Mass Spectrometry
LC-MS / MS / LC-MS Bottom-Up / MS Bottom-Up / LC-MS Top-Down / MS Top-Down
Related files:
-
🔬 Background doc: More details about this type.
- 📝 Excel template: For metadata entry.
- 📝 TSV template: Alternative for metadata entry.
This schema is for liquid chromatography mass spectrometry (LCMS).
v2 adds mass_resolving_power, mz_resolving_power, ion_mobility, spatial_type, spatial_sampling_type, spatial_target, and resolution_{x/y}_{value/unit}. In the case of datasets in which more than one analyte_type was interrogated (e.g. lipids plus metabolytes), those datasets should be split into one dataset per analyte.
v3 adds dms and label_name fields, and negative and positive ion mode as a polarity option.
Metadata schema
Version 3 (use this one, release date 2021-12-06)
Shared by all types
version
description
donor_id
tissue_id
execution_datetime
protocols_io_doi
operator
operator_email
pi
pi_email
assay_category
assay_type
analyte_class
is_targeted
acquisition_instrument_vendor
acquisition_instrument_modelUnique to this type
dms
ms_source
polarity
mz_range_low_value
mz_range_high_value
mass_resolving_power
mz_resolving_power
ion_mobility
data_collection_mode
ms_scan_mode
labeling
label_name
section_prep_protocols_io_doi
lc_instrument_vendor
lc_instrument_model
lc_column_vendor
lc_column_model
lc_resin
lc_length_value
lc_length_unit
lc_temp_value
lc_temp_unit
lc_id_value
lc_id_unit
lc_flow_rate_value
lc_flow_rate_unit
lc_gradient
lc_mobile_phase_a
lc_mobile_phase_b
spatial_type
spatial_sampling_type
spatial_target
resolution_x_value
resolution_x_unit
resolution_y_value
resolution_y_unit
processing_search
processing_protocols_io_doi
overall_protocols_io_doi
contributors_path
data_path
Shared by all types
version
Version of the schema to use when validating this metadata.
| constraint | value |
|---|---|
| enum | 3 |
| required | True |
description
Free-text description of this assay.
| constraint | value |
|---|---|
| required | True |
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* |
| required | True |
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.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
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.
| constraint | value |
|---|---|
| enum | mass_spectrometry |
| required | True |
assay_type
Bottom-up refers to analyzing proteins in a sample by digesting them to peptides. Top-down refers to analyzing whole proteins without digestion. LC-MS and 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.
| constraint | value |
|---|---|
| enum | LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | protein, metabolites, lipids, peptides, phosphopeptides, or glycans |
| required | False |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
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.
| constraint | value |
|---|---|
| required | True |
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.
| constraint | value |
|---|---|
| required | True |
Unique to this type
dms
Was differential mobility spectrometry used in this assay?
| constraint | value |
|---|---|
| type | boolean |
| required | True |
ms_source
The ion source type used for surface sampling.
| constraint | value |
|---|---|
| enum | ESI |
| required | True |
polarity
The polarity of the mass analysis (positive or negative ion modes)
| constraint | value |
|---|---|
| enum | negative ion mode, positive ion mode, or negative and positive ion mode |
| required | True |
mz_range_low_value
The low value of the scanned mass range for MS1. (unitless)
| constraint | value |
|---|---|
| type | number |
| required | True |
mz_range_high_value
The high value of the scanned mass range for MS1. (unitless)
| constraint | value |
|---|---|
| type | number |
| required | True |
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) Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
mz_resolving_power
The peak (m/z) used to calculate the resolving power. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
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). Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | TIMS, TWIMS, FAIMS, DTIMS, or SLIMS |
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).
