Mass Spectrometry

LC-MS / MS / LC-MS Bottom-Up / MS Bottom-Up / LC-MS Top-Down / MS Top-Down

Related files:

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_model

Unique 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

Version 0 (use this one)
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]