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. SenNet 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)

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 SenNet 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

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
source_id Textfield SenNet Display ID of the source of the assayed tissue.   True
tissue_id Textfield SenNet 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/∆m where ∆m 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

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
source_id Textfield SenNet Display ID of the source of the assayed tissue.   True
tissue_id Textfield SenNet 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/∆m where ∆m 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

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
source_id Textfield SenNet Display ID of the source of the assayed tissue.   True
tissue_id Textfield SenNet 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

Version 0

Attribute Type Description Allowable Values Required
source_id Textfield SenNet Display ID of the source of the assayed tissue.   True
tissue_id Textfield SenNet 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