| constraint | value |
|---|---|
| enum | DDA, DIA, MRM, or PRM |
| required | True |
ms_scan_mode
Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)
| constraint | value |
|---|---|
| required | True |
labeling
Indicates whether samples were labeled prior to MS analysis (e.g., TMT)
| constraint | value |
|---|---|
| required | True |
label_name
If the samples were labeled (e.g. TMT), provide the name/ID of the label on this sample. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
section_prep_protocols_io_doi
DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
lc_instrument_vendor
The manufacturer of the instrument used for LC. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_instrument_model
The model number/name of the instrument used for LC. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_column_vendor
OPTIONAL: The manufacturer of the LC Column unless self-packed, pulled tip capilary is used. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_column_model
The model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter “Pulled tip capilary”. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_resin
Details of the resin used for lc, including vendor, particle size, pore size. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_length_value
LC column length. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_length_unit
units for LC column length (typically cm) Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | um, mm, or cm |
| required | False |
| required if | lc_length_value present |
lc_temp_value
LC temperature. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_temp_unit
units for LC temperature. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | C |
| required | False |
| required if | lc_temp_value present |
lc_id_value
LC column inner diameter (microns) Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_id_unit
units of LC column inner diameter (typically microns) Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | um, mm, or cm |
| required | False |
| required if | lc_id_value present |
lc_flow_rate_value
Value of flow rate. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_flow_rate_unit
Units of flow rate. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | nL/min or mL/min |
| required if | lc_flow_rate_value present |
lc_gradient
LC gradient. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_mobile_phase_a
Composition of mobile phase A. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_mobile_phase_b
Composition of mobile phase B. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
spatial_type
Specifies whether or not the analysis was performed in a spatialy targeted manner and the technique used for spatial sampling. For example, Laser-capture microdissection (LCM), Liquid Extraction Surface Analysis (LESA), Nanodroplet Processing in One pot for Trace Samples (nanoPOTS). Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | LCM, LESA, nanoPOTS, or microLESA |
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. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | profiling or imaging |
spatial_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. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
resolution_x_value
The width of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
resolution_x_unit
The unit of measurement of the width of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | resolution_x_value present |
resolution_y_value
The height of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
resolution_y_unit
The unit of measurement of the height of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | resolution_y_value present |
processing_search
Software for analyzing and searching LC-MS/MS omics data.
| constraint | value |
|---|---|
| required | True |
processing_protocols_io_doi
DOI for analysis protocols.io for this assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
overall_protocols_io_doi
DOI for protocols.io for the overall process for this assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Version 2
Shared by all types
version
Version of the schema to use when validating this metadata.
| constraint | value |
|---|---|
| enum | 2 |
| required | True |
description
Free-text description of this assay.
| constraint | value |
|---|---|
| required | True |
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* |
| required | True |
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.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
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.
| constraint | value |
|---|---|
| enum | mass_spectrometry |
| required | True |
assay_type
Bottom-up refers to analyzing proteins in a sample by digesting them to peptides. Top-down refers to analyzing whole proteins without digestion. LC-MS and 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.
| constraint | value |
|---|---|
| enum | LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | protein, metabolites, lipids, peptides, phosphopeptides, or glycans |
| required | False |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
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.
| constraint | value |
|---|---|
| required | True |
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.
| constraint | value |
|---|---|
| required | True |
Unique to this type
ms_source
The ion source type used for surface sampling.
| constraint | value |
|---|---|
| enum | ESI |
| required | True |
polarity
The polarity of the mass analysis (positive or negative ion modes)
| constraint | value |
|---|---|
| enum | negative ion mode, positive ion mode, or negative and positive ion mode |
| required | True |
mz_range_low_value
The low value of the scanned mass range for MS1. (unitless)
| constraint | value |
|---|---|
| type | number |
| required | True |
mz_range_high_value
The high value of the scanned mass range for MS1. (unitless)
| constraint | value |
|---|---|
| type | number |
| required | True |
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) Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
mz_resolving_power
The peak (m/z) used to calculate the resolving power. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
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). Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | TIMS, TWIMS, FAIMS, DTIMS, or SLIMS |
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).
