Imaging Mass Spectrometry (IMS)
MALDI-IMS / SIMS-IMS / NanoDESI / DESI
Related files:
-
🔬 Background doc: More details about this type.
- 📝 Excel template: For metadata entry.
- 📝 TSV template: Alternative for metadata entry.
This schema is for imaging mass spectrometry (IMS).
Metadata schema
Version 2 (use this one)
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
ms_source
polarity
mz_range_low_value
mz_range_high_value
mass_resolving_power
mz_resolving_power
ion_mobility
ms_scan_mode
resolution_x_value
resolution_x_unit
resolution_y_value
resolution_y_unit
preparation_type
preparation_instrument_vendor
preparation_instrument_model
preparation_maldi_matrix
desi_solvent
desi_solvent_flow_rate
desi_solvent_flow_rate_unit
section_prep_protocols_io_doi
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 | 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_imaging |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | MALDI-IMS, SIMS-IMS, NanoDESI, or DESI |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay.
| constraint | value |
|---|---|
| enum | protein, metabolites, lipids, peptides, phosphopeptides, or glycans |
| required | True |
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, nanoDESI or SIMS).
| constraint | value |
|---|---|
| enum | MALDI, MALDI-2, LDI, LA, SIMS-C60, SIMS-H2O, DESI, or nanoDESI |
| 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)
| constraint | value |
|---|---|
| type | number |
| required | True |
mz_resolving_power
The peak (m/z) used to calculate the resolving power.
| constraint | value |
|---|---|
| type | number |
| required | True |
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 |
ms_scan_mode
Scan mode refers to the number of steps in the separation of fragments.
| constraint | value |
|---|---|
| enum | MS, MS/MS, or MS3 |
| required | True |
resolution_x_value
The width of a pixel.
| constraint | value |
|---|---|
| type | number |
| required | True |
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.
| constraint | value |
|---|---|
| type | number |
| required | True |
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 |
preparation_type
Common methods of depositing matrix for MALDI imaging include robotic spotting, electrospray deposition, and spray-coating with an airbrush. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
preparation_instrument_vendor
The manufacturer of the instrument used to prepare the sample for the assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
preparation_instrument_model
The model number/name of the instrument used to prepare the sample for the assay. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
preparation_maldi_matrix
The matrix is a compound of crystallized molecules that acts like a buffer between the sample and the laser. It also helps ionize the sample, carrying it along the flight tube so it can be detected. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
desi_solvent
Solvent composition for conducting nanospray desorption electrospray ionization (nanoDESI) or desorption electrospray ionization (DESI). Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
desi_solvent_flow_rate
The rate of flow of the solvent into a spray. Leave blank if not applicable.
| constraint | value |
|---|---|
| type | number |
| required | False |
desi_solvent_flow_rate_unit
Units of the rate of solvent flow. Leave blank if not applicable.
| constraint | value |
|---|---|
| required | False |
| enum | uL/minute |
| required if | desi_solvent_flow_rate present |
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/ |
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.
| constraint | value |
|---|---|
| required | True |
| 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
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_imaging |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | MALDI-IMS |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay.
| constraint | value |
|---|---|
| enum | protein, metabolites, or lipids |
| required | True |
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 |
|---|---|
| enum | MALDI, MALDI-2, DESI, SIMS, or nESI |
| 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 |
resolution_x_value
The width of a pixel.
| constraint | value |
|---|---|
| type | number |
| required | True |
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.
| constraint | value |
|---|---|
| type | number |
| required | True |
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 |
preparation_type
Common methods of depositing matrix for MALDI imaging include robotic spotting, electrospray deposition, and spray-coating with an airbrush.
| constraint | value |
|---|---|
| required | True |
preparation_instrument_vendor
The manufacturer of the instrument used to prepare the sample for the assay.
| constraint | value |
|---|---|
| required | True |
preparation_instrument_model
The model number/name of the instrument used to prepare the sample for the assay.
| constraint | value |
|---|---|
| required | True |
preparation_maldi_matrix
The matrix is a compound of crystallized molecules that acts like a buffer between the sample and the laser. It also helps ionize the sample, carrying it along the flight tube so it can be detected.
| 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/ |
overall_protocols_io_doi
DOI for protocols.io for the overall process.
| constraint | value |
|---|---|
| required | True |
| 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
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_imaging |
| required | True |
assay_type
The specific type of assay being executed.
| constraint | value |
|---|---|
| enum | MALDI-IMS |
| required | True |
analyte_class
Analytes are the target molecules being measured with the assay.
| constraint | value |
|---|---|
| enum | protein, metabolites, or lipids |
| required | True |
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 |
|---|---|
| enum | MALDI, MALDI-2, DESI, SIMS, or nESI |
| 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 |
resolution_x_value
The width of a pixel.
| constraint | value |
|---|---|
| type | number |
| required | True |
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.
| constraint | value |
|---|---|
| type | number |
| required | True |
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 |
preparation_type
Common methods of depositing matrix for MALDI imaging include robotic spotting, electrospray deposition, and spray-coating with an airbrush.
| constraint | value |
|---|---|
| required | True |
preparation_instrument_vendor
The manufacturer of the instrument used to prepare the sample for the assay.
| constraint | value |
|---|---|
| required | True |
preparation_instrument_model
The model number/name of the instrument used to prepare the sample for the assay.
| constraint | value |
|---|---|
| required | True |
preparation_maldi_matrix
The matrix is a compound of crystallized molecules that acts like a buffer between the sample and the laser. It also helps ionize the sample, carrying it along the flight tube so it can be detected.
| 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/ |
overall_protocols_io_doi
DOI for protocols.io for the overall process.
| constraint | value |
|---|---|
| required | True |
| 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 |
|---|---|---|
csv/[^/]+\.csv |
Intensities M/Z values with Pixel location | |
imzML/[^/]+\.ibd |
✓ | Mass spec data saved in a binary format. |
imzML/[^/]+\.imzML |
✓ | Mass spec metadata saved in XML format. Index to .ibd file. |
metadata/[^/]+_LipidAssignments\.xlsx |
Microsoft Excel file containing the m/z, assignment, lipid class, etc. | |
metadata/[^/]+_meta\.json |
JSON file containing the machine parameters/settings | |
metadata/[^/]+_microscopy\.txt |
Transformations/map back to autofluorescence microscopy (related) data | |
ometiffs/[^/]+_multilayer\.ome\.tiff |
✓ | Aligned multilayer OME TIFF file of the IMS data |
ometiffs/separate/[^/]+_mz[^/]+\.ome\.tiff |
Each file is a different M/Z value. | |
extras\/.* |
Folder for general lab-specific files related to the dataset. [Exists in all assays] |