external metadata record for the dataset. The external record may be maintained independently and can support dataset traceability and provenance tracking. Leave this field empty if no such identifier exists. | ||
| preparation_protocol_doi * | The DOI for the protocols.io page that details the assay or the procedures used for sample procurement and preparation. For example, in the case of an imaging assay, the protocol may start with tissue section staining and end with the generation of an OME-TIFF file. The documented protocol should also include any image processing steps involved in producing the final OME-TIFF. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1 | ||
| dataset_type * | The specific type of dataset being produced. Example: RNAseq | 10X Multiome 2D Imaging Mass Cytometry 4i ATACseq Auto-fluorescence Cell DIVE CODEX COMET Confocal CosMx Proteomics CosMx Transcriptomics CyCIF CyTOF DART-FISH DBiT-seq DESI DNA Methylation Enhanced Stimulated Raman Spectroscopy (SRS) FACS GeoMx (nCounter) GeoMx (NGS) HiFi-Slide Histology iCLAP Illumina Spatial ver0 LC-MS Light Sheet MACSima MALDI MERFISH MIBI Molecular Cartography MPLEx MS Lipidomics MUSIC nanoSPLITS Olink PhenoCycler Pixel-seqV2 Raman Imaging Resolve RNAseq RNAseq (with probes) Second Harmonic Generation (SHG) Seq-Scope seqFISH SIMS Singular Genomics G4X SNARE-seq2 STARmap Stereo-seq Thick section Multiphoton MxIF Virtual Histology Visium (no probes) Visium (with probes) Visium HD Xenium |
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| analyte_class * | The analyte class which is the target molecule that the assay is measuring. Example: DNA | Chromatin Collagen DNA DNA + RNA Endogenous fluorophore Fluorochrome Lipid Lipid + metabolite Lipid + metabolite + protein Metabolite Nucleic acid + protein Peptide Polysaccharide Protein RNA RNA + protein Saturated lipid Unsaturated lipid |
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| is_targeted * | Indicates whether a specific molecule or set of molecules is targeted for detection or measurement by the assay. Example: Yes | Yes No |
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| acquisition_instrument_vendor * | The company that manufactures or supplies the acquisition instrument. An acquisition instrument is a device equipped with signal detection hardware and signal processing software. It captures signals produced by assays, such as variations in light intensity or color, or signals corresponding to molecular mass. If the instrument was custom-built or developed internally, enter “In-House”. Example: Illumina | 10x Genomics 3DHISTECH Akoya Biosciences Andor BGI Genomics Bruker Complete Genomics Cytek Biosciences Cytiva Element Biosciences Evident Scientific (Olympus) GE Healthcare Hamamatsu Huron Digital Pathology Illumina In-House Ionpath Keyence Leica Biosystems Leica Microsystems Microscopes International Miltenyi Biotec Motic NanoString Resolve Biosciences Revvity Sciex Singular Genomics Standard BioTools (Fluidigm) Thermo Fisher Scientific Vizgen Waters Zeiss Microscopy |
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| acquisition_instrument_model * | The specific model of the acquisition instrument, as manufacturers often offer various versions with differing features or sensitivities. These differences may be relevant to the processing or interpretation of the data. If the instrument was custom-built or developed internally, enter “In-House”. If the model is unknown, enter “Unknown”. Example: HiSeq 4000 | Aperio AT2 Aperio CS2 AVITI Axio Observer 3 Axio Observer 5 Axio Observer 7 Axio Scan.Z1 Axio Zoom.V16 Biomark HD BZ-X710 BZ-X800 BZ-X810 Cell DIVE CosMx Spatial Molecular Imager Custom: Multiphoton Cytek Northern Lights CyTOF 2 CyTOF XT Digital Spatial Profiler DM6 B DMi8 DNBSEQ-T7 EVOS M7000 G4X Spatial Sequencer Helios HiSeq 2500 HiSeq 4000 Hyperion Imaging System IN Cell Analyzer 2200 In-House Juno System Lightsheet 7 LSM 710 Confocal Microscope MACSima System MALDI timsTOF Flex Prototype MERSCOPE MERSCOPE Ultra MIBIscope MoticEasyScan One NanoZoomer 2.0-HT NanoZoomer 2.0-RS NanoZoomer S210 NanoZoomer S360 NanoZoomer S60 NanoZoomer-SQ NextSeq 2000 NextSeq 500 NextSeq 550 Not applicable NovaSeq 6000 NovaSeq X NovaSeq X Plus Opera Phenix HCS Opera Phenix Plus HCS Orbitrap Eclipse Tribrid Orbitrap Fusion Lumos Tribrid Orbitrap Fusion Tribrid Pannoramic MIDI II Digital Scanner Panoramic 150 Digital Scanner Phenocycler-Fusion 1.0 Phenocycler-Fusion 2.0 PhenoImager Fusion Q Exactive Q Exactive HF Q Exactive HF-X Q Exactive UHMR QTRAP 5500 Resolve Biosciences Molecular Cartography SCN400 solariX STELLARIS 5 SYNAPT G2-Si timsTOF FleX timsTOF FleX MALDI-2 timsTOF HT timsTOF Pro timsTOF Pro 2 timsTOF SCP timsTOF Ultra timsTOF Ultra 2 TissueScope LE Slide Scanner Unknown uScopeHXII-20 VS200 Slide Scanner Xenium Analyzer Zeiss LightSheet Z.1 Zyla 4.2 sCMOS |