| constraint | value |
|---|---|
| enum | DDA, DIA, MRM, or PRM |
| required | True |
ms_scan_mode
Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)
| constraint | value |
|---|---|
| required | True |
labeling
Indicates whether samples were labeled prior to MS analysis (e.g., TMT)
| constraint | value |
|---|---|
| required | True |
section_prep_protocols_io_doi
DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
lc_instrument_vendor
The manufacturer of the instrument used for LC. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_instrument_model
The model number/name of the instrument used for LC. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_column_vendor
OPTIONAL: The manufacturer of the LC Column unless self-packed, pulled tip capilary is used. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_column_model
The model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter “Pulled tip capilary”. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_resin
Details of the resin used for lc, including vendor, particle size, pore size. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_length_value
LC column length. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_length_unit
units for LC column length (typically cm) Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | um, mm, or cm |
| required | False |
| required if | lc_length_value present |
lc_temp_value
LC temperature. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_temp_unit
units for LC temperature. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | C |
| required | False |
| required if | lc_temp_value present |
lc_id_value
LC column inner diameter (microns) Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_id_unit
units of LC column inner diameter (typically microns) Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | um, mm, or cm |
| required | False |
| required if | lc_id_value present |
lc_flow_rate_value
Value of flow rate. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_flow_rate_unit
Units of flow rate. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | nL/min or mL/min |
| required if | lc_flow_rate_value present |
lc_gradient
LC gradient. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_mobile_phase_a
Composition of mobile phase A. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_mobile_phase_b
Composition of mobile phase B. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
spatial_type
Specifies whether or not the analysis was performed in a spatialy targeted manner and the technique used for spatial sampling. For example, Laser-capture microdissection (LCM), Liquid Extraction Surface Analysis (LESA), Nanodroplet Processing in One pot for Trace Samples (nanoPOTS). Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | LCM, LESA, nanoPOTS, or microLESA |
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. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | profiling or imaging |
spatial_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. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
resolution_x_value
The width of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
resolution_x_unit
The unit of measurement of the width of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | resolution_x_value present |
resolution_y_value
The height of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
resolution_y_unit
The unit of measurement of the height of a pixel. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | nm or um |
| required | False |
| required if | resolution_y_value present |
processing_search
Software for analyzing and searching LC-MS/MS omics data.
| constraint | value |
|---|---|
| required | True |
processing_protocols_io_doi
DOI for analysis protocols.io for this assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
overall_protocols_io_doi
DOI for protocols.io for the overall process for this assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Version 1 (deprecated)
Shared by all types
version
Version of the schema to use when validating this metadata.
| constraint | value |
|---|---|
| enum | 1 |
| required | True |
description
Free-text description of this assay.
| constraint | value |
|---|---|
| required | True |
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | (([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)(,([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)?)* |
| required | True |
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.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
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.
| constraint | value |
|---|---|
| enum | mass_spectrometry |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | LC-MS (metabolomics), LC-MS/MS (label-free proteomics), or MS (shotgun lipidomics) |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | protein, metabolites, or lipids |
| required | False |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
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.
| constraint | value |
|---|---|
| required | True |
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.
| constraint | value |
|---|---|
| required | True |
Unique to this type
ms_source
The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)
| constraint | value |
|---|---|
| required | True |
polarity
The polarity of the mass analysis (positive or negative ion modes)
| constraint | value |
|---|---|
| enum | negative ion mode, positive ion mode, or negative and positive ion mode |
| required | True |
mz_range_low_value
The low value of the scanned mass range for MS1. (unitless)
| constraint | value |
|---|---|
| type | number |
| required | True |
mz_range_high_value
The high value of the scanned mass range for MS1. (unitless)
| constraint | value |
|---|---|
| type | number |
| required | True |
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).
