Mass Spectrometry

CE-MS

Related files:

🔬 Background doc: More details about this type.
📝 Excel template: For metadata entry.
📝 TSV template: Alternative for metadata entry.

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
ce_interface
ce_capillary_coating
ce_background_electrolyte
ce_instrument_vendor
ce_instrument_model
ce_electroosmotic_flow
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	`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`

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	`CE-MS`
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 technique used for sampling and ionization of the sample.

constraint	value
enum	`nanoflex` or `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 the data were generated using MS, MS/MS or MS3.

constraint	value
enum	`MS`, `MS/MS`, or `MS3`
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/`

`ce_interface`

Method by which the separation capillary interfaces with mass spectrometer and enables electrospray ionization while completing the separation circuit. The two most prevalent commercial interfaces are sheathless and sheath-flow.

constraint	value
enum	`sheath-flow` or `sheathless`
required	`True`

`ce_capillary_coating`

Treatment of surface of separation capillary. Capillary coating affects the absorption of analytes on capillary inner walls and regulates electroosmotic flow. Entries should indicate the charge of the coating and chemical composition (e.g. “Neutral; Polyacrylamide” or “Positive; Polyethyleneimine” or “Uncoated”).

constraint	value
required	`True`

`ce_background_electrolyte`

Chemical composition of the background electrolyte that fills the separation capillary (e.g. “3% acetic acid”).

constraint	value
required	`True`

`ce_instrument_vendor`

The manufacturer of the instrument used for capillary zone electrophoresis. Capillary electrophoresis is used to separate complex biological mixtures prior to performing MS-based analyses. Separations are performed based the analytes migrate through an electrolyte solution in the presence of an electric field.

constraint	value
required	`True`

`ce_instrument_model`

The model name of the instrument used for capillary zone electrophoresis.

constraint	value
required	`True`

`ce_electroosmotic_flow`

Properties of the electroosmotic flow (EOF). Normal EOF is defined as flow towards the cathode, reversed EOF is defined as flow towards the anode, and suppressed EOF involves marginal to almost no flow (e.g. when a neutral coating is used).

constraint	value
enum	`suppressed`, `normal`, or `reversed`
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`

`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`

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]