LC-MS Metadata Attributes
Fields that are collected for LC-MS data, available at dataset.metadata.<attribute>
* indicates a required field
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| parent_sample_id * | 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 | ||
| lab_id | A locally assigned identifier provided by the data provider for the dataset. It is used to reference an external metadata record that may be maintained independently, enabling traceability and supporting provenance tracking. Example: Visium_9OLC_A4_S1 | ||
| preparation_protocol_doi * | 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 | ||
| dataset_type * | 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 |
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| analyte_class * | 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 |
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| is_targeted * | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay. | ||
| acquisition_instrument_vendor * | 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 |
|
| acquisition_instrument_model * | 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 |
|
| source_storage_duration_value * | How long was the source material stored, prior to this sample being processed? For assays applied to tissue sections, this would be how long the tissue section (e.g., slide) was stored, prior to the assay beginning (e.g., imaging). For assays applied to suspensions such as sequencing, this would be how long the suspension was stored before library construction began. | ||
| source_storage_duration_unit * | The time duration unit of measurement | hour month day minute year |
|
| time_since_acquisition_instrument_calibration_value | The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture. | ||
| time_since_acquisition_instrument_calibration_unit | The time unit of measurement | Column-by-column Not applicable Row-by-row Snake-by-columns Snake-by-rows |
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| contributors_path * | Relative path to file with ORCID IDs for contributors for this dataset. | ||
| data_path * | Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions. | ||
| ms_ionization_technique * | 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 |
|
| ms_scan_mode * | Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT) | MS1 MS2 MS3 |
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| mass_analysis_polarity * | The polarity of the mass analysis (positive or negative ion modes). | 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. (unitless) | ||
| mass_to_charge_range_high_value | The high value of the scanned mass-to-charge range, for MS1. (unitless) | ||
| mass_resolving_power | The MS1 resolving power defined as m/∆m where ∆m is the FWHM for a given peak with a specified m/z (m). (unitless) | ||
| mass_to_charge_resolving_power | The peak (m/z) used to calculate the resolving power. | ||
| ion_mobility | 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 SLIM FAIMS DTIMS cIMS TWIMS |
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| data_collection_mode * | Mode of data collection in tandem MS assays. Either DDA (Data-dependent acquisition), DIA (Data-independent acquisition), MRM (multiple reaction monitoring), or PRM (parallel reaction monitoring). | DDA PRM DIA SRM |
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| label_name | If the samples were labeled (e.g. TMT), provide the name/ID of the label on this sample. | ||
| lc_instrument_vendor | The manufacturer of the instrument used for LC | Thermo Fisher Scientific Sciex In-House Agilent Technologies Waters Bruker Evosep |
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| lc_instrument_model | The model number/name of the instrument used for LC | ||
| lc_column_vendor | OPTIONAL: The manufacturer of the LC Column unless self-packed, pulled tip capilary is used | Thermo Fisher Scientific In-House Waters Bruker Evosep IonOpticks |
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| lc_column_model | The model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter “Pulled tip capilary” | ||
| lc_resin | Details of the resin used for lc, including vendor, particle size, pore size | ||
| lc_column_length_value | Liquid chromatography column length. | ||
| lc_column_length_unit | Units for liquid chromatography column length (typically cm). | um mm cm |
|
| lc_temperature_value | Liquid chromatography temperature. | ||
| lc_temperature_unit | The unit of measurment for the LC temperature value. If the temperature is not specified, this field may be left blank. | celsius |
|
| 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. | um mm cm |
|
| lc_flow_rate_value | Value of flow rate. | ||
| lc_flow_rate_unit | Units of flow rate. | nL/min mL/min |
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| lc_gradient_value | Liquid chromatography gradient. | ||
| 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 | Composition of mobile phase B | ||
| spatial_sampling_technique | The spatially targeted technique used to isolate or analyze specific regions of a sample. Techniques may include Laser-Capture Microdissection (LCM), Liquid Extraction Surface Analysis (LESA), or Nanodroplet Processing in One Pot for Trace Samples (nanoPOTS), among others. | nanoSPLITS nanoPOTS LESA microPOTS LCM microLESA |
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| spatial_sampling_target | 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. | ||
| spatial_sampling_type | 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 |
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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 | ||
| acquisition_protocol_doi | DOI for protocols.io referring to the protocol for this assay. | ||
| metadata_schema_id * | 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 |
Deprecated Attributes
These attributes were supported by older metadata version specifications. They are no longer collected but there may be some older datasets that contain data for these attributes.
| Attribute | Type | Description | Allowable Values |
|---|---|---|---|
| assay_category | 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. | sequence |
|
| description | Free-text description of this assay. | ||
| donor_id | HuBMAP Display ID of the donor of the assayed tissue. | ||
| execution_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. | ||
| operator | Name of the person responsible for executing the assay. | ||
| operator_email | Email address for the operator. | ||
| protocols_io_doi | DOI for protocols.io referring to the protocol for this assay. | ||
| overall_protocols_io_doi | DOI for protocols.io for the overall process for this assay. | ||
| pi | Name of the principal investigator responsible for the data. | ||
| pi_email | Email address for the principal investigator. | ||
| processing_search | Software for analyzing and searching LC-MS/MS omics data | ||
| labeling | Indicates whether samples were labeled prior to MS analysis (e.g., TMT) | ||
| dms | Was differential mobility spectrometry used in this assay? | ||
| resolution_x_unit | The unit of measurement of the width of a pixel. | mm um nm |
|
| resolution_x_value | The width of a pixel. | ||
| resolution_y_unit | The unit of measurement of the height of a pixel. | mm um nm |
|
| resolution_y_value | The height of a pixel | ||
| version | Version of the schema to use when validating this metadata. | 1 |