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| source_storage_duration_value * | The length of time the sample was stored prior to processing it. For assays performed on tissue sections, this refers to how long the tissue section (e.g., slide) was stored before the assay began (e.g., imaging). For assays performed on suspensions, such as sequencing, it refers to how long the suspension was stored before library construction started. Example: 12 | ||
| source_storage_duration_unit * | The unit of measurement used to specify the source storage duration value. Example: hour | day hour minute month year |
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| time_since_acquisition_instrument_calibration_value | The length of time since the acquisition instrument was last serviced or calibrated. This provides a metric for assessing drift in data capture. Example: 10 | ||
| time_since_acquisition_instrument_calibration_unit | The unit of measurement used to specify the time since acquisition instrument calibration value. Example: month | day month year |
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| contributors_path * | The name of the file containing the ORCID IDs for all contributors to this dataset. Example: ./contributors.csv | ||
| data_path * | The top-level directory containing the raw and/or processed data. For a single dataset upload, this might be represented as “.”, whereas for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For example, if the data is within a directory named “TEST001-RK”, use the syntax “./TEST001-RK” for this field. If there are multiple directory levels, use the format “./TEST001-RK/Run1/Pass2”, where “Pass2” is the subdirectory where the single dataset’s data is stored. This is an internal metadata field used solely for data ingestion. Example: ./TEST001-RK | ||
| ms_ionization_technique * | The ionization technique used in imaging mass spectrometry, which refers to the method employed to probe the sample. Example: MALDI | DESI ESI HESI LA LDI MALDI MALDI-2 nanoDESI nESI SIMS-C60 SIMS-H20 |
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| ms_scan_mode * | The mode of mass spectrometry (MS) scanning, which refers to the number of steps involved in the separation of fragments during the analysis. Example: MS1 | MS1 MS2 MS3 |
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| mass_analysis_polarity * | The polarity mode used in mass analysis, indicating whether positive or negative ion modes are employed. Example: Positive ion mode | Negative and positive ion mode Negative ion mode Positive ion mode |
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| mass_to_charge_range_low_value | The low value of the scanned mass-to-charge range for MS1. This value is unitless. Example: 100 | ||
| mass_to_charge_range_high_value | The high value of the scanned mass-to-charge range, for MS1. (unitless) | ||
| mass_resolving_power | The mass resolving power, denoted as m/∆m, where ∆m is defined as the full width at half-maximum (FWHM) for a given peak with a specified mass-to-charge ratio (m/z). This measurement is unitless. Example: 60000 | ||
| mass_to_charge_resolving_power | The peak mass-to-charge ratio (m/z) used to calculate the resolving power. Example: 400.2 | ||
| ion_mobility | The specific technology employed for ion mobility spectrometry. Available technologies include 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). Example: TIMS | cIMS DTIMS FAIMS SLIM TIMS TWIMS |