| constraint | value |
|---|---|
| enum | DDA, DIA, MRM, or PRM |
| required | True |
ms_scan_mode
Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)
| constraint | value |
|---|---|
| required | True |
labeling
Indicates whether samples were labeled prior to MS analysis (e.g., TMT)
| constraint | value |
|---|---|
| required | True |
section_prep_protocols_io_doi
DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
lc_instrument_vendor
The manufacturer of the instrument used for LC. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_instrument_model
The model number/name of the instrument used for LC. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_column_vendor
OPTIONAL: The manufacturer of the LC Column unless self-packed, pulled tip capilary is used. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_column_model
The model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter “Pulled tip capilary”. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_resin
Details of the resin used for lc, including vendor, particle size, pore size. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_length_value
LC column length. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_length_unit
units for LC column length (typically cm) Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | um, mm, or cm |
| required | False |
| required if | lc_length_value present |
lc_temp_value
LC temperature. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_temp_unit
units for LC temperature. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | C |
| required | False |
| required if | lc_temp_value present |
lc_id_value
LC column inner diameter (microns) Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_id_unit
units of LC column inner diameter (typically microns) Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | um, mm, or cm |
| required | False |
| required if | lc_id_value present |
lc_flow_rate_value
Value of flow rate. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_flow_rate_unit
Units of flow rate. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | nL/min or mL/min |
| required if | lc_flow_rate_value present |
lc_gradient
LC gradient. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_mobile_phase_a
Composition of mobile phase A. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_mobile_phase_b
Composition of mobile phase B. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
processing_search
Software for analyzing and searching LC-MS/MS omics data.
| constraint | value |
|---|---|
| required | True |
processing_protocols_io_doi
DOI for analysis protocols.io for this assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
overall_protocols_io_doi
DOI for protocols.io for the overall process for this assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Version 0 (deprecated)
Shared by all types
donor_id
HuBMAP Display ID of the donor of the assayed tissue. Example: ABC123.
| constraint | value |
|---|---|
| pattern (regular expression) | [A-Z]+[0-9]+ |
| required | True |
tissue_id
HuBMAP Display ID of the assayed tissue. Example: ABC123-BL-1-2-3_456.
| constraint | value |
|---|---|
| pattern (regular expression) | ([A-Z]+[0-9]+)-[A-Z]{2}\d*(-\d+)+(_\d+)? |
| required | True |
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.
| constraint | value |
|---|---|
| type | datetime |
| format | %Y-%m-%d %H:%M |
| required | True |
protocols_io_doi
DOI for protocols.io referring to the protocol for this assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
operator
Name of the person responsible for executing the assay.
| constraint | value |
|---|---|
| required | True |
operator_email
Email address for the operator.
| constraint | value |
|---|---|
| format | email |
| required | True |
pi
Name of the principal investigator responsible for the data.
| constraint | value |
|---|---|
| required | True |
pi_email
Email address for the principal investigator.
| constraint | value |
|---|---|
| format | email |
| required | True |
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.
| constraint | value |
|---|---|
| enum | mass_spectrometry |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | LC-MS (metabolomics), LC-MS/MS (label-free proteomics), or MS (shotgun lipidomics) |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | protein, metabolites, or lipids |
| required | False |
is_targeted
Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay.
| constraint | value |
|---|---|
| type | boolean |
| required | True |
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.
| constraint | value |
|---|---|
| required | True |
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.
| constraint | value |
|---|---|
| required | True |
Unique to this type
ms_source
The ion source type used for surface sampling (MALDI, MALDI-2, DESI, or SIMS) or LC-MS/MS data acquisition (nESI)
| constraint | value |
|---|---|
| required | True |
polarity
The polarity of the mass analysis (positive or negative ion modes)
| constraint | value |
|---|---|
| enum | negative ion mode, positive ion mode, or negative and positive ion mode |
| required | True |
mz_range_low_value
The low value of the scanned mass range for MS1. (unitless)
| constraint | value |
|---|---|
| type | number |
| required | True |
mz_range_high_value
The high value of the scanned mass range for MS1. (unitless)
| constraint | value |
|---|---|
| type | number |
| required | True |
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).
