Mass Spectrometry

GC-MS

Related files:

This schema is for gas chromatography - mass spectrophotometry (GCMS).

Metadata schema

Version 1 (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_model

Unique to this type

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
section_prep_protocols_io_doi
column_vendor
column_model
column_length_value
column_length_unit
column_temp_value
column_temp_unit
internal_standard
ion_source
guard_column
spatial_type
spatial_sampling_type
spatial_target
resolution_x_value
resolution_x_unit
resolution_y_value
resolution_y_unit
processing_search
section_prep_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 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 GC-MS
required True

analyte_class

Analytes are the target molecules being measured with the assay.

constraint value
enum 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.

constraint value
enum MALDI, MALDI-2, DESI, SIMS, nESI, or EI
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/

column_vendor

The manufacturer of the GC column.

constraint value
required True

column_model

The model of the GC column used.

constraint value
required True

column_length_value

GC column length.

constraint value
type number
required True

column_length_unit

Unit for GC column length. Leave blank if not applicable.

constraint value
enum cm
required False
required if column_length_value present

column_temp_value

GC column temperature.

constraint value
type number
required True

column_temp_unit

Units for GC column temperature. Leave blank if not applicable.

constraint value
enum C
required False
required if column_temp_value present

internal_standard

Specifies if internal standard was utilized and designates what standard was used. Leave blank if not applicable.

constraint value
required True

ion_source

Specifies the ion source used.

constraint value
required True

guard_column

Specifies if guard column was used.

constraint value
required True

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

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

Version 0.0 (use this one)
pattern required? description
TODO ✓ Directory structure not yet specified.
extras\/.*   Folder for general lab-specific files related to the dataset. [Exists in all assays]