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| data_collection_mode | The mode of data collection used in tandem MS assays, which can include options such as Data-dependent acquisition (DDA), Data-independent acquisition (DIA), multiple reaction monitoring (SRM), or parallel reaction monitoring (PRM). Example: PRM | DDA DIA PRM SRM |
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| label_name | The name or identifier of the chemical label used on this sample if labeling was applied. This is typically required for multiplexed experiments using techniques like Tandem Mass Tag (TMT). If sample was not labeled, this field may be left blank. Example: TMT126 | ||
| lc_instrument_vendor | The company that manufactures the instrument used for liquid chromatography. If the instrument was custom-built or developed internally, enter “In-House”. Example: Bruker | Agilent Technologies Bruker Evosep In-House Sciex Shimadzu Thermo Fisher Scientific Waters |
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| lc_instrument_model | The model number or name of the instrument used for liquid chromatography. Example: Bruker Elute LC-MS | ||
| lc_column_vendor | The manufacturer of the liquid chromatography column used, unless a self-packed or pulled tip capillary is employed. If the column was custom-made or developed internally, enter “In-House”. Example: Bruker | Agilent Technologies Bruker Evosep In-House IonOpticks Millipore Thermo Fisher Scientific Waters |
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| lc_column_model | The model number or name of the liquid chromatography column used. If a custom self-packed, pulled tip capillary is utilized, enter “Pulled tip capillary”. Example: Thermo Scientific Vanquish UHPLC | ||
| lc_resin | The details of the resin used in liquid chromatography, including information about the vendor, particle size, and pore size. Example: Thermo Fisher Scientific, Acclaim PepMap 100 C18, 3 µm, 100 Å | ||
| lc_column_length_value | Liquid chromatography column length. | ||
| lc_column_length_unit | Units for liquid chromatography column length (typically cm). | cm mm um |
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| lc_temperature_value | The temperature at which the liquid chromatography (LC) process is conducted. Example: 40 | ||
| lc_temperature_unit | celsius |
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| lc_inner_diameter_value | Liquid chromatography column inner diameter. | ||
| lc_inner_diameter_unit | The unit of measurment for the LC inner diameter value. If the diameter is not specified, this field may be left blank. Example: um | cm mm um |
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| lc_flow_rate_value | Value of flow rate. | ||
| lc_flow_rate_unit | Units of flow rate. | mL/min nL/min |
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| lc_gradient_value | The liquid chromatography (LC) gradient used in the assay. Example: 120 | ||
| lc_gradient_unit | Unit for liquid chromatography gradient | minute |
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| lc_mobile_phase_a | Composition of mobile phase A. | ||
| lc_mobile_phase_b | |||
| spatial_sampling_technique | LCM LESA microLESA microPOTS nanoPOTS nanoSPLITS |
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| spatial_sampling_target | The cell type or functional tissue unit (FTU) that is the focus of the spatial profiling experiment. If the data are generated in imaging mode without targeting a specific structure, this field may be left blank. Example: Proximal tubule epithelial cell | ||
| spatial_sampling_type | The type of spatial targeting used in the analysis. Spatial profiling focuses on selected tissue regions without necessarily producing images, while spatial imaging captures data across a regular grid of pixels, enabling visualization as ion intensity heat maps—also referred to as molecular images. Leave this field blank if the data originate from bulk (non-spatial) analysis. Example: Imaging | Imaging Profiling |
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| analysis_protocol_doi * | 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 | ||
| metadata_schema_id * | The unique string identifier for the metadata specification version, which is easily interpretable by computers for purposes of data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9 |