| constraint | value |
|---|---|
| enum | DDA, DIA, MRM, or PRM |
| required | True |
ms_scan_mode
Indicates whether experiment is MS, MS/MS, or other (possibly MS3 for TMT)
| constraint | value |
|---|---|
| required | True |
labeling
Indicates whether samples were labeled prior to MS analysis (e.g., TMT)
| constraint | value |
|---|---|
| required | True |
section_prep_protocols_io_doi
DOI for protocols.io referring to the protocol for preparing tissue sections for the assay.
| constraint | value |
|---|---|
| required | True |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
lc_instrument_vendor
The manufacturer of the instrument used for LC. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_instrument_model
The model number/name of the instrument used for LC. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_column_vendor
OPTIONAL: The manufacturer of the LC Column unless self-packed, pulled tip capilary is used. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_column_model
The model number/name of the LC Column - IF custom self-packed, pulled tip calillary is used enter “Pulled tip capilary”. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_resin
Details of the resin used for lc, including vendor, particle size, pore size. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_length_value
LC column length. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_length_unit
units for LC column length (typically cm) Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | um, mm, or cm |
| required | False |
| required if | lc_length_value present |
lc_temp_value
LC temperature. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_temp_unit
units for LC temperature. Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | C |
| required | False |
| required if | lc_temp_value present |
lc_id_value
LC column inner diameter (microns) Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_id_unit
units of LC column inner diameter (typically microns) Leave blank if not applicable.
| constraint | value |
|---|---|
| enum | um, mm, or cm |
| required | False |
| required if | lc_id_value present |
lc_flow_rate_value
Value of flow rate. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
lc_flow_rate_unit
Units of flow rate. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | nL/min or mL/min |
| required if | lc_flow_rate_value present |
lc_gradient
LC gradient. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_mobile_phase_a
Composition of mobile phase A. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
lc_mobile_phase_b
Composition of mobile phase B. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
processing_search
Software for analyzing and searching LC-MS/MS omics data.
| constraint | value |
|---|---|
| required | True |
processing_protocols_io_doi
DOI for analysis protocols.io for this assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
overall_protocols_io_doi
DOI for protocols.io for the overall process for this assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| pattern (regular expression) | 10\.17504/.* |
| url | prefix: https://dx.doi.org/ |
contributors_path
Relative path to file with ORCID IDs for contributors for this dataset.
| constraint | value |
|---|---|
| required | True |
data_path
Relative path to file or directory with instrument data. Downstream processing will depend on filename extension conventions.
| constraint | value |
|---|---|
| required | True |
Directory schemas
| pattern | required? | description |
|---|---|---|
raw_data/[^/]+\.(raw|mzML|d) (example: raw_data/20200707_rmi049_75umPLRPS_Kidney_GF10pc_VAN0003LK32_biorep05_techrep02.raw) |
✓ | Raw mass spectrometry data from an assay of LC-MS, MS, LC-MS Bottom-Up, MS Bottom-Up, LC-MS Top-Down, or MS Top-Down that describes an analyte class of protein, metabolites, lipids, peptides, phosphopeptides, or glycans. |
ID_search_results/[^/]+\.(txt|csv) |
✓ | Identification results. Annotated data describing (qualitative or quantitative) the proteins, metabolites, lipids, peptides, phosphopeptides, or glycans identified from the corresponding raw data. |
ID_metadata/[^/]+\.(csv|tsv|txt|xml) |
✓ | Identification search parameters/metadata. Software settings used during the analyte identification process (e.g., from MaxQuant or Proteome Discoverer). |
QC_results/[^/]+\.(xml|txt|html|pdf|log|yaml) |
Output file resulting from QC analysis. A list of metrics with the score of the current dataset that shows the quality of data collection. | |
extras\/.* |
Folder for general lab-specific files related to the dataset. [Exists in all assays] |